GSE135170
RNA-Sequencing of epithelium and colonoids from patients with pediatric inflammatory bowel disease
Objective: Children with very early onset inflammatory bowel disease (VEO IBD) present with more extensive, severe, and refractory disease than older children and adults with IBD. In the current study, we evaluated functional and transcriptomic differences in epithelial cells from patients with VEO and older onset IBD compared to controls. Design: We established enteroids and colonoid lines from patients with VEO and older onset IBD and control patients. We evaluated crypt conversion (initial growth efficiency) compared to histopathological and clinical parameters. We performed RNA-sequencing on colonoids followed by validation via qPCR and flow cytometry in additional patients and in colonoids after multiple passages. Results: Control enteroids and colonoids exhibited consistently high crypt conversion, whereas patients with VEO and older onset IBD exhibited decreased crypt conversion associated with higher inflammation scores. Transcriptomic analysis revealed increased expression of LYZ, reported previously in colonoids from adult patients with ulcerative colitis, as well as antigen presentation genes HLA-DRB1 and HLA-DRA, which persisted after prolonged passaging as verified by flow cytometry. Conclusion: We present the first functional comparison of enteroids and colonoids from patients with VEO and older onset IBD, a subset of which exhibit poor initial growth. Enhanced and persistent expression of epithelial antigen presentation genes in patient colonoids supports the notion that epithelial cell-intrinsic differences may result from or contribute to disease. Analyses of colonoids from pediatric patients with IBD will contribute to a greater understanding of epithelial cell-autonomous defects in patients with VEO and older onset IBD and will be an important tool for understanding novel disease variants in the future. Overall design: mRNA profiles from colonoids of 3 patients with older onset IBD, 4 patients with VEO IBD and 7 controls and epithelial tissue of 2 patients with older onset IBD, 3 patients with VEO IBD and 1 control