Correlation of Biomarker Expression in Colonic Mucosa with Disease Phenotype in Crohn's Disease and Ulcerative Colitis

Abstract

Background: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are characterized by chronic intestinal inflammation due to immunological, microbial, and environmental factors in genetically predisposed individuals. Advances in the diagnosis, prognosis, and treatment of IBD require the identification of robust biomarkers that can be used for molecular classification of diverse disease presentations. We previously identified five genes, RELA, TNFAIP3 (A20), PIGR, TNF, and IL8, whose mRNA levels in colonic mucosal biopsies could be used in a multivariate analysis to classify patients with CD based on disease behavior and responses to therapy.

Aim: We compared expression of these five biomarkers in IBD patients classified as having CD or UC, and in healthy controls.

Results: Patients with CD were characterized as having decreased median expression of TNFAIP3, PIGR, and TNF in non-inflamed colonic mucosa as compared to healthy controls. By contrast, UC patients exhibited decreased expression of PIGR and elevated expression of IL8 in colonic mucosa compared to healthy controls. A multivariate analysis combining mRNA levels for all five genes resulted in segregation of individuals based on disease presentation (CD vs. UC) as well as severity, i.e., patients in remission versus those with acute colitis at the time of biopsy.

Conclusion: We propose that this approach could be used as a model for molecular classification of IBD patients, which could further be enhanced by the inclusion of additional genes that are identified by functional studies, global gene expression analyses, and genome-wide association studies.

Keywords: Colonic mucosa; Crohn’s disease; Multivariate analysis; Ulcerative colitis; mRNA biomarkers.

Fig. 1

Expression of 5 biomarkers in colonic mucosa of UC patients and healthy controls. CD and UC patients were sub-classified as being in remission or with acute inflammation, based on macroscopic evidence of localized tissue inflammation during colonoscopy. For the purpose of this analysis, biopsies were obtained from regions of the colon of CD and UC patients that were not visibly inflamed, and absence of inflammation in these biopsies was confirmed microscopically. Levels of mRNA were measured by qRT-PCR and normalized to β2-microglobulin. Horizontal lines indicate the median level of mRNA for each group. Significant differences among groups were determined by the Mann-Whitney non-parametric test.

Fig 2

Principal component analysis of gene expression in colonic mucosa. Levels of mRNA for 5 biomarkers were analyzed as described for Fig. 1, combined for all subjects, then reduced to 2 principal components (PCs) for each individual based on the sum of the normalized expression level multiplied by the weighting coefficient for each gene (Table 4). Symbols denote individual subjects, including healthy controls (green), CD patients (red) and UC patients (yellow). CD or UC patients in remission are denoted by squares, and patients with acute inflammation are denoted by triangles. Individuals were distributed into 4 quadrants based on their scores for PC1 and PC2: A, PC1 < 0, PC2 < 0; B, PC1 > 0, PC2 < 0; C, PC1 > 0, PC2 > 0; D, PC1 < 0, PC2 > 0.