Fig. 1

Decreased epithelial Paneth cell α-defensins signature in pediatric iCD ≥10 years at diagnosis. a Venn diagram shows an overlap between the previously reported 1340 core iCD gene signature¹⁹ and the 365 genes that were differentially expressed in the ileum between older (A1b) and younger (A1a) iCD (FDR correction [0.05], fold-change ≥1.5). 124 of these 365 genes including α-defensins and REG3A were not included in the core iCD gene list. b Unsupervised hierarchical clustered heat map of the 365 genes differentially expressed genes between older and younger iCD with upregulated genes in red and down-regulated genes in blue. Above the heat map, younger Ctl (light blue), older Ctl (dark blue), younger CD (orange), and older CD (red) samples are indicated. c TPM ileal gene expression is shown for the indicated genes for the indicated groups stratified by age-of-diagnosis with Kruskal-Wallis test with Dunn's multiple comparisons. d Immunohistochemistry in representative CD patients and non-IBD controls. Relatively high DEFA5 staining is shown for older non-IBD control (i) and younger CD (ii) that correlated with transcripts per million (TPM) values of >10,000 and 6143 for gene expression by RNASeq, respectively, and relatively low DEFA5 staining in older CD that correlated with transcripts per million (TPM) values of 1239 for gene expression by RNASeq. Images were captured using an Olympus BX51 light microscope and digitally recorded at ×20 magnification. e Averaged and unsupervised hierarchical clustering heat map of 121 of 365 (top third differentially expressed genes between older and younger iCD) stratified by yearly age-of-diagnosis as indicated. Number of patients for each age group is indicated adjacent to the heat map