Fig. 2

B cell heterogeneity among the primary and metastatic tumors in the liver. A UMAP plot of scRNA-seq profile from B cells which are separated into 5 cell clusters. Cells are colored according to different clusters. B UMAP plot showing 5 B cell clusters in NTs, PTs and MTs. C Feature plots showing the typical markers of memory B cells (top) and plasma cells (bottom). D Dotplot showing the percentage of expressed cells and average expression levels of marker genes of the 5 B cell clusters. E Tissue prevalence of major B cell clusters estimated by Ro/e scores. Ro/e, the ratios of the observed versus expected cell numbers. F Heatmap showing the normalized expression (z-score) of B cell function-associated gene sets in each cell cluster. G Violin plots showing the immune activation (top) and B cell receptor signaling (bottom) levels of 5 B cell clusters in NTs, PTs and MTs. Wilcox test was used to assess the difference between groups. “**”, “*” and “ns” represent “P < 0.01”, “P < 0.05” and “not significant”, respectively. H Violin plots showing the normalized expression (z-score) of inhibitory-associated genes in memory B cells clusters among three groups. Wilcox test was used to assess the difference between groups. “****”, “***”, “**”, “*” and “ns” represent “P < 0.0001”, “P < 0.001”, “P < 0.01”, “P < 0.05” and “not significant”, respectively. I–K Semi-supervised pseudotime trajectory of B cell clusters inferred by Monocle2. I Trajectory is colored by the pseudotime. J Trajectory is colored by cell clusters. K Ridgeline plot showing the order of appearance of cell clusters in time, colored by cell clusters (top), and the Heatmap showing the fluctuation of genes along the pseudotime (bottom). L Box plots showing the proportion changes of early and late B cells in NTs, PTs and MTs, respectively. T-test was used to assess the difference between groups. “****” and “**” represent “P < 0.0001” and “P < 0.01”, respectively. M Volcano plot showing the differential expressed genes (DEGs) between late B cells and early B cells. The red dots represent the statistically significant up-regulated genes, the blue ones represent the down-regulated genes, and the grey ones represent the non-significant genes. N Bar plots showing the GO biological processes enriched by the signature genes of late B cells (red) and early B (blue) cells, respectively. APP antigen processing and presentation