Genome-wide Pathway Analysis Using Gene Expression Data of Colonic Mucosa in Patients with Inflammatory Bowel Disease

Abstract

Background: Ulcerative colitis (UC) and Crohn's disease (CD) share some pathogenetic features. To provide new steps on the role of altered gene expression, and the involvement of gene networks, in the pathogenesis of these diseases, we performed a genome-wide analysis in 15 patients with CD and 14 patients with UC by comparing the RNA from inflamed and noninflamed colonic mucosa.

Methods: Two hundred ninety-eight differentially expressed genes in CD and 520 genes in UC were identified. By bioinformatic analyses, 34 pathways for CD, 6 of them enriched in noninflamed and 28 in inflamed tissues, and 19 pathways for UC, 17 in noninflamed and 2 in inflamed tissues, were also highlighted.

Results: In CD, the pathways included genes associated with cytokines and cytokine receptors connection, response to external stimuli, activation of cell proliferation or differentiation, cell migration, apoptosis, and immune regulation. In UC, the pathways were associated with genes related to metabolic and catabolic processes, biosynthesis and interconversion processes, leukocyte migration, regulation of cell proliferation, and epithelial-to-mesenchymal transition.

Conclusions: In UC, the pattern of inflammation of colonic mucosa is due to a complex interaction network between host, gut microbiome, and diet, suggesting that bacterial products or endogenous synthetic/catabolic molecules contribute to impairment of the immune response, to breakdown of epithelial barrier, and to enhance the inflammatory process. In patients with CD, genes encoding a large variety of proteins, growth factors, cytokines, chemokines, and adhesion molecules may lead to uncontrolled inflammation with ensuing destruction of epithelial cells, inappropriate stimulation of antimicrobial and T cells differentiation, and inflammasome events.

FIGURE 1

Real-time polymerase chain reaction analysis for the genes CREM, ICAM3, JAK2, PTRF, PUS10, AK3, CEBPA, SULT1A2, THRA, and CYLD in inflamed versus not inflamed CD (n = 40). Box plot indicates the expression levels of all tested samples. Data were expressed as 2^-ΔΔCt.

FIGURE 2

UC, pathways enriched in UC; Real-time polymerase chain reaction analysis for the genes CREM, ICAM3, JAK2, PTRF, PUS10, LRRK2, MAP4K4, REXO2, TNFRSF9, and CDH3 in inflamed versus not inflamed UC (n = 40). Box plot indicates the expression levels of all tested samples. Data were expressed as 2^-ΔΔCt.

FIGURE 3

Nodes denote enriched gene sets or “annotation terms/categories”; node size is proportional to the number of genes in each gene set. Node color (red: enriched pathways in inflamed tissues; green: enriched pathways in noninflamed tissues) denotes the gene set enrichment score. Only significantly enriched (P < 0.01) gene sets are shown. Pathways shared by both diseases have at least one P < 0.01 and the other one P < 0.05. CD, pathways enriched in CD; IBD, pathways enriched shared between CD and UC; UC, pathways enriched in UC.