Proteomics of immune cells from liver tumors reveals immunotherapy targets [tumor]

Elucidating the mechanisms by which immune cells become dysfunctional in tumors is critical to developing next-generation immunotherapies. We profiled proteomes of cancer cells, as well as monocyte/macrophages, and CD4+ and CD8+ T cells isolated from tumors, livers, and blood of 48 patients with hepatocellular carcinoma. We found that tumor macrophages induce the sphingosine-1-phospate-degrading enzyme SGPL1, which dampened their inflammatory phenotype and anti-tumor function in vivo. We further discovered that the signaling scaffold protein AFAP1L2 is upregulated in chronically activated CD8+ T cells in tumors but is not present during the canonical T cell activation program. Ablation of AFAP1L2 in CD8+ T cells increased their viability upon repeated stimulation and enhanced their antitumor activity synergistically with PD-L1 blockade in mouse models. Our data revealed new targets for immunotherapy and provide a resource on immune cell proteomes in liver cancer (www.immunomics.ch/liver). Fresh tumor tissue samples were collected. Tumors were enzymatically digested. Cell suspensions were filtered through, and mononuclear immune cells were separated from tumor, stromal cells and red blood cells by Ficoll gradient centrifugation. Mononuclear immune cells were stained with antibodies to CD45 and CD14, plus antibodies to CD8, CD4, CD56 to exclude other cell types and sorted. Cell pellets were washed and snap frozen in liquid nitrogen.