Genome-wide CRISPR screen reveals cancer cell resistance to NK cells induced by NKderived IFN-γ

Abstract

Abstract The anti-leukemia activity of NK cells is important for preventing relapse during HSCT in leukemia patients. However, the factors that determine susceptibility of leukemia cells in the context of NK-mediated killing are not well established. Here we performed a genome wide CRIPSR screen in the human CML cell line K562 to identify genes that regulate vulnerability of leukemia cells to killing by primary human NK cells. Distribution of gRNAs in K562 cells that survived co-incubation with NK cells showed that loss of NCR3LG1 (encodes B7H6), the ligand of the activating receptor NKp30, predominantly protected K562 cells from killing. It indicates that B7H6 is a major ligand on K562 cells. In contrast, loss of genes that regulate pathways for antigen-presentation (B2M, HLA-I, PSMB5, TAP1, TAPBP) and IFN-γ signaling (IFNGRs, JAKs, STATs) increased the vulnerability of K562 cells. MHC-I on K562 cells was upregulated after co-culture with NK. Addition of IFN-γ neutralizing antibody during the co-culture increased the susceptibility of K562 cells to NK-mediated lysis. The results suggest that cancer cells respond to NK-derived IFN-γ and lead to NK-resistance and immune evasion. Moreover, Analysis of RNA-seq data from The Cancer Genome Atlas (TCGA) showed that low IFNGR2 expression in cancer tissues associated with improved overall survival in AML patients, indicating that the IFNGR-JAK-STAT pathway can be a contributor to worse prognosis of cancer patients, potentially related to IFN-γ–induced NK-resistance, despite the fact that IFN-γ signaling promotes T cell mediated immune surveillance. Our results suggest that targeting IFN-γ responses might be a promising approach to enhance NK cell anti-cancer efficacy.