Gene expression profile at single cell level of patient-derived colon fibroblasts induced by different cytokine cocktails to become inflammation-associated fibroblasts (IAFs)

IAFs are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. One major problem is that IAFs do not persist after in vitro culture. Here we used single cell RNA sequencing (scRNA-seq) to validate and analyze the diversity of different cytokine-induced IAFs. Eight patient-derived colon fibroblast lines were generated and treated with no treatment (earlier passage), no treatment (older passage), IL1β+TNFα, IL4+IL13+TNFα, or TNFα for 96hrs. After treatment, fibroblasts were dissociated and sorted into single cells and analyzed using scRNAseq.