mRNA expression, functional profiling and multivariate classification of colon biopsy specimen by cDNA overall glass microarray

World J Gastroenterol. 2006 Nov 21;12(43):6998-7006. doi: 10.3748/wjg.v12.i43.6998.


Aim: To understand the local pathophysiological alterations and gene ontology-based functional classification of colonic biopsies into inflammatory and neoplastic diseases.

Methods: Total RNA was extracted from frozen biopsies and amplified by T7-method. Expression profile was evaluated by Atlas Glass 1K microarrays. After microarray quality control, applicable data were available from 10 adenomas, 6 colorectal adenocarcinomas (CRCs), and 6 inflammatory bowel diseases (IBDs). Multivariate statistical and cell functional analyses were performed. Real-time RT-PCR and immunohistochemistry were used for validation.

Results: Discriminant analysis of selected genes, could correctly reclassify all 22 samples using 4 parameters (heat shock transcription factor-1, bystin-like, calgranulin-A, TRAIL receptor 3). IBD samples were characterized by overregulated chemokine (C-X-C motif) ligand 13, replication protein A1, E74-like factor 2 and downregulated TNF receptor-associated factor 6, BCL2-interacting killer genes. In adenomas upregulation of TNF receptor-associated factor 6, replication protein A1, E74-like factor 2 and underexpression of BCL2-associated X protein, calgranulin-A genes were found. CRC cases had significantly increased epidermal growth factor receptor, topoisomerase-1, v-jun, TNF receptor-associated factor 6 and TRAIL receptor 3, and decreased RAD51 and RAD52 DNA repair gene, protein phosphatase-2A and BCL2-interacting killer mRNA levels. Epidermal growth factor receptor RT-PCR and immunohistochemistry, topoisomerase-1 RT-PCR confirmed the chip results.

Conclusion: Different histological alterations can be reclassified by functional, multivariate analysis using cDNA microarrays. Further studies with expanded sample number are needed for subclassification of pathological alterations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenocarcinoma / diagnosis
  • Adenocarcinoma / genetics
  • Adenocarcinoma / metabolism
  • Aged
  • Aged, 80 and over
  • Analysis of Variance
  • Biopsy
  • Cluster Analysis
  • Colon / metabolism
  • Colon / pathology*
  • Colorectal Neoplasms / diagnosis
  • Colorectal Neoplasms / genetics
  • Colorectal Neoplasms / metabolism
  • DNA / genetics
  • DNA, Neoplasm / genetics
  • Female
  • Gene Expression Profiling / methods*
  • Genetic Markers
  • Humans
  • Male
  • Middle Aged
  • Multivariate Analysis
  • Oligonucleotide Array Sequence Analysis / methods*
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Reproducibility of Results


  • DNA, Neoplasm
  • Genetic Markers
  • RNA, Messenger
  • DNA