Inflammation, adenoma and cancer: Objective classification of colon biopsy specimens with gene expression signature

摘要

Abstract. Gene expression analysis of colon biopsies using high-density oligonucleotide microarrays can contribute to the understandingnof local pathophysiological alterations and to functional classification of adenoma (15 samples), colorectal carcinomasn(CRC) (15) and inflammatory bowel diseases (IBD) (14). Total RNA was extracted, amplified and biotinylated fromnfrozen colonic biopsies. Genome-wide gene expression profile was evaluated by HGU133plus2 microarrays and verified bynRT-PCR. We applied two independent methods for data normalization and used PAM for feature selection. Leave one-outnstepwise discriminant analysis was performed. Top validated genes included collagenIVα1, lipocalin-2, calumenin, aquaporin-8ngenes in CRC; CD44, met proto-oncogene, chemokine ligand-12, ADAM-like decysin-1 and ATP-binding casette-A8 genes innadenoma; and lipocalin-2, ubiquitin D and IFITM2 genes in IBD. Best differentiating markers between Ulcerative colitis andnCrohn’s disease were cyclin-G2; tripartite motif-containing-31; TNFR shedding aminopeptidase regulator-1 and AMICA. Thendiscriminant analysis was able to classify the samples in overall 96.2% using 7 discriminatory genes (indoleamine-pyrrole-2,3-ndioxygenase, ectodermal-neural cortex, TIMP3, fucosyltransferase-8, collectin sub-family member 12, carboxypeptidase D, andntransglutaminase-2). Using routine biopsy samples we successfully performed whole genomic microarray analysis to identifyndiscriminative signatures. Our results provide further insight into the pathophysiological background of colonic diseases. Thenresults set up data warehouse which can be mined further.