Fig. 1

Dissection and clustering of tumor-related immune cells in melanoma. A Flow chart of the steps in the performed analyses. B The t-SNE projection of 2068 single T cells, 515 B cells and 126 macrophages from 19 patients, showing the formation of 9 main clusters of T cells, including 5 for CD8 + T cells and 3 for CD4 + T cells (left), 4 main clusters of B cells, including 1 for regulatory B cells and 3 for non-regulatory B cells (top right), and 2 main clusters of M1 and M2 macrophages (bottom right). Each dot corresponds to one single cell, colored according to cell cluster. C Heatmap showing the z-score normalized mean expression of selected T cell function-associated genes (row) in each T-cell cluster (C0-C8, column) of the 9 main clusters identified in (B). The T cell function-associated genes covering five different classes, including cytotoxic, exhausted, regulatory and naïve types. The T-cell clusters are colored according to those shown in (B). Blue boxes highlight the key markers and the numbers in brackets represent the total times appeared in literature. D-E Z-score normalized mean expression of the selected B cell function-associated genes (row) in each B-cell cluster (C0-C3, column) of the 4 main clusters (D) and z-score normalized mean expression of the selected macrophage function-associated genes (row) in each cell cluster (C0-C1, column) of the 2 main macrophage clusters (E). The B cell function-associated genes covering five different classes, including anti-apoptosis, regulatory B cell, germinal center, pro-apoptosis and naïve/memory types. The macrophage function-associated genes covering two different classes of M1 and M2 types. The B-cell and macrophage clusters are colored according to those shown in (B). Blue boxes highlight the key markers and the numbers in brackets represent the total times appeared in literature