A transcriptome anatomy of human colorectal cancers

Abstract

Background: Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile.

Methods: In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of beta-catenin and. 7 novel genes in colorectal cancers.

Results: The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers.

Conclusion: Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers.

Figure 1

Total ESTs, UniGene transcripts, and Genes in 4 colorectal libraries. The number 1, 2, 3 and 4 in the X-axis stand for total ESTs, validated ESTs that could be clustered in to UniGene, UniGene transcripts and genes, respectively. The exact counts of each category in different states are shown in the Y-axis. Z-axis reflects different status in colon, i.e., normal (N), inflammatory bowel disease (IBD), adenoma (A) and colorectal cancer (T) as indicated by different colours in the figure. This figure implies that the increased ESTs in these libraries might be positively associated with gene redundancy in these profiles.

Figure 2

Comparison of gene distribution in 4 gene expression profiles. As depicted in the figure, area within the red, green, blue and grey circle is representative for the profile of N (normal), IBD (inflammatory bowel disease), A (adenoma) and T (cancer), respectively. Genes in A, IBD and N were all found in T, implying heterogeneity of colorectal cancer. Overlapping areas as filled by different colours are interpreted as the common genes among profiles. For example, the black area means the coexpressed genes in N, IBD and A, and the number "186" on it represents the total of related genes.

Figure 3

Level 4 categories under biological_process in the T library as compared with the total genes in the whole human genome. Red bar: genes in T (colorectal cancer) library; Blue bar: whole genes in the human genome. The different biological categories are labeled along the X-axis and the gene numbers in each catalogue are in the Y-axis. Catalogues with significantly enriched gene numbers is indicated by red words as compared with genes in the whole human genome (p < 0.01, Hypergeometric test).

Figure 4

Expression of SOX9 and β-catenin in colorectal cancers. Semi-quantitative RT-PCR shows SOX9 and β-catenin expression in colorectal cancer tissues (Left) and cell lines (Right). Representative names of each sample or cell line are listed under the figure. T stands for cancer tissue and N for matched normal colonic mucosa. GAPDH is used as the normalization control and given at the bottom of the figure. Up-regulation of SOX9 and β-catenin is present in case 1, 2, 3, 4 and 6, and down-regulation only in 5. All cell lines have the expression of both genes.