Integrative Transcriptomic and Metabonomic Molecular Profiling of Colonic Mucosal Biopsies Indicates a Unique Molecular Phenotype for Ulcerative Colitis

Ulcerative colitis is the most prevailing entity of several disorders under the umbrella term inflammatory bowel disease, with potentially serious symptoms and devastating consequences for affected patients. The exact molecular etiology of ulcerative colitis is not yet revealed. In this study, we characterized the molecular phenotype of ulcerative colitis through transcriptomic and metabonomic profiling of colonic mucosal biopsies from patients and controls. We have characterized the extent to which metabonomic and transcriptomic molecular phenotypes are associated with ulcerative colitis versus controls and other disease-related phenotypes such as steroid dependency and age at diagnosis, to determine if there is evidence of enrichment of differential expression in candidate genes from genome-wide association studies and if there are particular pathways influenced by disease-associated genes. Both transcriptomic and metabonomic data have previously been shown to predict the clinical course of ulcerative colitis and related clinical phenotypes, indicating that molecular phenotypes reveal molecular changes associated with the disease. Our analyses indicate that variables of both transcriptomics and metabonomics are associated with disease case and control status, that a large proportion of transcripts are associated with at least one metabolite in mucosal colonic biopsies, and that multiple pathways are connected to disease-related metabolites and transcripts

Box plot of RT-PCR results.

<p>Real time RT-PCR quantification of genes differentially expressed in inflamed CD smokers and non-smokers. Transcript copy numbers for ring finger protein 138 (RFP138), phosphoglucomutase 2-like 1 (PGM2L1), metallothionein 2A (MT2A), STEAP family member 3 (STEAP3), and potassium inwardly-rectifying channel, subfamily J, member 2 (KCNJ2) were measured in RNA extracted from all inflamed CD biopsy samples. The copy numbers of ribosomal protein L10 were used for normalization between samples. The box border represents the interquartile range, and the horizontal line in the box is the median. *, significant difference between smokers and non-smokers.</p

Clinical details.

<p>CD: Crohn's disease, CDAI: Crohn's Disease Activity Index.</p

Differential expressed genes on DNA micro-arrays in CD inflamed smokers vs. CD inflamed non-smokers.

<p>The significance level for the Wilcoxon's rank sum was set at 2×10⁻⁴.</p><p>The Q value is the minimum <i>false discovery rate</i> set at 0.15.</p><p>Fold Change: up-regulated (+), down-regulated (−) in the smokers.</p