Fig 2: The degree of inflammation in correlation with the staining pattern and intensity. A-C demonstrate the periphery of active inflammation and D-F show regions of massive inflammation and necrosis. Expression of OLFM4 and LYZ was higher and included more intestinal epithelial and immune cells in regions with high inflammation and necrosis in comparison to regions in the periphery of active inflammation

Fig 3: Expression of OLFM4 and LYZ in controls (intestinal tissue with volvulus). A, B OLFM4 was clearly expressed in the crypts (thin arrow in A, arrow in B) and in the intestinal epithelial cells (thick arrow in A). C Paneth cells at the base of a crypt showed expression of LYZ. Immune cells (e.g., neutrophils) also expressed LYZ (C), invading the crypts (thin arrow in C) after leaving the vessels (thick arrows in C)

Fig 4: Expression of OLFM4 and LYZ in NEC tissue. A-C NEC in a preterm infant (gestational age at birth: 26 weeks, birth weight: 800 g). OLFM4 was highly expressed in the crypts (arrow in B) and in the intestinal epithelial cells (arrow in A) and in immune cells, dispersed in the whole intestinal wall (A). LYZ was expressed in Paneth cells of the crypts (thin arrow in C) and in immune cells (e.g., macrophages, thick arrow in C). D-F NEC in a preterm infant (gestational age at birth: 31 weeks; birth weight: 1490 g). Massive expression of OLFM4 and extensive OLFM4 and LYZ staining of macrophages (arrows in E & F). G-I Expression of OLFM4 and LYZ in immune cells during NEC. G OLFM4 positive immune cells attached to the endothelial cells of a large vessel in the intestinal wall. H Neutrophils with expression of OLFM4 located in the intestinal wall. I LYZ-positive immune cells in the intestinal wall migrated from vessels into intramural tissue

Fig 5: The immune landscape of colonic tumor subtypes(A) Regulon-based UMAP representation of non-epithelial cells.(B) Heatmap of marker genes defining each cell type in (A). T - T cell, PLA - Plasma B cell, MYE - Myeloid, MAS - Mast, FIB - Fibroblast cell, END - Endothelial cell, B - B cell.(C) Scatterplots of cell type representation of (top) polyp and (bottom) CRC subtypes. Points represent individual specimens. Error bars represent SEM of n = 28 for AD, n = 17 for SER, n = 66 for NL, n = 33 for MSS, and n = 34 for MSI-H.(D and E) Scatterplots of (D) CD4+ T cell and (E) tumor cell-specific signature scores, with each point representing a single cell. Error bars depict SEM of single cells.(F) MxIF images of CD8+ cells in polyps.(G) Image quantification of intraepithelial CD8+ cells for n = 20 polyps per type.(H) MxIF images of CD68+ and MUC5AC+ in cells in polyps.(I) MxIF scans of intratumoral heterogeneous regions within CRCs (OLFM4+ stem regions versus MUC5AC+ metaplastic regions). MSS CRC only has stem regions. MxIF images of CD8 and CD3 within stem and metaplastic regions. The inset is the quantification of CD8-positive pixels in these regions from MxIF scans of n = 15 MSS and n = 10 MSI-H CRCs.*p < 0.05, **p < 0.01, ***p < 0.001. See also Figure S6 and Tables S3, S4, and S5.