Fig. 3: Spatially resolved multicellular coordination in CMs.
From: Cross-tissue multicellular coordination and its rewiring in cancer
a–c, Visium analysis of the ileum showing spatial distribution of CMs (a), their component cell subsets (b), and cellular niches identified by CellCharter (c). H&E, haematoxylin and eosin. d,e, Representative Xenium imaging (d) and quantification (e; n = 6) of CM02 and CM03 in intestinal mucosal sections (Methods). Scale bar, 100 μm. Two-tailed paired Wilcoxon tests. Epi, epithelium; LP, lamina propria. f, Spatial colocalization and cellular composition of CMs. Top, CM colocalization scores across Visium samples (n = 34) coloured by tissue (Methods and Supplementary Table 3). CMs are ordered by the median of colocalization scores across samples. Bottom, proportion of different cell lineages in all cell-subset nodes within CM networks shown in Fig. 2b. None, 0; 0 < low <0.2; 0.2 ≤ medium < 0.4; high ≥ 0.4. g, CellPhoneDB cell–cell interaction (CCI) counts within CMs, measured in single-cell samples with high (for example, CMT02) or low (others) CM activities. Dots represent unique subset pairs within CMs and black lines link the average counts. CM02, n = 90; CM04, n = 90; CM05, n = 90; CM06, n = 72; CM08, n = 72; CM09, n = 90. Two-tailed paired Wilcoxon tests. h, Cytokine responsiveness in CM02, CM03 and CM05, as inferred using the Immune Dictionary28. The CM-level false discovery rate (FDR) denotes the minimum FDR value among all subsets within the CM (Methods). i, Expression of cytokine genes that are enriched in CM02, CM03 or CM05 across the ileum cellular niches in c. Only cytokines detected by Visium data are shown. j, Spatial distribution of selected cytokines (labelled in red in h,i) in the Visium section of the ileum shown in a–c. For box plots in e,f, the centre line represents the median, the box limits delineate the top and bottom quartiles, and the whiskers extend to the highest and lowest values within 1.5× the interquartile range.
