Molecular profiling of a rat model of colitis: validation of known inflammatory genes and identification of novel disease-associated targets

Inflamm Bowel Dis. 2006 Oct;12(10):950-66. doi: 10.1097/01.mib.0000231575.11678.8c.


Background: Inflammatory bowel disease (IBD) is a disease of unknown etiology characterized by acute and chronic relapsing inflammation. The most suitable animal model for studying this disease is still under debate. Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in both the human condition and animal models.

Aim: To identify differentially expressed genes in the 2,4,6-trinitrobenzene sulfonic acid (TNBS) model of experimental colitis and compare gene expression profiles with that reported in patients.

Methods: Colitis was induced by TNBS administration (30 mg in 50% ethanol) in female Sprague-Dawley rats. Controls received the vehicle. Seventy-two hours later, the animals were killed, the colons were removed and scored for damage, and total RNA was isolated. Gene expression levels were analyzed after hybridizing experimental and control cDNA to PIQOR Toxicology Rat Microarrays containing 1,252 genes. Genes with 2-fold or more higher or 0.5-fold or less lower expression levels were selected as significantly differentially expressed. Results were validated using real-time reverse-transcription polymerase chain reaction (RT-PCR).

Results: We observed increased expression of genes that have previously been shown to be up-regulated in IBD patients, including chemokines/cytokines, extracellular matrix/remodeling genes, transcription factors and tumor necrosis factor family members. Using real-time RT-PCR, we validated 9 of 10 critical genes identified by DNA microarray. Fibulin 2 and lysyl oxidase are among some of the novel genes not previously associated with IBD that could potentially be related to the pathogenesis of this condition.

Conclusion: We provide evidence supporting the TNBS colitis model as an appropriate tool to study the pathology of IBD and identify molecular targets with clinical relevance.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Validation Study

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Colitis / chemically induced
  • Colitis / genetics*
  • Colitis / metabolism
  • Disease Models, Animal
  • Electronic Data Processing
  • Female
  • Gene Expression Profiling / methods*
  • Inflammation Mediators / metabolism*
  • Oligonucleotide Array Sequence Analysis / methods
  • Rats
  • Rats, Sprague-Dawley
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Trinitrobenzenesulfonic Acid


  • Biomarkers
  • Inflammation Mediators
  • Trinitrobenzenesulfonic Acid