Fig. 6

Summarizing cartoon. Using high throughput mRNA and 16s rRNA amplicon sequencing of treatment naïve newly diagnosed ileal biopsies from CD cases we identify 365 genes that were robustly differentially expressed between older iCD (10–16 years) and younger iCD <10 years). Those differentially expressed genes showed increased Th1-related IFNγ profile associated with amplified innate myeloid inflammatory activation, and enhanced extracellular matrix and collagen signatures in older iCD cases. Remarkably, these signatures for enhanced immune activation was associated with a specific reduction in epithelial Paneth cell α-defensin expression in older iCD, and was not associated with systematic changes in the local mucosal microbial communities