Figure 4.

Landscape of lymphocytes and innate lymphoid cells in breast cancer liver and brain metastases. a) t‐SNE plot of the T cell and NK cell landscape colored by subcluster. b) Feature plots showing the normalized expression of canonical marker genes in each T cell and NK cell subcluster. c) t‐SNE plot of the B cell landscape colored by subcluster. d) Feature plots showing the normalized expression of canonical marker genes in each B cell subcluster. e) Dot plot showing the expression level of canonical marker genes across all lymphocyte and innate lymphoid cell subtypes. f) Heatmap showing the gene set score of each T cell and NK cell according to GSVA. Gene sets included MHC molecules, T cell cytotoxicity, T cell exhaustion, inflammatory pathway, regulatory cytokines, and immune checkpoint pathway sets. g) Heatmap showing the expression of core genes in each gene set. h) The cytotoxicity and dysfunction of each T cell and NK cell cluster were analyzed and quantified based on gene signature scores. i) Exhaustion scores of CD8_T_cells_c1_GZMK and CD8_T_cells_c2_ZNF683 in liver and brain metastases of breast cancer. j,k) The potential biological functions and relevant signaling pathways of T, B, and NK cell subclusters were evaluated by GO and KEGG analyses. l) Monocle pseudotime trajectory analysis of CD8+ T cells (CD8_T_cells_c1_GZMK, CD8_T_cells_c2_ZNF683, CD8_T_cells_c3_KLRB1, and CD8_T_cells_c4_IFIT3) with highly variable gene expression. l) Monocle pseudotime trajectory analysis of B cells (Pre‐B_cells_VPREB3, Naive_B_cells_TCL1A, Mature_B_cells_MS4A1, and Plasma_cells_MZB1) with highly variable gene expression. o) Violin plot showing the expression level of immune checkpoint genes in four CD8+ T cell subclusters. o) Dot plot showing the expression level of immune checkpoint genes in each lymphocyte and innate lymphoid cell subcluster. p) Feature plots showing the normalized expression of immune checkpoint genes in lymphocytes and innate lymphoid cells.