Gene expression profiling of colorectal tissues in the early adenoma-carcinoma sequence

Colorectal cancer (CRC) is the third most common cancer worldwide. Colorectal polyps are pre-cursors of CRC; however hyperplastic polyps (HPs) lack malignant potential. The aim of this thesis was to describe differences in gene expression and pathway activation between colorectal tissues (normal mucosa and polyp) from early stages of CRC development and to validate novel candidate genes identified by qRT-PCR. Differential gene expression was investigated in 48 colorectal tissues from the early stages of the adenoma-carcinoma sequence using DASL Whole-Genome expression microarrays and appropriate bioinformatics. Particular emphasis was placed on the comparison between Adenomatous polyps (APs) and HPs as lesions with and without malignant potential. In the comparison between HP and AP tissues 1633 significantly differentially expressed genes (DEGs) (p<0.05) and 33 pathways were identified, which confirms the fundamental differences between these polyps. Moreover, DEGs associated with Wnt-Signalling, MAPK Signalling, p53 Signalling, cell cycle and apoptosis were noted between HPs and APs. In addition, a novel network was created using COXPRESSdb, which found connections between genes comparing HP and AP tissues. Six candidate genes were selected based on their differential expression across the range of colorectal tissues; ASCL2, ANXA2, AXIN2, ETS2, G3BP1 and TFF2. qRT-PCR was employed to investigate expression of these candidate genes in a larger Validation Set (n=143) of colorectal tissues. With the exception of TFF2, significant differential expression was identified for all genes, which supported the results of the DASL microarray. Again the most significant differences identified were between HPs and APs. In conclusion, HPs and APs have different malignant potential, with associated differential gene expression profiles, which could be exploited for screening and to provide potential therapeutic candidates.