Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays

Using an oligonucleotide array containing sequences complementary to simila r to 3200 full-length human tDNAs and 3400 expressed sequence tags (GeneChi p, Affymetrix), mRNA expression patterns were probed in 18 colon adenocarci nomas and 4 adenomas, Paired normal tissue was available and analyzed for e ach of the tumors. Relatively few changes in transcript expression are asso ciated with colon cancer. Nineteen transcripts (0.48% of those detected) ha d at least 4-10.5-fold higher mRNA expression in carcinoma compared with pa ired normal samples, whereas 47 transcripts (1.3% of those detected) had at least 4-38-fold or lower expression in tile tumor tissue compared with the normal samples. Some of these differences were confirmed by reverse transc ription-PCR. Many of these transcripts were already known to be abnormally expressed in neoplastic tissue in general, or colon cancer in particular, a nd several of these differences were also observed in premalignant adenoma samples. A two-way hierarchical clustering algorithm successfully distingui shed adenoma from adenocarcinoma and normal tissue, generating a phylogenet ic tree that appropriately represented the clinical relationship between th e three tissue types included in the analysis. This supports the concept th at genome-wide expression profiling may permit a molecular classification o f solid tumors.