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Background Collagenous colitis (CC) is a common inflammatory bowel disease that exhibits chronic watery diarrhoea. Treatment with the glucocorticoid budesonide is effective to induce and maintain clinical remission in most cases; however, few patients do not respond to treatment. To distinguish between different CC subgroups on a molecular level, we performed genome-wide RNA sequencing (RNAseq) analysis on mucosal samples. Methods We collected colonic biopsies from healthy controls (Hc) and CC patients with active disease. Additionally, we obtained matched samples from budesonide-responsive patients (clinical remission) under treatment with budesonide (9 mg/day, 8 weeks), and biopsies from budesonide-refractory patients (n = 9 patients/group). Ulcerative colitis (UC) samples were included as a separate control. Total RNA was isolated for RNAseq. Whole-genome expression data were analysed by principal component analysis (PCA) and differential gene expression (DGE) using R software. The Benjamini–Hochberg FDR method adjusted p values, considering &amp;lt;0.05 as statistically significant. Gene-set enrichment analysis (GSEA) was performed using GSEA software and visualised in Cytoscape. Results were validated in tissue samples from the same patients by immunohistochemistry (IHC). Results PCA of all samples identified three principal components which separated sample groups into distinct clusters of gene expression, explaining 31% of the transcriptional variation. PCA clearly demarcated UC samples from Hc and CC. Mucosal samples from budesonide-refractory patients exhibited a discrete RNA expression profile that was distinct from all other groups. Moreover, PCA of budesonide-responsive persons also separated active from treated CC. Subsequent DGE analysis revealed differential expression of 395 genes in patients with active CC compared with Hc, and that these genes were mainly involved in immune response, cell cycle and apoptosis, according to GSEA. Using IHC, we confirmed the impaired proliferation and immune response on the protein level. In samples from budesonide-treated patients, 75 genes were differentially regulated compared with controls. A paired comparison of matched samples from CC patients before and after induction of remission showed an expression change of 337 genes, mainly involved in DNA recognition. Conclusion CC is a transcriptionally homogeneous disease that can be characterised by differential gene expression. Unique gene expression profiles describe patient sub-populations, which could define budesonide-refractory CC as a distinct disease entity. Further study of the transcriptional landscape of CC may reveal pathogenic mechanisms and therapeutic targets for this common, debilitating inflammatory bowel disease.

P008 Whole-genome RNA sequencing in collagenous colitis: a subgroup analysis