Figure 1.

Digital spatial RNA profiling reveals elevated inflammatory signals in colitis-associated dysplasia

Formalin-fixed paraffin embedded mucosal biopsies (3 dysplastic and 7 paired non-dysplastic, uninflamed tissues) were included from 3 patients enrolled in surveillance.

(A) Masks for epithelium (panCK⁺) and immune cells (CD45⁺) were generated, for 3 regions per biopsy. Scale bars represent 1 mm.

(B) Epithelial and (C) immune cell gene expression-based pathway analysis of uninflamed versus dysplastic biopsies. Top 20 of KEGG human pathway enrichment, most significant processes are highlighted in red, and the less significant processes are highlighted in blue according to −log10(FDR). Dot size indicates number of genes involved: larger dots in the graph correspond to a greater number of genes.

(D) Volcano plots showing differential gene expression with genes enriched in uninflamed (left) or in dysplastic tissue (right). Significance is indicated by color: p < 0.05 (light blue), FDR<0.05 (dark blue), FDR<0.001 (orange, and names indicated).

(E) Gene expression level of IL-17 family (type 3 inflammation) cytokines compared between dysplastic and uninflamed epithelial regions and immune cells. Displayed are IL-17A, IL-17F, and IL-21. Student’s t test was performed. p values are indicated in the graphs. See also Tables S1A and S1B and Figure S1.