Fig. 4: ECs generate a proximal-to-distal gene expression pattern in surrounding fibroblasts.
a,b, Representative visualization of spatially profiled 2D (a) and 3D (b) co-culture with transcripts for fibroblast marker PDGFRB, and endothelial marker PECAM1, overlaid on DAPI. Schematic summarizing the spatial distribution of fibroblast transcripts based on EC proximity on the right. c,f,j,m, Example images of gene expression distribution overlaid on labeled cell types, to a maximum of randomly selected 1,500 transcripts per gene, with Notch target genes shown in c, fibrogenic markers in f, TGFB ligands in j and TGFB receptors in m. d,g,k,n, Line plots representing average expression of transcripts per fibroblast relative to the EC distance, with Notch target genes shown in d, fibrogenic markers in g, TGFB ligands in k and TGFB receptors in n. Solid line shows the mean; shaded regions show one standard deviation. e,h,l,o, Distance to the nearest EC in the top-versus-bottom quantile of cells by expression of each gene, with Notch target genes shown in e, fibrogenic markers in h, TGFB ligands in l and TGFB receptors in o. Statistics by two-sided Wilcoxon tests comparing distances from ECs for the top-versus-bottom quantiles of cells in expression of each gene. i, Heat map representing expression of TGFB ligands and receptors by cell type in the co-culture. Scale bars, 200 µm (a–c, f, j and m). Schematic in b created with BioRender.com.
