Fig. 2

R-loop score positively correlated with anti-PD-1 immunotherapy response. A Changes in immune escape molecular profiles of malignant cells from GEO datasets (GSE123904 and GSE131907) between subgroups with high and low R-loop scores, and the difference in the score of enriched immunogenic cell death (ICD) pathways between two different scoring subgroups, using single-sample gene set enrichment analysis (ssGSEA, Wilcoxon rank test). B Proportions of immune cells, malignant cells, and other cells from samples with high R-loop scores and those with low R-loop scores. C Proportions of eight immune cell types and naive, cytotoxic, and dysfunctional T cells from patients with high R-loop scores and those with low R-loop scores (Wilcoxon rank test). D The difference in the NK cell exhaustion score between malignant cells with high and low R-loop scores (Wilcoxon rank test). E T-distributed stochastic neighbor embedding (t-SNE) plot of 11,515 cells from the single-cell RNA-sequencing data (GSE146100) colored according to cell types or individual patients. F R-loop scores for each cell type such as malignant cells, endothelial cells, fibroblasts, epithelial cells, and immune cells (Wilcoxon rank test). G Uniform manifold approximation and projection (UMAP) of malignant cells colored according to the treatment response or R-loop score. H The difference in the R-loop score between patients who responded to cancer treatment and those who did not (Wilcoxon rank test). (*p < .05, **p < .01, ***p < .001)