Figure 2.

Immune heterogeneity in spatial intratumor subgroups. A, Bar chart of the proportion of deconvoluted immune cell types between intratumor subgroups (G1 and G2) in tumor ROIs in aggregated 10 GeoMx DSP samples (left of the vertical line) and in each individual sample (right). Samples were selected based on the number of tumor ROIs. Colors represent five different immune cell types, including myeloid, T, plasma, B, and NK cells. B, Representative stained slides of mIHC for tumor core (left) and tumor edge regions (right) in TMA sample S03729. Blue represents nuclei, red represents CD3, and green represents CK/EpCAM. The length of the scale bar represents 30 μm. C, Bar plot of the proportion of CD3⁺ T cells in tumor core and tumor edge ROIs by TMA mIF. Colors represent different tumor regions. D, Violin plot of scaled ssGSEA scores of immune exhaustion signatures (comprising genes such as LAG3, TIGIT, and PD1) on G1 and G2 subregions in two representative samples. Stars represent the statistical significance of the Wilcoxon test. Bars represent median values of the scaled ssGSEA score. E, Heatmap of log₂ fold changes (log₂ FC) in expression of inhibitory immune checkpoints between intratumor subgroups (G2 vs. G1) in 10 GeoMx DSP samples. Each row represents an immune checkpoint, and each column represents a GeoMx DSP sample. Colors represent log₂ FC values between G2 and G1. F, Heatmap of log₂ FCs in expression of inhibitory chemokines between intratumor subgroups (G2 vs. G1) in 10 GeoMx DSP samples. Each row represents an immune checkpoint, and each column represents a GeoMx DSP sample. Colors represent log₂ FC values between G2 and G1. G, Violin plot of scaled ssGSEA scores of inhibitory immune chemokines on tumor core and tumor edge ROIs using the gastric cancer TMA cohort. Stars represent statistical significance of the Wilcoxon test. Bars represent median values of scaled ssGSEA scores. H, Violin plot of scaled ssGSEA scores of inhibitory cytokines on tumor core and tumor edge ROIs using the gastric cancer TMA cohort. Stars represent statistical significance of the Wilcoxon test. Bars represent median values of scaled ssGSEA scores. I, Violin plot of scaled ssGSEA scores of an immune checkpoint blockade resistance signature on G1 and G2 subregions in aggregated 10 samples. Stars represent the statistical significance of the Wilcoxon test. Bars represent the median values of the scaled ssGSEA score. (*, P < 0.05; **, P < 0.01; ***, P < 0.001; absence of a star represents non-significance, P ≥ 0.05).