Fig. 4: Spatial transcriptomics identifies distinct inflammatory cytokine and IFN signaling niches in lung adenocarcinoma following Treg cell depletion.
a, Tumor region identification in KP LuAd sections using Visium ST. The fraction of tumor cell RNA in each Visium spot (top right) was determined by BayesPrism deconvolution, binarized (bottom right; Methods), and compared to histological H&E images (left). b, Factor scores and Bonferroni-adjusted two-sided t-test P values differentially expressed factors between control and Treg cell-depleted conditions in ST. c,d, Representative tissue sections from control (left) or Treg cell-depleted (right) conditions. Tumor regions are outlined, and spots are colored by factor score. Scores represent IC (c; 18 genes) or IFN (d; 103 genes) gene programs shared across all lineages (Br, bronchi; A/V, artery/vein; LV, lymphatic vessel; IAs, immune cell aggregates). e, ST analysis revealed distinct signaling niches. Spots were assigned to niches based on thresholding a gamma distribution fitted to IC or IFN signaling module scores across all spots (Methods). f, Enrichment of cell-type RNA fractions in signaling niches. Adjusted empirical P value corresponds to the probability of obtaining the mean observed RNA fraction for that cell type (Methods). Fractions with adjusted P > 0.01 are not shown. In a and c–e, images are representative of, and analysis performed on (b and f), one of two serial sections for each of four samples (DT and Ctrl, two biological replicates each).
