Figure 1.

Characterization of healthy human colonic epithelium samples

(A) Representative images of live colonoscopy (top) and histological analysis (bottom) confirming ulceration in the epithelium of UC patients (bottom). Histological samples were stained for the gastrointestinal epithelium marker KRT20 and counterstained with hematoxylin. Scale bar: 100 μm.

(B) UMAP plot of 11,035 colonic epithelial cells profiled from healthy samples following annotation based on expression of cell lineage markers.

(C) UMAP plots highlighting expression of known lineage markers in the cell type clusters identified in (B).

(D) Cell type trajectory graph based on over-clustering. Nodes represent clusters colored by cell type of origin, while connecting edges indicate the similarity degrees.

(E) RNA velocity measurements projected onto the UMAP embedding shown in (B).

(F) Immunostaining for TFF3 (blue), PCNA (red), and β-Catenin (green) in the healthy colonic epithelium. Arrow indicates a TFF3/PCNA double-positive cell. Scale bar: 100 μm.

(G–I) Spatial distribution of RNA molecules for MUC2 (red), HMGB2 (blue), KRT20 (orange), and CEACAM1 (green). DNA was counterstained with DAPI (gray). (G) and (H) show the entire crypts length. Scale bar: 50 μm. (I) shows a zoomed-in region of interest of crypt-top area. CT colonocyte (arrow) and goblet cell (arrowhead) are indicated. Scale bar: 10 μm (H).