Figure 5.

Nearest-neighbor-smoothed histological scores reveal the most and least inflammatory cells

(A) Schematic illustration showing the histological scores from the endoscopically least and most inflamed paired colonic biopsies used for scRNA-seq.

(B) Pie chart showing the total number of cells from areas of different histological scores from all 12 pIBD colon biopsy samples.

(C) The raw histological score of each cell derived from each sample depicted onto the main UMAP from Figure 2B.

(D) Schematic illustration of the Euclidean neighbor smoothing. Each cell was given the average histological scores of its 100 transcriptionally closest neighbors. These smoothed histological scores were used for the subsequent analysis.

(E) Histogram showing the cell type distribution across the histological scores derived from the nearest-neighbor analysis. Cells were categorized into 3 groups: ≤4 (least inflamed), 5–8 (intermediate), and ≥9 (most inflamed).

(F) Visualization of cells from the nearest-neighbor smoothing on the main UMAP with cells derived from the ≥9 histological (histo) score (most inflamed) and ≤4 histo score (least inflamed) groups, which also have neighbors from at least 5 samples.

(G and H) Violin plots showing the expression level of selected DEGs (log2 fold change [FC] > 0.10 and adjusted p value [adj. p value] < 0.05) upregulated in the most (G) and least (H) inflamed cells versus the rest of the cells in each cluster.

(I) Frequencies of CD4⁺CD69⁺, CD4⁺CD161⁺CD69⁺, CD8⁺CD69⁺, and CD8⁺CD161⁺CD19⁺ cells in colonic adult non-IBD (n = 8) and IBD samples (n = 8). Mann-Whitney test (p < 0.05), mean with SD. The samples were analyzed in two independent experiments.