Extended Data Fig. 12: Myeloid cell spatial modelling and cell-cell communication.

a, Median standardized importances (>0) of the cell-state scores of myeloid cells (colocalization) in the prediction of fibroblast cell-state scores in spatial transcriptomics. b, Spatial mapping of cell-type niches in a control and an ischaemic sample. Arrows in the IZ sample show niche 4 and how it surrounds niche 5. c, Distribution of myofibroblasts and SPP1+ macrophages marker gene expression (state-score) across cell-type niche 4 and 5. Each dot represents a spatial transcriptomics spot belonging to a molecular niche across samples (n = 12,427 for niche 4, n = 4,375 for niche 5) (two-sided Wilcoxon rank sum test, adj P-value = 6.02e-133 for myofibroblast, adj P-value = 0 for SPP1+ monocytes). Data are represented as boxplots where the middle line is the median, the lower and upper hinges correspond to the first and third quartiles, the upper whisker extends from the hinge to the largest value no further than 1.5 × IQR from the hinge (where IQR is the inter-quartile range) and the lower whisker extends from the hinge to the smallest value at most 1.5 × IQR of the hinge, while data beyond the end of the whiskers are outlying points that are plotted individually. d, Cell-cell communication network representing number of ligand-receptor interactions (edge richness), expression of ligand-receptor pairs (LR scores; colour gradients) and cell centrality (Pagerank; node size) as estimated in snRNA-seq of myogenic, ischaemic and fibrotic samples. e, Sankey plots summarizing the top 50 ligand-receptor interactions for selected source and target cells and contrast. These ligand-receptor pairs are selected by absolute value of the difference in LRscore, as provided by CellPhoneDB method implemented in Liana. f. Sankey plot summarizing top 50 TGFbeta ligand-receptor interactions from Fib2 to SPP1+ Mac. cells. g, In situ hybridization mRNA (RNAscope) staining of CD163 (myeloid), POSTN (myofibroblast) and SPP1 on human cardiac MI tissue (crop-out in Fig. 6n). Arrows indicate CD163+SPP1+ macrophages near myofibroblasts. Scale: 25 µm.