Identification of colorectal cancer, adenoma, and inflammatory bowel disease specific gene expression patterns using whole genomic oligonucleotide microarray system

Abstract

Discrimination and classification of colorectal diseases (adenoma, colorectal cancer, inflammatory bowel disease) using biopsy samples and expression microarrays, has not been solved yet, nevertheless, it can contribute to the understanding of the colonic diseases. Total ribonucleic acid was extracted, amplified and biotinylated from frozen colonic biopsies of 15 patients with colorectal cancer, 15 with adenoma, 14 with inflammatory bowel disease and 8 normal controls. Genome-wide gene expression profile was evaluated by Human Genome U133 Plus 2.0 microarrays. Two independent methods were used for data normalization and "Prediction Analysis of Microarrays" was performed for feature selection. Leave one-out stepwise discriminant analysis was performed. The expression results were verified by real-time polymerase chain reaction. Top validated genes included CD44 antigen, met proto-oncogene, chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette-A8 genes in adenoma; collagen IValpha1, lipocalin-2, calumenin, aquaporin-8 genes in colorectal cancer; and lipocalin-2, ubiquitin D and interferon induced transmembrane protein 2 genes in inflammatory bowel disease. The discriminant analysis was able to classify the samples in overall 96.2% using 7 discriminatory genes. The expression of 94% of the 52 genes measured by Taqman real-time polymerase chain reaction correlated with the results obtained using Affymetrix microarrays at a significance of p < 0.05. We successfully performed whole genomic microarray analysis to identify discriminative signatures using routine biopsy samples. The results set up data warehouse which can be further mined.