Fig. 2: Cellular deconvolution and spatiotemporal associations in regeneration.

A Schematic illustration of the cellular deconvolution approach using spatial transcriptomic and single-cell sequencing data from human skeletal muscle (Created in BioRender. Farup, J. (2025) https://BioRender.com/uxex51k). B Fractional distribution of specific cell type transcripts during the course of regeneration shows FAPs and monocytes/macrophages to constitute the two cell populations with largest relative increase (n = 3, biological replicates, curves represents means). C Change in cell content during regeneration quantified from tissue homogenate by flow cytometry. Monocyte content was increased in the early phase of regeneration whereas lymphocyte, Muscle stem cell (MuSC), Fibro-adipogenic progenitors (FAP) and endothelial cell content was increased at later time points (# = p < 0.05 pre vs. 2dpi; (* = p < 0.05 pre vs. 8dpi; + = p < 0.05 pre vs. 30dpi) (Monocyte, MuSCs, endothelial cells, lymphocytes: n = 10; FAPs: n = 9, biological replicates, one-way ANOVA with Dunnett’s test for multiple comparisons, graph represents median ± interquartile range). D Cell-cell proportion correlation revealed that FAPs were spatiotemporally correlated with monocytes/macrophages, lymphocytes, and endothelial cells (n = 3, biological replicates). E Spatial distribution of spots containing FAP and monocyte/macrophage transcript at different time points. F Immunostaining of FAPs (PDGFR-α) and macrophages (CD68) 8dpi shows a close spatial proximity in injured areas (this was repeated at baseline and day 8 for n = 10 subjects with similar results depending on the magnitude of tissue regeneration). Scale bar represents 62.5 µm. Arrows mark PDGFR-α expressing cells (dpi = days post injury). Source data are provided as a Source Data file.