Extended Data Fig. 10: Spatial analyses of IL-1β+ TAMs and T1RS+ PDAC cells.
From: IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer
a, UMAP plot of scRNA-Seq data of PDAC cells from chemotherapy-naïve patients. Colors and numbers indicate cluster identity. b, Left panels. Selected region of interest (LPDAC30 B2_1) showing expression (Molecular Cartography) of all (563,761) detected transcripts or KRT19, as well as signal intensity (IF staining) of KRT19. Right panels. UMAP of spatial gene expression data (Molecular Cartography) of cells from all sections collected from patient LPDAC30. Colors and numbers indicate cluster identity and corresponding annotations. c, Heatmaps of spatial correlation of gene expression (see Methods) with CXCL1 of genes of the spatial transcriptome panel (left) or of marker genes of TAM subsets (right). d, Heatmap of spatial neighborhood significance between the indicated clusters (see Methods). e, Selected regions of interest (LPDAC30 C2_1, left. LPDAC30 D2_1, right) showing co-localization of IL-1β+ TAMs (red) and T1RS+ PDAC cells (light blue) in spatial gene expression analyses. Numbers indicate insets and their magnifications. f, UMAP showing expression (scRNA-Seq) of IL1R1 in PDAC cells from chemotherapy-naïve patients. g, UMAP of scRNA-Seq data (left) and violin plot showing mean expression of T1RS genes (right) of PDAC cells selected for pseudotime analysis. Colors and numbers indicate cluster identity. Significance is computed by two-sided Mann-Whitney test. h, Heatmaps (NicheNet) of ligand activity (Pearson correlation coefficient) of top-ranking ligands expressed by IL-1β+ TAMs (left) and their regulatory potential on predicted target genes expressed by T1RS+ PDAC cells (right).