title: Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas.
abstract: To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e-7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node-negative and lymph node-positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/beta-catenin signaling cascade, suggesting similar pathogenic pathways.
authors.affiliation: Department of General Surgery, University Medical Center, Robert-Koch-Strasse 40, 37075 Göttingen, Germany.
authors.forename: Marian
authors.initials: M
authors.lastname: Grade
authors.forename: Patrick
authors.initials: P
authors.lastname: Hörmann
authors.forename: Sandra
authors.initials: S
authors.lastname: Becker
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Hummon
authors.forename: Danny
authors.initials: D
authors.lastname: Wangsa
authors.forename: Sudhir
authors.initials: S
authors.lastname: Varma
authors.forename: Richard
authors.initials: R
authors.lastname: Simon
authors.forename: Torsten
authors.initials: T
authors.lastname: Liersch
authors.forename: Heinz
authors.initials: H
authors.lastname: Becker
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Difilippantonio
authors.forename: B Michael
authors.initials: BM
authors.lastname: Ghadimi
authors.forename: Thomas
authors.initials: T
authors.lastname: Ried
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000782:Aneuploidy; D003106:Colon / Q000378:metabolism / Q000502:physiology; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D007413:Intestinal Mucosa / Q000378:metabolism / Q000502:physiology; D008198:Lymph Nodes / Q000473:pathology*; D008207:Lymphatic Metastasis; D008297:Male; D008875:Middle Aged; D005810:Multigene Family; D009367:Neoplasm Staging; D020133:Reverse Transcriptase Polymerase Chain Reaction