Extended Data Fig. 4: Xenium spatial transcriptomic mapping of macrophages and chemokine co-localization.
From: Chemokine-defined macrophage niches establish spatial organization of tumor immunity
(a) Xenium H&E-stained section of four lungs of WT C57BL/6 mice 16 days after intravenous injection of 4×105 KPAR1.3 adenocarcinoma (n = 2) and B16F10 melanoma cells (n = 2). Scale bar, 1000 µm. (b) Stromal cell spatial map (same samples as in a). ImageDimPlot highlighting endothelial, epithelial and tumor cell populations. Cell type identities were assigned by matching graph-based clusters to known markers (Supplementary Figs 3-4), illustrating the anatomical distribution of airway/bronchial epithelial structures and vascular endothelium in each sample. Scale bar, 1000 µm. (c) Spatial localization (same samples as in a) of chemokine transcripts, spatial molecule plot showing per-molecule transcript coordinates for Cxcl9, Cxcl10, Cxcl13, and Ccl2 detected in each sample. Molecules are overlaid on the cell segmentation map. Spatial distributions highlight chemokine-producing regions within each tumor, allowing direct comparison of inflammatory niches between KPAR and B16F10 models. Scale bar, 1000 µm. (d) Myeloid cell spatial map (same samples as in a). ImageDimPlot visualizing four major macrophage and monocyte-derived populations: AMs; CD206hi IMs; CD206lo IMs; recMacs. Cluster-to-cell type assignments were performed using sample-specific marker-enriched clusters defined a priori (Supplementary Figs 3-4). Plots show the spatial localization of each myeloid subset within the TME, revealing region-specific enrichment patterns across KPAR and B16F10 samples. Scale bar, 1000 µm. (e) Spatial distances (same samples as in a) between myeloid cell subsets and tumor or bronchovascular structures. Violin plots show the distribution of nearest-neighbor distances from individual myeloid cells AMs, CD206hi IMs, CD206lo IMs, and recMacs to the closest tumor cell. Distances were calculated in two-dimensional space as the Euclidean distance from each myeloid cell centroid to its nearest target cell centroid. Values are plotted as log1p-transformed distances. Violin plots represent the full distribution of single-cell distances. Box plots indicate the median (center line), the 25th and 75th percentiles (box), and whiskers extending to the minimum and maximum values; outliers are shown as individual points.
