Fig. 5

Characterization of the heterogeneity of myeloid cells in primary and metastatic tumors in the liver. A UMAP plot of scRNA-seq profile from myeloid cells separated into 13 cell clusters. Cells are colored according to different clusters. B UMAP plot showing 13 cell clusters in different types of tissues. C Heatmap showing the normalized expression (z-score) of myeloid cell function-associated gene sets in each cell cluster. D Tissue prevalence of myeloid cell clusters estimated by Ro/e scores. E Forest plot showing the prognostic values of each myeloid cell cluster infiltration in the primary HCC cohort (TCGA-LIHC; n = 346) and the metastatic liver tumors cohort (MT2020; n = 198). The HRs with 95% CIs and P values were determined by univariate Cox proportional hazards regression analyses. F–H Semi-supervised pseudotime trajectory of tumor-associated macrophages clusters inferred by Monocle 2. Trajectory is colored by the pseudotime (F) or cell clusters (G). H Ridgeline plot showing the order of appearance of cell clusters in time colored by clusters (top) and the heatmap showing the fluctuation of genes along the pseudotime (bottom). I Heatmap showing the average activities of the top 5 significant TFs identified by SCENIC in each macrophage cluster. J Feature plots showing the activities of WDR45B+ TAM-specific TF CEBPD (top) and expression levels of CEBPD (bottom). K Volcano plot showing the DEGs between WDR45B+ TAMs and the other TAMs. The red dots represent the significantly up-regulated genes, the blue ones represent the down-regulated genes, and the grey ones represent the non-significant genes. L Violin plots showing the M2 scores of WDR45B+ TAMs across different types of tissues. Wilcox test was used to assess the statistic difference between groups. “****” and “***” represent “P < 0.0001” and “P < 0.001”, respectively. M Violin plot showing the GSVA scores of WDR45B+ TAMs signature genes across NTs and PTs from the TCGA-LIHC cohort (NTs, n = 50; PTs, n = 374) and metastatic liver tumors from the M2020 cohort (n = 198). Wilcox test was used to assess the difference between groups. “****” and “*” represent “P < 0.0001” and “P < 0.05”, respectively. N Spatial distribution of the whole myeloid cells and WDR45B+ TAMs in a metastatic liver tumor (L1) determined by the spatial transcriptomic data (GSE225857). O Heatmap showing the scaled expression levels of a series of immune checkpoint genes in myeloid cell clusters. Genes are grouped as receptor or ligand, inhibitory or stimulatory status and expected major lineage cell types known to express the gene (lymphocyte and myeloid)