Fig. 3: Detailed characterization of immune cells in TME of HPC.

a Identification of cell subtypes in immune cells. b Average gene expression heatmap of functional markers in T/NK subtypes. c Violin plots showing the expression scores of naive, cytotoxic, and inhibitory/exhausted signature gene sets of four CD8 + T-cell subtypes (n = 9989). Inside black points denote median values, and lines denote the corresponding interquartile ranges. d Heatmap showing the activity of TF regulons across four CD8 + T-cell subtypes. e Proportion differences of all CD8 + T subtypes among RBT, NBT, and NAT groups. f 2D density dot plots showing the changes of the cytotoxicity and exhaustion states of all CD8 + T cells among RBT, NBT and NAT groups. Cells were partitioned into four parts according to the mean scores of two states with quadrantal percentages shown in the plots. g Violin plots showing the expression scores of naive, TregStability and related chemokine signature gene sets of three CD4 + Treg cell subtypes (n = 4103). Inside black points denote median values and lines denote the corresponding interquartile ranges. Source data are provided as a Source Data file. h 2D density dot plots showing the changes of the TregStability and chemokines states of all Treg cells among RBT, NBT and NAT groups. Cells were partitioned into four parts according to the mean scores of two states, with quadrantal percentages shown in the plots. i Scatter plot showing the scores of M1 and M2 signatures for each macrophage cell. j Violin plots showing the expression levels of different marker genes between subtypes of macrophageM1 and macrophageM2. k 2D density dot plots showing the changes of the M1 and M2 signature states of all macrophages among RBT, NBT, and NAT groups. Cells were partitioned into four parts according to the mean scores of two states, with quadrantal percentages shown in the plots.