Figure 3.

Emergence of new cell states in the ulcerated epithelium

(A) UMAP of epithelial cells from the combined datasets from healthy individuals, and patient-derived healthy margin and ulcerated samples. Colors indicate different cell cluster types. Arrows indicate the inflammation-associated cell clusters.

(B) UMAP of the combined datasets from healthy, healthy margin, and ulcerated epithelial cells colored by cell type and dataset of origin.

(C) Bar plots showing cell fractions within the indicated lineages in the healthy, healthy margin, and ulcerated datasets, including the IA cell states. Colonocytes, BEST4+, and goblet cell lineages include TA and CT populations. Significance tested with two-sided Mann-Whitney U test. Each dot represents an individual donor. Bars represent the mean ± SEM. UC-HM, UC patient-derived healthy margin; UC-UL, patient-derived ulcerated samples.

(D) (Left) Venn diagrams indicating the number of shared upregulated and downregulated genes between the stem cell clusters from the ulcerated and healthy margin samples (when compared to the healthy state). (Right) bar plots showing top 10 terms from GO term overrepresentation analyses of the shared differentially expressed genes. Numbers in each bar indicate the fraction of genes within that GO term found in the shared differentially expressed genes (DEGs).

(E) Analysis of CD74 expression in the indicated samples. (Top) UMAP plots with heatmaps of normalized expression of the CD74 gene in the integrated dataset split by sample type of origin. (Bottom) Representative immunohistochemistry images for CD74 in tissue biopsies. Scale bars: 100 μm.

(F) Similarity correlation matrix between healthy, ulcerated, and healthy margin samples. The last was split into CD74-positive and negative fractions (cutoff value based on the third quartile of CD74 expression in the healthy dataset). Similarity among samples calculated based on first 50 principal components using Pearson correlation. Dendrogram lines on the left shows hierarchical clustering of the sample types.

(G) Trajectory graph of cell type clusters in the integrated datasets. Pie charts indicate proportions of cells in each cell-cycle phase. Outer ring colors match cell type clusters in (A).

(H and I) Violin plots showing normalized enrichment score of the indicated signatures and expression levels of the indicated lineage-specific genes (CA1 and MUC2) in the stem cell, IA colonocyte, and IA goblet clusters from the ulcerated samples. Significance was tested with two-sided Mann-Whitney U test.