Figure 4 from Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer

Neutrophil infiltration in LUSC is associated with distinct metabolic and immunosuppressive phenotypes. A, Gene Ontology (GO) biological processes enriched among upregulated genes in the TS:Neutrophil high TME class (n = 10 cores) compared with other TME classes combined (n = 28 cores) in LUSC (FDR < 0.01, gene ratio > 0.05). B, GSEA of hallmark gene sets compared between tumor cores from the Tumor/Stroma:Neutrophil high TME class and other TME classes combined, using the t-statistic derived from the limma–voom model on TMM-normalized gene expression. Significantly enriched pathways were colored by type of pathway (FDR < 0.05). C, Normalized enrichment score derived from single-sample GSEA visualized for TS:Neutrophil high and cores from other TME classes. The P value is derived from GSEA of LUSC as shown in A and adjusted for other hallmark pathways using the Benjamini–Hochberg method. D, Proportion of tumor cells assigned MCT4⁺ in TS:Neutrophil high tumor cores compared with tumor cores from other TME classes combined in LUSC. E, Spearman correlation coefficient and P value comparing the proportion of MCT4⁺ and CAIX⁺ tumor cells in TS:Neutrophil high LUSC TMEs. F, Median distance between LUSC tumor cells to their nearest endothelial cell per core in TS:Neutrophil high TME class compared with all other TME classes combined. G, Single-channel images and composite image alongside cell type map displaying tumor cells, neutrophils (MPO, yellow), endothelial cells (CD31, magenta), and regions of hypoxia (CAIX, cyan) and MCT4 (green) expression. Boxplots show median and lower and upper quartile values, and whiskers extend up to 1.5 × IQR above and below the quartiles. P values for D and F were calculated in a linear mixed-effects model with patient as the random-effect covariate. LUSC, lung squamous cell carcinoma; TS, tumor/stroma; FDR, false discovery rate; TMM, trimmed mean of M-values; panCK, pancytokeratin; *, P < 0.05; **, P < 0.01; ***, P < 0.001.