Comparative study of gene expression in human colorectal cancer tissues and normal mucosa

The purpose of our study was to better understand the genetic mechanism of oncogenesis for human colorectal cancer and to identify potential new tumour markers of use in clinical practice. Results: Comparing cancerous tissues with normal colonic mucosa we identified 584 known genes (3%) differentially expressed to a significant degree (p<0.001). Many of the transcripts that were more abundant in tumours than in non-neoplastic tissues appear to reflect important events for colon carcinogenesis. For example, a significant number of these genes serve as apoptotic inhibitors (e.g. BFAR, BIRC1, BIRC6). Furthermore, we observed the simultaneous upregulation of HLA-E and the downregulation of b2-microglobulin; these genes strongly support a potential tumour escape strategy from immune surveillance in colon cancer tissues. Conclusions: Our study provides new gene candidates in the pathogenesis of human CRC disease. From our results we hypothesise that CRC cells escape immune surveillance through a specific gene expression alteration; moreover, overexpression of several survival genes seems to confer a more anti-apoptotic phenotype. These genes are involved in pathways not previously implicated in CRC pathogenesis and they may provide new targets for therapy. Keywords: disease state analysis We used cDNA microarrays to compare gene expression profiles of colorectal biopsies from 25 CRC patients and 13 normal mucosa from adjacent noncancerous tissues. Normal samples were pooled in equimolar amounts to generate a single standard reference RNA employed as a control in each microarray hybridisation. For half of microarray hybridisations, total RNA isolated from each tumour sample were retrotranscribed and labelled with Cy5-dCTP and cDNA obtained from the standard reference RNA was labelled with Cy3-dCTP; the fluorochromes were inverted in the second half of microarrays with the purpose of reducing dye bias. Findings were validated by real time PCR; in addition, western blotting and immunochemistry analysis were carried out as further confirmation of differential expression at a protein level.