Fig. 1 |. Inflamed CD14⁺PDGFRA⁺ cells and scRNA-seq orthologies suggest key roles for myeloid–stromal clusters.

a, Expression (log₂(cluster expression/cluster averages)) of genes (columns) across myeloid and stromal cell subsets (rows) from scRNA-seq data of PBMCs and inflamed ileum from individuals with Crohn’s disease ileum (n = 11). DC, dendritic cells (including plasmacytoid and classical dendritic cells). b, Gene expression in CD14⁺PDGFRA⁺ versus CD14⁻ fraction from uninflamed versus inflamed tissue (n = 3 biological replicates). Data are mean ± s.e.m. *P < 0.05, **P < 0.1; two-tailed paired Student’s t-test. c, scRNA-seq of DSS-treated and untreated larval intestines (n = 5 replicates; 25 pooled intestines per replicate (80,098 cells in total)), and innate immune, epithelial and stromal cells from individuals with Crohn’s disease (24,364 cells in total). Uniform manifold approximation and projection (UMAP) shows joint clustering of 28 clusters between zebrafish (F) and human (H) cells. ILCs, innate lymphoid cells; ILC3s, type-3 ILCs; LREs, lysosome-rich enterocytes. d, Confusion matrices of a human random-forest model applied to actual human (top) and zebrafish (bottom) scRNA-seq datasets, showing the proportion of actual and model-predicted cells. M, macrophages; S1, activated fibroblasts; S2, residential fibroblasts; S3, smooth muscle cells; S4, endothelial cells; S5, mesothelial cells (zebrafish only). e, Top, haematoxylin and eosin staining of 1× DSS-treated nod2^+/+ (nod2^WT) (left) and nod2^mss13/mss13 (nod2^mss13) (right) larvae. Red arrows, leukocyte staining in anterior intestine. Scale bar, 100 μm (main panels), 50 μm (insets). Bottom, quantification of the number of leukocytes per 1.5 × 3.5-cm area in larvae treated with 1× (left) or 2× (right) DSS or untreated controls (ctrl). For 1× DSS, n = 3 (nod2^+/+, treated), 5 (nod2^+/+, control), 6 (nod2^mss13, control) or 8 (nod2^mss13 treated); for 2× DSS, n = 4 (nod2^+/+, control), 5 (nod2^mss13, control), 6 (nod2^mss13, treated) or 10 (nod2^+/+, treated). Data are mean ± s.e.m. *P < 0.05, **P < 0.01; one-way analysis of variance (ANOVA) with Tukey’s multiple comparisons.