Fig. 7

Single-cell RNA sequencing (scRNA-seq) data combined with deconvolution analysis unveil that CD244 plays a role in determining the destiny of monocytes/macrophages differentiation and influences melanoma patient survival. The scRNA-seq data of 16,291 immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors (GSE120575) was downloaded and subjected to re-analysis. (A) UMAP plot showing seven subclusters (C0–6) of monocytes/macrophages identified from scRNA-seq data. (B) UMAP plot showing CD244-expressing monocytes/macrophages (left) and CD244 expression levels in three cell groups (C0–1, C2–3 and C4–6) (right). (C) Heatmap showing DEGs between CD244⁺ and CD244⁻ monocytes/macrophages in C0–1. (D) Cellular pathways enriched by 221 genes upregulated in CD244⁻ monocytes/macrophages. (E) The expression of genes preferentially involved in the innate immune response, phagosome/antigen presentation, and autophagy was assessed in CD244⁺ and CD244⁻ monocytes/macrophages (F) A schematic representation is provided to illustrate the classification of patients based on the expression level of CD244 in monocytes/macrophages (left). The UMAP plot demonstrates the distribution of CD8 T cells among patients classified as CD244 low and high, based on the expression levels of monocytes/macrophages (right). (G) Cellular pathways enriched by the genes upregulated in CD8 T cells of CD244 low patients (based on monocytes/macrophages); presented as –log₁₀ (P-value). (H) Genes predominantly upregulated in C2–3, C4–6, CD244⁺ and CD244⁻ monocytes/macrophages in the C0–1. (I) DEGs in C2–3, C4–6 and CD244⁺ and CD244⁻ within the C0–1 were deconvoluted to TCGA-SKCM bulk RNA-seq data. The estimated survival of patients was analyzed based on the presence or absence of CD244-negative monocytes/macrophages. The overall survival of patients with primary tumors (left) or metastatic tumors (right) was assessed. ***P < 0.001; one-way ANOVA (B) or Kaplan–Meier (log rank) test (G)