Abstract Background Intestinal epithelia is key in ulcerative colitis (UC) pathogenesis. However, epithelial models that capture the human variations for pre-clinical screening of epithelial-directed interventions are limited. We aimed to determine whether ex-vivo colonoids derived from different UC patients, maintain inflammatory signals associated with UC. Methods Rectal biopsies-derived epithelial colonoids were maintained through 4-9 passages (>1 month in culture) using an L-WRN-conditioned medium, differentiated for 48h, and were either left untreated or treated with inflammatory cocktails for an additional 24h. ELISA quantified CXCL1 secretion, mRNAseq and qPCR assessed mRNA levels Results 7 controls and 9 UC colonoids were generated from different subjects (median age was 16 years, 56% females). After 4-9 passages, untreated colonoids from UC patients secreted significantly higher levels of the CXCL1 chemokine compared to colonoids obtained from non-IBD controls (Fig. 1A). This phenomenon was also observed when colonoids were treated with INFγ and TNFα to mimic gut inflammation (Fig. 1B). mRNAseq further confirmed differences between UC and non-IBD colonoids. Unsupervised PCA analyses indicated the separation of 4/8 UC organoids from control organoids on PC1 (explaining 39% variance) and toward organoids treated ex-vivo with INFγ and TNFα (Fig. 1C). Differential expression (fold change >1.5 and FDR <0.05) identified 800 genes significantly upregulated, and 263 genes downregulated in untreated UC compared to control colonoids following passaging (Fig. 2A). Upregulated genes included DUOX2, DUOXA2, VDAC2, TJP1 (ZO1), TGM2, CXCL1, and IL8, as previously observed in mucosal biopsies from UC (PMID: 36655602) (Fig. 2B). Functional annotation of the upregulated genes highlighted pathways related to responses to wounding, bacterial signals, and cell-cell junctions (FDR<1E-10) (Fig. 2C). Conversely, downregulated genes included lipoprotein lipase (LPL), a key enzyme in lipid metabolism, the sulfate/anion transporter gene SLC26A1, and the mitochondrial coenzyme A transporter SLC25A42 (Fig. 2A-B). Functional enrichment analysis of the downregulated genes revealed associations with rRNA binding (FDR=1E-12) and mitochondrial gene expression (FDR=1E-6), all of which are relevant to UC pathogenesis (Fig. 2C). The expression of these genes and pathways were further induced with inflammatory triggering (Fig. 2D). Conclusion UC epithelial cells maintain a heightened inflammatory response ex-vivo after several passaging. This suggests an "inflammatory" epithelial transcriptional memory that may contribute to UC chronicity, justifying the use of this model for testing interventions targeted at the epithelium.
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