Extended Data Fig. 8: Molecular differences of phagocytes between EOPC and LOPC in the validation.

(a) Phagocytes distribution of EOPC versus LOPC, with abundance represented by the ratio of observed to expected (Ro/e). (b) Heatmap showing the mean AUCell scores for macrophage subtypes by myeloid functional sets (M1/M2 polarization and suppressive, angiogenesis, and phagocytosis activity). (c) Boxplot comparing the AUCell scores of M2 and MDSC functional sets between EOPC (n = 1,718) and LOPC (n = 377) Macro_APOE cells. Box-and-whisker plots showed the minimum, 25th percentile, median, 75th percentile and maximum (two-sided Wilcoxon tests). (d) Boxplot comparing the GSVA scores of fatty acid and cholesterol pathways among myeloid subtypes (n = 434, 69, 1,182, 71, 729, 821, 166, 930, 1,145, 626, 2,095, 423 and 435 for pDC_JCHAIN, cDC1_CLEC9A, cDC2_CD1C, cDC3_LAMP3, Mono_IL1B, Mono_FCN1, Macro_CXCL11, Macro_C3, Macro_RGS1, Macro_FOLR2, Macro_APOE, Macro_MT1A and Macro_Ribosome, respectively). Box-and-whisker plots showed the minimum, 25th percentile, median, 75th percentile and maximum. (e) Chord plots showing the interactions between AR-MP_High malignant epithelia and Macro_APOE cells in EOPC versus LOPC inferred by CellPhoneDB, and Dot plot showing the ligand‒receptor pairs from Macro_APOE to AR-MP_High malignant epithelia shared in EOPC samples. (f) Spatially illustration of different cell types (Left), APOE expression level (Middle) and AR-MP AUCell score (Right) for Rep-EOPC4-ST. (g) Violin-and-box plots comparing the stimulatory and inhibitory AUCell scores of CD4+ T cells (n = 5,348 and 2,459 for EOPC and LOPC, respectively) and CD8+ T cells (n = 8,110 and 7,161 for EOPC and LOPC, respectively) between EOPC and LOPC. Box-and-whisker plots showed the minimum, 25th percentile, median, 75th percentile and maximum (two-sided Wilcoxon tests). P-values were not adjusted for multiple comparisons.