Comprehensive Immune Cell Profiling in Tumors

CIBERSORT method used to quantify infiltrating immune cell ratio (https://cibersort.stanford.edu/) (20 (link)). The proportion of 22 immune cells (B-naive cells, B-cell memory, plasma cells, T-cell CD8, T-cell CD4 naive, T-cell follicular helper cells, T-cell CD4 memory resting, T-cell CD4 memory activation, regulatory T cells (Tregs), γδ cells, monocytes, activation) was calculated by CIBERSORT method NK cells, resting NK cells, macrophage M0, macrophage M1, macrophage M2, resting dendritic cells, activated dendritic cells, resting mast cells, activated mast cells, eosinophils, and neutrophils). Samples with P<0.05 indicated that the proportion of immune cells calculated by CIBERSORT was correct. The tumor purity, stromal score, immune score and ESTIMATE scorewere calculated for each tumor sample by R package “ESTIMATE” (21 (link)). A single sample Gene set enrichment analysis (ssGSEA) algorithm was used to assess the immune infiltration between the two groups based on 28 immune cell types. XCELL, QUANTISEQ, MCPCOUNTER, EPIC and CIBERSORT-ABS software were also used to quantify the relative proportion of immune cell infiltration.