Fig. 5: PDGFRA⁺CD142^low/− fibroblasts guide monocyte to macrophage transition through GM-CSF.

a Overview of the co-culture, for gating see Supplementary Fig. 7. b Phenograph clusters of HLA-DR⁺lin⁻ cells in UMAP space across the three conditions. c Percentage of total HLA-DR⁺lin⁻ cells per cluster across the three conditions. d Cell frequencies across conditions in the three largest clusters of monocytes only condition (upper panels) or monocytes cultured with fibroblast conditions (lower panels). e Heatmap of marker expression across clusters. f Expression of selected markers across conditions in total CD11b⁺CD14⁺ monocyte/macrophage pool; same data ± TNF in Supplementary Fig. 8e. g Distribution and annotation of Phenograph clusters ± TNF. h Cell frequencies across conditions in selected clusters, +TNF. i Soluble factors in supernatants from sorted fibroblasts stimulated with OSM, TNF, and LPS for 24 h. j CD206 levels on monocytes/macrophages ± blocking antibodies against IL-34, IL-33, GM-CSF, or M-CSF. k Concatenated HLA-DR⁺lin⁻ cells in UMAP space; transwell (left) and contact (right) condition, ± anti-GM-CSF. l Cell frequencies across conditions of monocyte cluster #1 and macrophage cluster #10, ±anti-GM-CSF. m Double staining of intestinal PDGFRAB⁺ fibroblasts and GM-CSF in inflamed submucosa of three representative patients with IBD, scale bar indicates 20 µm (see Supplementary Fig. 9). n Concatenated total intestinal CD11b⁺CD14⁺ monocytes/macrophages from 96 mucosal ex vivo biopsy samples in UMAP space; expression of CD206 and FOLR2, and gating strategy shown. o Quantification of GM-CSF receptor (CD116) and PDL1 in intestinal CD206⁻ monocytes/macrophages (pink), CD206⁺ macrophages (blue), and FOLR2⁺ macrophages (green) gated as shown in (n). p Heatmap of marker expression across intestinal monocyte/macrophage subsets in non-inflamed or inflamed samples. Data from three (i), four (j), five (b, d, f, h–l), and 96 (o) biologically independent samples were examined. Mean with SD in (i) and (j), mean with SE in (o); differences among three groups were assessed using one-way ANOVA with Holm–Šídák’s multiple comparisons tests (d, f, h, i, j, l) and Kruskal-Wallis with Dunn’s multiple comparisons tests (o, p); significance in (p): *p < 0.05, **p < 0.01, ***p < 0.001 and ****p < 0.0001; for p values see Supplementary Fig. 8m.