Profiling Immune Landscapes in Cancer

To estimate the signature of MHC-II antigen presentation in cancer cells, we calculated the enrichment scores for each cell using the AddModuleScore function in Seurat with the gene list from the REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION pathway (c2.cp.reactome.v7.2.symbols.gmt, download from https://www.gsea-msigdb.org/gsea/index.jsp). To explore the cytotoxic and exhausted functions of T and NK cells, we calculated the cytotoxic score and exhausted score for each cell using the canonical cytotoxic (GZMA, GZMB, GZMK, GNLY, IFNG, PRF1, and NKG7) and exhausted (LAG3, TIGIT, PCCD1, HAVCR2, CTLA4, LAYN, and ENTPD1) markers, respectively. With the same method, we used the gene list (Additional file 3: Table S2) in “LM22.xls” from CIBERSORT [22 (link)] to estimate the phenotype (M0, M1, or M2) for each macrophage. We also calculated the antigen presentation score for DCs with the previously reported markers (Additional file 3: Table S2) [23 (link)]. A mean value of module scores of a cell cluster (≥ 10 cells) from an individual sample was calculated to present the signature level.