Inflammatory gene signature in ulcerative colitis with cDNA macroarray analysis

Aliment Pharmacol Ther. 2005 May 1;21(9):1091-7. doi: 10.1111/j.1365-2036.2005.02443.x.


Background: Most array analyses of ulcerative colitis have focused on identifying susceptibility genes for ulcerative colitis.

Aim: To clarify the changes in gene expression during inflammation in ulcerative colitis colon mucosa using cDNA macroarray.

Methods: From 23 ulcerative colitis patients, 16 each of inflamed and non-inflamed specimens (total 32 samples for individual analysis) were obtained by colonoscopic biopsy. Eighteen of the 32 samples, used for pairwise analysis, consisted of nine sample pairs, each pair being from the same patient. We examined expression profiles of approximately 1300 genes with cDNA macroarray. Comparisons were made using two kinds of statistics, t-test and significance analysis of microarray in both analyses. The reproducibility of significant genes from the macroarray analysis was confirmed by real-time ploymerase chain reaction.

Results: We detected five upregulated genes, categorized into proinflammatory genes (MRP14, GRO gamma and SAA1) and anti-inflammatory genes (TIMP1 and Elafin) in inflamed mucosa, and one upregulated gene (L-FABP) in non-inflamed mucosa.

Conclusions: As the cDNA macroarray analysis in this study exactly reflects the total profile of gene expression in the clinical setting of ulcerative colitis, the genes identified will be directly applicable to diagnostics or as novel therapeutic targets in active ulcerative colitis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acrosome
  • Adult
  • Antigens / genetics
  • Calgranulin B / genetics
  • Carrier Proteins / genetics
  • Chemokine CXCL1
  • Chemokines, CXC / genetics
  • Colitis, Ulcerative / genetics*
  • DNA, Complementary / analysis*
  • DNA, Complementary / genetics
  • Fatty Acid-Binding Proteins
  • Genes / genetics*
  • Humans
  • Inflammation / genetics
  • Intercellular Signaling Peptides and Proteins / genetics
  • Isoantigens
  • Oligonucleotide Array Sequence Analysis
  • Proteinase Inhibitory Proteins, Secretory
  • Proteins / genetics
  • RNA / analysis
  • RNA / genetics
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Seminal Plasma Proteins
  • Tissue Inhibitor of Metalloproteinase-1 / genetics
  • Up-Regulation / genetics


  • Antigens
  • CXCL1 protein, human
  • Calgranulin B
  • Carrier Proteins
  • Chemokine CXCL1
  • Chemokines, CXC
  • DNA, Complementary
  • FABP1 protein, human
  • Fatty Acid-Binding Proteins
  • Intercellular Signaling Peptides and Proteins
  • Isoantigens
  • Proteinase Inhibitory Proteins, Secretory
  • Proteins
  • SPACA1 protein, human
  • Seminal Plasma Proteins
  • Tissue Inhibitor of Metalloproteinase-1
  • RNA