Fig. 5: Immunosuppressive myeloid cells are enriched in prostate tumors.

a, b Joint embedding showing the detailed annotation of the myeloid subpopulations (a) and the expression of select gene markers for each subpopulation (b). c Gene expression pattern: boxplots representing the average gene expression pattern of monocyte, macrophage, inflammatory, antigen processing and presentation, MDSC gene signatures, and M2-macrophages gene signature across the different myeloid subpopulations (top). Heatmap showing the average gene expression of representative genes across the different myeloid subpopulations in healthy, adj-normal, and tumor prostate samples (bottom). See Supplementary Data 4 for the genes defining the above-mentioned signatures. d Boxplot comparing the average expression of MDSC gene signature in tumor-inflammatory monocytes (TIMo) across the three different samples (healthy n = 5, adj-normal n = 14, and tumor n = 18). e Boxplot representing the cell fraction of different myeloid subpopulations across the healthy (n = 5), tumor (n = 18), and their adj-normal (n = 14) prostate tissues. Boxplots in c–e include centerline, median; box limits, upper and lower quartiles; and whiskers are highest and lowest values no >1.5× interquartile range. Statistical significance was accessed using two-sided Wilcoxon rank-sum test (*p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001), p values could be found in Supplementary Data 6. f Top: multiplex fluorescence immunohistochemistry (mFIHC) staining of prostate tumor tissue (bottom) and its adj-normal tissue (top) collected from a prostatectomy case of Gleason score 5 + 5. Samples are labeled with PD-1 (Clone EH33) (color Red), FOXP3 (color Orange), CD8 (color Yellow), CD68 (color Magenta), CD3 (color Cyan), CD163 (color Green), and DAPI (Blue) by using mFIHC. Bottom: quantification of absolute number of macrophages (left) and M2-macrophages (right) from mIHC data comparing tumor tissues to their matched adj-normal tissues collected from prostatectomy cases of different Gleason scores. Red circles represent the tumor samples and black circles represent their matched adj-normal samples. Source data are provided as a Source Data file.