Journal: Cell Reports

Article Title: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease

doi: 10.1016/j.celrep.2022.111439

Figure Lengend Snippet: A gradient of cytokine-responsive transcriptional signatures stratifies patients with IBD into distinct molecular phenotypes (A) Activation of cytokine-responsive transcriptional signatures in whole colonic biopsies of patients with UC (UNIFI trial, n = 550) and colonic CD (UNITI2 trial, n = 126) (demographics shown in Table S1 ). Enrichment of cytokine-responsive transcriptional signatures was evaluated in the transcriptome of colonic biopsies using gene set variation analysis. A score of +1 suggests that all transcripts are upregulated, while a score of −1 suggests that all transcripts are downregulated (showing median and interquartile range [IQR], Mann Whitney test, ∗∗∗ p < 0.001). (B, C, and D) Gradient of cytokine-responsive transcriptional signature activation in IBD. Each column represents a single patient. The sum of all four scores per subject is also depicted as the total enrichment score (TES). Columns have been clustered by Euclidean distance (method: average, tree ordering: original, figure generated with ClustVis). Cohorts: UNITI2 (n = 126), UNIFI (UC, n = 550), and PROgECT (UC, n = 84). (E and F) Cytokine-responsive transcriptional signature association to clinical indices of human colonic inflammation in UC (UNIFI cohort, n = 550) and cCD (UNITI2 cohort, n = 126). All clinical data were collected prospectively as part of the trials’ protocol ( Feagan et al., 2016 ; Sands et al., 2019 ; Telesco et al., 2018 ).

Article Snippet: Human intestinal biopsies for whole transcriptome profiling (microarray) , Janssen Pharmaceuticals , UNITI2, NCT01369342 UNIFI, NCT02407236 PROgECT, NCT01988961.

Techniques: Activation Assay, MANN-WHITNEY, Generated

Journal: Cell Reports

Article Title: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease

doi: 10.1016/j.celrep.2022.111439

Figure Lengend Snippet:

Article Snippet: Human intestinal biopsies for whole transcriptome profiling (microarray) , Janssen Pharmaceuticals , UNITI2, NCT01369342 UNIFI, NCT02407236 PROgECT, NCT01988961.

Techniques: Microarray, Recombinant, Cell Recovery, Sequencing, Software