P667. Dissecting the role of unfolded protein response pathway in inflammatory bowel disease: in silico mRNA-miRNA co-expression analysis
O. Palmieri1, F. Bossa1, M.T. Creanza2, T. Latiano1, G. Corritore1, D. Scimeca1, G. Biscaglia1, V.C. Liuzzi2, R. Anglani2, M. Carella3, V. Annese4, A. Andriulli1, A. Latiano1, 1IRCCS ‘Casa Sollievo della Sofferenza’ Hospital, Division of Gastroenterology, San Giovanni Rotondo, Italy, 2CNR, Istituto di Studi sui Sistemi Intelligenti per l'Automazione, Bari, Italy, 3IRCCS ‘Casa Sollievo della Sofferenza’ Hospital, Division of Medical Genetics, San Giovanni Rotondo, Italy, 4AOU Careggi, SOD2, Division of Gastroenterolgy, Firenze, Italy
Genetic models, specifically in the intestinal epithelium, have provided avenues to understand the diverse pathways whereby intestinal epithelial cells direct the mucosal immune state in IBD. Among these pathways of note is the unfolded protein response (UPR) induced by stress in the endoplasmic reticulum (ER). Moreover, inflammation modulates the expressions of miRNAs that influence the production of mRNAs or proteins. We performed a gene expression, miRNA profile, pathways and in silico mRNA-miRNA co-expression analyses in biopsies of IBD patients.
Paired expression levels of mRNAs and miRNAs were measured on 15 Crohn's Disease (CD) and 15 ulcerative colitis (UC) inflamed and in the corresponding non-inflamed tissues, using Human Gene 1.0 ST Array and miRNA 2.0 Array, on Affymetrix platform. Differential expression (DE), for both mRNA and miRNA profiles, was evaluated by performing paired t-tests, and the False Discovery Rate (FDR) by the Benjamini and Hochberg procedure. The gene set Reactome Unfolded Protein Response was analyzed in terms of enrichment with respect to differential expression by using RS Method.
Comparing inflamed vs non inflamed tissues by pathway analysis, the whole UPR pathway, that comprises 20 genes, was associated to both UC (P < 0.00001) and CD (P < 0.04). In inflamed UC and CD biopsies, 14 (P < 0.016, FDR <0.09) and 7 (P < 0.027, FDR <0.16) genes, respectively, were up regulated. A bipartite network was constructed linking one gene with a miRNA when they result differentially correlated (DC) with a P < 0.01. In UC patients 23 miRNAs were DE (P < 0.05) and also DC with at least one gene in UPR pathway. Of these, 5 were DC with at least 3 genes: miR-194*, miR-200C, miR-595, miR-627, miR-548I. In CD patients 32 miRNAs DE (P < 0.05) were also DC with at least one gene in the pathway. Of these, 6 were DC with at least 3 genes: miR-369–5P, miR-380, miR-493*, miR-503, miR-675 and miR-2355. By analyzing in UC specimens the three major arms of UPR pathway, corresponding to ATF4, ATF6 and XBP1 genes, we found that these genes were DC with 2, 3 and 6 miRNAs, respectively; in CD, ATF6 was DC with 7, and XBP1 with 14 miRNAs. Among hub genes identified for specific miRNAs, the XPB1 gene was the most enriched of connections.
Using a miRNA-mRNA integrated expression analysis, we find that the UPR pathway is involved in the pathogenic mechanisms, principally in UC patients, shedding a new light on the paradigm of the ER stress and inflammation.