Fig. 5: Single-cell and spatial transcriptomic features of myeloid subsets of GC with varying TLS status.

a Sub-clustering of all myeloid cells generated 11 subsets. b Dot plot showing the expression level of canonical cell-type-specific marker genes in 11 myeloid cell subsets. c Heatmap showing the relative cell abundance of myeloid subsets across GC with varying TLS status (****p < 0.0001). Relative enrichment of myeloid subsets across TLS distributions in GC was assessed by the Ro/e metric. Significance was evaluated using a two-sided Fisher’s exact test with FDR correction. Source data are provided as a Source data file. d Boxplot showing the expression level of PD1 (upper) and 41-BB (CD137) (bottom) immune checkpoint-related signal pathway in different myeloid subtypes. Significance was assessed by a two-sided Wilcoxon rank-sum test. Boxplots show median (line), interquartile range (box), and range (whiskers). e Bubble plot showing the expression of cellular interaction between LAMP3⁺ DC and TLC subsets. Bubble size represents communication probability, and color denotes P value (two-sided Wilcoxon rank-sum test, P < 0.01). f H&E staining and ST-seq analysis showing the spatial distribution of TLS, CXCL13⁺ TLC, and LAMP3⁺ DC in GC with varying TLS status. g ST-seq analysis showing the colocalization of ligands (CXCL16 and CCL19) secreted by LAMP3⁺ DC and the receptors (CXCR5 and CCR7) secreted by CXCL13⁺ TLC in GC with varying TLS status. h Multiplex immunostaining showing the cell interaction guided by PD1 and PDL1 between LAMP3⁺ DCs and TLC in iTLS^-GC. i Kaplan–Meier survival plot showing the OS (upper panel) and PFS (bottom panel) according to the relative abundance of LAMP3⁺ DC in GC with anti-PD1 immunotherapy, p values were calculated by the log-rank test.