Extended Data Fig. 6: Detailed response profiles of monocytes upon regorafenib-nivolumab treatment.

a, Volcano plot showing proportional changes in monocyte subclusters at C1D1 among long-term responders (LR; n = 15) versus early progressors (EP; n = 13). The unpaired T test was performed for unpaired groups. b, Gating strategy of monocytes from PBMCs in LR and EP. c, Representative flow cytometry plots for classical (CD14⁺CD16⁻), intermediate (CD14⁺CD16⁺) and non-classical (CD14^dimCD16⁺) monocytes among total monocytes. d, Proportions of classical, intermediate and non-classical monocytes among total monocytes, before and after regorafenib-nivolumab treatment, in LR (n = 7) and EP (n = 8). Analyses of monocyte clusters from an independent HCC cohort treated with anti-PD-1 monotherapy (Chuah et al. 2022) (e-i). e, UMAP of monocyte clusters. f, Dot plots showing the average normalized expressions of marker genes used for subclustering of monocyte clusters. g, Bar plots showing the proportion of each cell type among monocyte clusters in individual samples. (h-i), Violin plots showing module scores for the gene sets upregulated in each monocyte cluster according to treatment outcomes at pre- and post-treatment; gene sets upregulated in by regorafenib in M0 condition (h), upregulated in CSF1R KO (i). *P < 0.05, **P < 0.01, ***P < 0.005, ****P < 0.001, according to a two-sided Wilcoxon signed-rank test for paired groups, and two-sided Mann-Whitney U test for unpaired groups. Data are presented as mean ± standard deviation.