Fig. 5: Stereopy integrates spatial multi-sample data and reveals 3D regulatory mechanisms related to cardiac development. | Nature Communications

Fig. 5: Stereopy integrates spatial multi-sample data and reveals 3D regulatory mechanisms related to cardiac development.

From: Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Fig. 5

a Stereopy-NicheReg3D workflow. This approach focuses on identifying regulatory networks that are responsive to cell-niche interactions in a spatial manner, through extracting the cellular niche in 3D and connecting intracellular regulations with intercellular communications (highlighted in green). b Stereopy-NicheReg3D illustrating multi-hierarchically transcriptomic architecture, ranging from heart organ meshes, heart cell types and clusters, spatially variable genes (Myl2), spatially specific regulons (Mef2c(+)), and niche-specific L-R pairs (Igf2-Igf2r) from left to right. c Spatial distribution of VCM’s niche compositions including neighboring ACM, blood, EC, EP, and FM cells in the boundary. d Circos plot showing bidirected cell-cell interactions in five niches. The width of an arrow correlates with the number of significant L-R pairs. e Heatmap showing the CCC intensities without niche restriction, different from (d). f, g Bubble plots demonstrating cell-type-specific L-R pairs: f niches to VCM. g VCM to niches. Circle color indicates the communication score of each L-R pair, while circle size indicates its p-value of permutation test. h Sankey plot connecting intercellular L-R interactions from sender niche cells to receiver VCM cells to VCM intracellular downstream TFs via deductive signaling pathways. Bandwidth indicates the mean expression of the two genes at both ends. i Regulatory network showing inferred intracellular signaling paths from receptor Itgb1 to downstream TFs. j Shared and specific TGs in Pdlim5(+) and Mllt10(+) regulons showing the 3D co-regulation function. k GO enrichment analysis indicating the collective function of shared targets of regulons (shared, Pdlim5(+), and Mllt10(+) from left to right). l The 3D regulation model of extracellular signaling to intracellular gene regulatory network. The protein structure of RBPMS (PDB code: 5CYJ) was downloaded from Protein Data Bank and rendered in PyMOL. Source data are provided as a Source Data file.

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