Fig. 3: Niche-specific functional states of T cells.

a, The expression of naive/memory, cytotoxic and exhaustion markers in T cells from different spatial niches. Statistically significant DEGs are highlighted in dashed boxes. b, A representative FOV from CosMx SMI dominated by CN1, with abundant expression of cytotoxic markers in T cells, as well as T cell chemotaxis molecules from APOE⁺C1Q⁺ TAMs, tumor B cells and FRCs. Cell cluster is colored according to Fig. 2a, and CN cluster is colored according to Fig. 2d. c, T cell chemotaxis molecules in APOE⁺C1Q⁺ TAMs, tumor B cells and FRCs from different spatial niches. d, The expression of MHC-II genes in APOE⁺C1Q⁺ TAMs residing in different spatial niches. e, Summary of T cell chemotaxis pathways in CN1 and CN5, created with Biorender.com. f, The expression of CXCL9 and CXCR3 in APOE⁺C1Q⁺ TAMs and T cells from the same FOV as panel b. g, Barplot depicting the normalized PD-L1–PD-1 interaction count in each spatial niche. P values were calculated with a Kruskal–Wallis test. h, A representative CN3-dominated FOV showing the PD-L1–PD-1 interaction between APOE⁺C1Q⁺ TAMs and T cells. Cell cluster is colored according to Fig. 2a, and CN cluster is colored according to Fig. 2d.