Fig 2: Perturbed immune cell transcriptomes and cellular interactions in prostate tumor(A) Violin plot of gene module score of GO term corresponding to antigen processing and presentation in tumor versus normal in myeloid cells. Kruskal-Wallis test was performed between normal and tumor for each cluster and p < 0.05 was considered statistically significant.(B) Pie chart of co-activating and co-inhibitory DEGs between normal (light colored sections) and tumor (dark colored sections) in myeloid clusters. Darker sections indicate genes that were that were upregulated in tumor versus normal and lighter section indicate upregulation is in normal versus tumor (> = 1.25 log2 fold change). Grey sections indicate < 1.25 log2 fold change.(C) Mean expression dot plot of costimulatory/coinhibitory molecules. Increasing expression corresponds with increasing gradient from white to red (MNP/B cell/epithelial/stromal) or white to blue (T/NK/B cell) corresponding to increasing expression value. Size of circles indicate the percentage of cells expression the gene.(D) Violin plot of gene set test (AUCell) results in CD8 cytotoxic T cell cluster for murine CD8 T cell exhaustion gene set curated from (Doering et al., 2012). Significance is denoted by ∗p < 0.05 (Mann-Whitney test).(E) GSEA of KEGG pathways for NK CD16neg tumor versus normal. Statistically significant pathways are colored and labeled.(F) Mean expression dot plot of leading edge genes in cytokine-cytokine receptor interaction as in (E). Only genes that are expressed by at least 20% of cells are plotted.(G) (Top) Expression of CCL5 and prediction/label transfer score of NK CD16neg cells in visium data of normal and tumor prostate sections. (Bottom) Spatial correlation of CCL5 with NK CD16neg cells in prostate cancer visium data. Only positive correlations are plotted; increasing value of correlation is shown as a gradient from white to red.(H) CellPhoneDB receptor-ligand interaction analysis between B cell and myeloid clusters.(I) Representative immunofluorescence confocal microscopy of BAFF and HLA-DR in human prostate tumor section. Scale bars, 20 μm.(J–L) (J) Expression of TNFSF13B and prediction/label transfer score of MAC-MT cells, and correlation of TNFSF13B with MAC-MT cells in prostate cancer visium data. Only positive correlations are plotted; increasing value of correlation is shown as a gradient from white to red. CellPhoneDB receptor-ligand interaction analysis between (K) fibroblasts and T cell clusters, and fibroblast and myeloid clusters and (L) myeloid clusters with LE clusters split by group (N = normal; T = tumor). The order of the receptor-ligand interactions corresponds to the order of the cell-types i.e., cell type A expressing molecule A interacts with cell type B expressing molecule B. Size of circles and color gradient corresponds to the receptor-ligand interaction score, which purple, blue, green to yellow for increasing values. Significant interactions (p < 0.05) are highlighted in red. See also Figure S7.

Fig 3: The spatial characteristics of APC, pro-Tex cells, and Tex cells in the head and neck squamous cell carcinoma (HNSCC) tumor microenvironment (TME).(a–b) Representative example of HNSCC tumor stained by multiplex IHC, with white triangles and rhombus showing the Texs and P-Tex aggregates in the APC area, respectively. (c) Measured distances to APC (MHCII+) cells from CD8+ T cells, CD8+ PD1+T cells (Tex cells) or CD8+ PD1+MKI67+/CDK4+ T cells (P-Tex cells) in five representative samples. The dashed lines represent the cutoff distance of 25 μm, which indicate that 90% of CD8+ T, Tex, or P-Tex cells are enriched within a distance of 25 µm from APCs.

Fig 4: Anticancer activity and improved tumor immune microenvironment of a combination of anti-PD-1 antibody and Met@Man-MPs in AOM/DSS-induced CAC mice.a Schematic schedule for anticancer experiment in AOM/DSS-induced CAC mice. b Numbers of tumors with size>3 mm and <3 mm in CAC mice after treatment with PBS, Man-MPs, Met@Man-MPs, anti-PD-1 antibody, a combination of Man-MPs and anti-PD-1 antibody, or combination of Met@Man-MPs and anti-PD-1 antibody at the anti-PD-1 antibody dosage of 100 µg per mouse and Met dosage of 10 mg kg−1 indicated in (a). Data are presented as mean ± s.d. (n = 5 mice per group; one-way ANOVA followed by Tukey’s HSD post-hoc test). c–j Percentages of M1-like TAMs (c), M2-like TAMs (d), CD8+ T cells (e), CD8+CD69+ T cells (f), CD4+ T cells (g), CD4+CD69+ T cells (h), MDSCs (i) and Tregs (j) in colon tumors of CAC mice after treatment with PBS, Man-MPs, Met@Man-MPs, anti-PD-1 antibody, a combination of Man-MPs and anti-PD-1 antibody, or combination of Met@Man-MPs and anti-PD-1 antibody at the anti-PD-1 antibody dosage of 100 µg per mouse and Met dosage of 10 mg kg−1 indicated in (a). Data are presented as mean ± s.d. (n = 5 mice per group; one-way ANOVA followed by Tukey’s HSD post-hoc test). Source data are provided as a Source Data file.

Fig 5: Anticancer activity and improved immune microenvironment of Met@Man-MPs in H22 tumor-bearing mice.a Tumor growth curves of H22 tumor-bearing mice after intravenous injection of PBS, MPs, Man-MPs, free Met, Met@MPs or Met@Man-MPs at the Met dosage of 10 mg kg−1, or high dosage of Met at 100 mg kg−1 every two days for six times. The black arrows indicate the injection time. Data are presented as mean ± s.e.m. (n = 5 mice per group; two-way ANOVA followed by Bonferroni’s multiple comparisons post-test). b Tumor weight at the end of the treatment indicated in (a). Data are presented as mean ± s.d. (n = 5 mice per group; one-way ANOVA followed by Tukey’s HSD post-hoc test). c Kaplan–Meier survival plot of H22 tumor-bearing mice after treatment indicated in (a) (n = 7 mice per group). d–k The numbers of M1-like TAMs (d), M2-like TAMs (e), CD8+ T cells (f), CD8+CD69+ T cells (g), CD4+ T cells (h), CD4+CD69+ T cells (i), MDSCs (j), and Tregs (k) in tumor tissues of H22 tumor-bearing mice after intravenous injection of PBS, MPs, Man-MPs, free Met, Met@MPs or Met@Man-MPs at the Met dosage of 10 mg kg−1, or high dosage of Met at 100 mg kg−1 every two days for six times. Data are presented as mean ± s.d. (n = 3 mice per group; one-way ANOVA followed by Tukey’s HSD post-hoc test). l–o The contents of IFN-γ (l), TNF-α (m), IL12p70 (n), and TGF-β (o) in tumor tissues of H22 tumor-bearing mice after intravenous injection of PBS, MPs, Man-MPs, free Met, Met@MPs or Met@Man-MPs at Met dosage of 10 mg kg−1, or high dosage of Met at 100 mg kg−1 every two days for six times. Data are presented as mean ± s.d. (n = 3 mice per group; one-way ANOVA followed by Tukey’s HSD post-hoc test). Source data are provided as a Source Data file.