Fig. 6

Signaling within the stem cell niche using spatial transcriptomics. a Pathway analysis of DEGs enriched with niche spatial spots relative to other spatial spots within the bone marrow. b Schematic of cell‒cell interactions. While scRNAseq can be used to predict ligand/receptor pairs between cell types, the addition of spatial information can distinguish biologically relevant interactions occurring between cells with close proximity (within circle, solid arrows) from those occurring between distant cells unlikely to occur in vivo (outside of circle, dotted arrows). c Predicted cell‒cell interactions using single-cell spatial transcriptomics. Genes were defined as showing enriched expression within select cell types (brown), encoding known receptors or ligands (yellow), predicted to communicate using CellChat (green), and being expressed by those cell types present within the stem cell niche (magenta). Genes were overlaid with spatial DEGs (blue). d Sample genes identified from cell‒cell interaction found to be spatially restricted to the niche but expressed by numerous different cell types (Cd44), genes expressed by only select cell type but present throughout the marrow (Cd74), and genes restricted both spatially and by cell type (Ryr1). e RNAscope of bone marrow showing Lepr-expressing SSPCs (red) and Cd44 (left), Cd74 (middle) and Ryr1 (right) (green). Bar, 10 µm. f Distribution of distances between the indicated niche cell markers and Lepr⁺ SSPCs. Numbers above the graph represent the average±SD of the distance between cells. n = 50 cells per marker. ^aP < 0.001 vs. Cd74, ^bP < 0.001 vs. Ryr1