Fig. 6: Spatial transcriptomics map developmentally distinct cell stages to spatially distinct tumor compartments. | Nature Communications

Fig. 6: Spatial transcriptomics map developmentally distinct cell stages to spatially distinct tumor compartments.

From: Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

Fig. 6

Dotplots showing the expression of the ten genes chosen for spatial transcriptomics in the snRNAseq- (a) and the smRNA-FISH-dataset (b) for each cluster, respectively. c Harmony corrected UMAP-clustering of smRNA-FISH-derived single cells shows distinct clusters (three samples, n = 110,508 cells). d–f Mapping single cells back to the original scans reveals spatially distinct localization of cells from each cluster with regard to the bicompartmental structure of MBEN. Color code corresponds to c. Each image represents one sample. g Network visualization quantifying the probability of co-localization of cells from each cluster. Red and blue colors indicate high and low probability for co-localization, respectively. (Proliferating) early CGNP-like and stromal/astrocytic cells are co-localizing, whereas early and late stages of the MBEN trajectory are spatially separated. h A scan of the sample MB295 shows clear correlation of the smRNA-FISH-derived clusters to spatially distinct regions of MBEN, as they were found in all three investigated samples. Lower panel left: Zoom-in with pseudo H.E. staining. Lower panel right: Corresponding mapping of single cells illustrates the spatial architecture of the transition zone between the two histological compartments of MBEN, which is mainly formed by early CGNP-like, migrating and stromal/astrocytic cells. Scale bars in d –f =200 µm. Scale bars in h =200 µm (large image), 100 µm (Zoom-ins). Source data are provided as a Source Data file.

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