Upon evaluating the cell–cell interaction status by jointly considering the gene expression pattern of immune checkpoint components in the complementary cells, e.g., PDCD1 (PD-1) in T cells, and CD274 (PDL1) and PDCD1LG2 (PDL2) in the tumor cells, we estimated the relative contribution of different co-stimulatory and co-inhibitory checkpoints in shaping the immunosuppressive landscape in HCC (Fig. 4a and Supplementary Fig. 11). Here, PDCD1 is linked to hepatocellular carcinoma.