Fig. 4: scRNA-seq analysis indicates C1QC⁺ RTM-mediated immune activation via MHC class II signaling.

a UMAP plot of broad cell types from the Li et al. cohort. b UMAP plot of the macrophages showing transcriptionally distinct clusters. c UMAP plots showing the expression of selected marker genes in macrophages. d–f The Resident tumor macrophage (RTM) score, M2 score and innate anti-PD-1 resistance (IPRES) score in distinct cell clusters. The one-way ANOVA test was adopted to evaluate the statistical significance. g Abundance of each macrophage cluster in the tissue of pCR and non-pCR groups was estimated via Ro/e analysis. h Cell cluster frequency shown as a fraction of total macrophages in pCR and non-pCR group. i C1QC⁺ RTM score calculated by single sample gene set enrichment analysis (ssGSEA) method on the basis of bulk transcriptome from pCR and non-pCR group. The Wilcoxon Rank-Sum Test was adopted to evaluate the statistical significance. j GO analysis of C1QC⁺ RTMs and the other three macrophage clusters. k Violin plot showing the expression levels of MHC-II molecules in C1QC⁺ RTMs and the other three macrophage clusters. l The outgoing and ingoing interaction strength of immune cells in pCR and non-pCR group. The x-axis and y-axis scales differ between the pCR and non-pCR groups. m The number of pair–ligand interactions between T cells and C1QC⁺ RTM in the pCR and non-pCR groups. n Differences in the MHC-II pathway interaction of various cell types. The thicker the line, the stronger the connection. o Up-regulated and down-regulated receptor–ligand pairs that differ significantly between pCR and non-pCR based on C1QC⁺ RTM and other cell clusters. Dot size indicates the P value, colored according to the communication probability of pathways.