Lawson and Sousa et al. performed genome-wide loss-of-function CRISPR screens in a panel of mouse cancer cell lines in the presence of CTLs and identified 182 genes associated with cancer-intrinsic immune evasion. Perturbation of IFNγ signaling regulators sensitized cancer cells to CTL killing, and Fitm2 or autophagy gene knockouts were sensitive to IFNγ and CTL killing. Unexpectedly, cells with combined Fitm2 and autophagy gene perturbations were resistant to IFNγ killing , but not to CTL killing. Loss of autophagy or NF-κβ signaling sensitized cell to TNF-mediated cell death. A pooled in vivo CRISPR screen showed a loss of autophagy-targeted cells.
Contributed by Shishir Pant
ABSTRACT: The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood(1-3). Here, to identify a phenotypically robust core set of genes and pathways that enable cancer cells to evade killing mediated by cytotoxic T lymphocytes (CTLs), we performed genome-wide CRISPR screens across a panel of genetically diverse mouse cancer cell lines that were cultured in the presence of CTLs. We identify a core set of 182 genes across these mouse cancer models, the individual perturbation of which increases either the sensitivity or the resistance of cancer cells to CTL-mediated toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated manner in which genes and pathways act in cancer cells to orchestrate their evasion of CTLs, and shows that discrete functional modules that control the interferon response and tumour necrosis factor (TNF)-induced cytotoxicity are dominant sub-phenotypes. Our data establish a central role for genes that were previously identified as negative regulators of the type-II interferon response (for example, Ptpn2, Socs1 and Adar1) in mediating CTL evasion, and show that the lipid-droplet-related gene Fitm2 is required for maintaining cell fitness after exposure to interferon-_ (IFN_). In addition, we identify the autophagy pathway as a conserved mediator of the evasion of CTLs by cancer cells, and show that this pathway is required to resist cytotoxicity induced by the cytokines IFN_ and TNF. Through the mapping of cytokine- and CTL-based genetic interactions, together with in vivo CRISPR screens, we show how the pleiotropic effects of autophagy control cancer-cell-intrinsic evasion of killing by CTLs and we highlight the importance of these effects within the tumour microenvironment. Collectively, these data expand our knowledge of the genetic circuits that are involved in the evasion of the immune system by cancer cells, and highlight genetic interactions that contribute to phenotypes associated with escape from killing by CTLs.