Fig. 2: Spatial transcriptomics defines compartment-specific signatures for nodular and infiltrative tumor–stroma interfaces. | Nature Communications

Fig. 2: Spatial transcriptomics defines compartment-specific signatures for nodular and infiltrative tumor–stroma interfaces.

From: Integrated multi-omics reveals cellular and molecular interactions governing the invasive niche of basal cell carcinoma

Fig. 2

a Immunofluorescence images of nodular and infiltrative BCC samples stained with DAPI and a panCK antibody showing the ROIs selection process and AOIs subdivision based on panCK staining. The table indicates the number of AOI for each tumor subtype (6 nodular and 6 infiltrative samples) and compartment (Tumor or Stroma). Scale bars indicate 300 µm (upper panels) and 100 µm (lower panels). b Volcano plot of the DEGs comparing the infiltrative to the nodular tumor AOIs. Eighty-six genes (highlighted in purple) show a log2 fold change (log2FC) >0.4 or <−0.4 with a p value <0.05. c Volcano plot of the DEGs comparing the infiltrative to the nodular stroma AOIs. Fifty-two genes (highlighted in green) show a log2FC > 0.4 or <−0.4 with a p value <0.05. d Violin plot of the spatial Tumor DEG signature (57 genes) enrichment in tumor and stroma AOIs. e Violin plot of the spatial Stroma DEG signature (46 genes) enrichment in tumor and stroma AOIs. f PCA plot and heatmap of the enrichment for the spatial Tumor DEG signature in individual tumor AOI. g PCA plot and heatmap of the enrichment for the spatial Stroma DEG signature in individual stroma AOI. p Values in d, e were calculated using unpaired two-sided Student’s t test. Tumor and Stroma AOIs in a, d, e are depicted in purple and green, respectively. AOI area of interest, panCK pan-cytokeratin, log2FC log2 fold change, DEG differentially expressed genes, PC principal component, PCA principal component analysis.

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