Fig. 3

Single-cell transcriptional profiling of immune cells in APC patients treated with NK cell-based therapy. a Schematic overview of the study design. Three nonresponders (NR, including the SD/PD samples P16, P20, and P21) and four responders (R, including the CR/PR samples P22, P24, P26, and P27) were sampled for scRNA-seq. Three responders (P24, P26, and P27) were enrolled for bulk TCR Vβ repertoire sequencing. b t-SNE plot visualization of circulating immune cell clusters. c Dot plot showing the expression levels of marker genes in the indicated immune cell types. d t-SNE plot showing the cell origins by color. Patient origin is shown in the left panel, and pretreatment (pre–all, n = 7) or posttreatment (post–all, n = 12) data are shown in the right panel. e Histogram indicating the proportion of annotated immune cells in each sample; neutrophils and unknown cells were excluded from the proportion analysis. f GO and KEGG analyses of differentially expressed genes (DEGs) between pre–all and post–all samples. DEGs were computed by Findmarkers with a |log2-fold change| > 0.25 and adjusted p value < 0.05. The top 10 enriched GO-BP terms (left panel) and the top 10 enriched KEGG pathways (right panel) upregulated in all the samples are shown. scRNA-seq single-cell RNA sequencing, TCR T-cell receptor, t-SNE t-distributed stochastic neighbor embedding, GO gene ontology, KEGG Kyoto Encyclopedia of Genes and Genomes, GO-BP GO-biological process