title: Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon.
abstract: In order to discover global gene expression patterns characterizing subgroups of colon cancer, microarrays were hybridized to labeled RNAs obtained from seventeen colonic specimens (nine carcinomas and eight normal samples). Using a hierarchical agglomerative method, the samples grouped naturally into two major clusters, in perfect concordance with pathological reports (colon cancer versus normal colon). Using a variant of the unpaired t-test, selected genes were ordered according to an index of importance. In order to confirm microarray data, we performed quantitative, real-time reverse transcriptase-polymerase chain reaction (TaqMan RT-PCR) on RNAs from 13 colorectal tumors and 13 normal tissues (seven of which were matched normal-tumor pairs). RT-PCR was performed on the gro1, B-factor, adlican, and endothelin converting enzyme-1 genes and confirmed microarray findings. Two hundred and fifty genes were identified, some of which were previously reported as being involved in colon cancer. We conclude that cDNA microarraying, combined with bioinformatics tools, can accurately classify colon specimens according to current histopathological taxonomy. Moreover, this technology holds promise of providing invaluable insight into specific gene roles in the development and progression of colon cancer. Our data suggests that a large-scale approach may be undertaken with the purpose of identifying biomarkers relevant to cancer progression.
authors.affiliation: Department of Medicine, Division of Gastroenterology and Greenebaum Cancer Center, University of Maryland School of Medicine and Baltimore VA Hospital, Baltimore, Maryland, MD 21201, USA.
authors.forename: Tong-Tong
authors.initials: TT
authors.lastname: Zou
authors.forename: Florin M
authors.initials: FM
authors.lastname: Selaru
authors.forename: Yan
authors.initials: Y
authors.lastname: Xu
authors.forename: Valentina
authors.initials: V
authors.lastname: Shustova
authors.forename: Jing
authors.initials: J
authors.lastname: Yin
authors.forename: Yuriko
authors.initials: Y
authors.lastname: Mori
authors.forename: David
authors.initials: D
authors.lastname: Shibata
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Sato
authors.forename: Suma
authors.initials: S
authors.lastname: Wang
authors.forename: Andreea
authors.initials: A
authors.lastname: Olaru
authors.forename: Elena
authors.initials: E
authors.lastname: Deacu
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Liu
authors.forename: John M
authors.initials: JM
authors.lastname: Abraham
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Meltzer
mesh_terms: D000368:Aged; D002277:Carcinoma / Q000145:classification* / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D003106:Colon / Q000378:metabolism; D003110:Colonic Neoplasms / Q000145:classification* / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D019295:Computational Biology / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis; D012334:RNA, Neoplasm / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D012333:RNA, Messenger; D012334:RNA, Neoplasm