Cancer Cell Resistance to IFNγ Can Occur via Enhanced Double-Strand Break Repair Pathway Activity [CRISPR screen]

The pleiotropic cytokine interferon-gamma (IFNγ) is known to be associated with cytostatic, anti-proliferation, and pro-apoptosis functions in cancer cells. However, cancer cells can become resistant to IFNγ, and the underlying mechanism is not fully understood. To investigate the potential IFNγ resistant mechanisms, we performed IFNγ sensitivity screens in more than 40 cancer cell lines and characterized the sensitive and resistant cell lines. By applying CRISPR screening and transcriptomic profiling in both IFNγ sensitive and resistant cells, we discovered that activation of double-strand break (DSB) repair genes could result in IFNγ resistance in cancer cells. In addition, suppression of single-strand break (SSB) repair genes increased the essentiality of DSB repair genes after IFNγ treatment. The relationship between the activation of DSB repair genes and IFNγ resistance was further confirmed in clinical tumor profiles from The Cancer Genome Atlas (TCGA) and immune checkpoint blockade (ICB) cohorts. Our study provides a comprehensive resource to elucidate IFNγ resistance in cancer and has the potential to inform combinational therapeutic strategies to overcome immunotherapy resistance. To further validate the molecular mechanisms related to IFNγ resistance, we performed CRISPR knockout (KO) screens on four IFNγ resistant cell lines (MCF7, 786O, HCT116, HUH6) and five sensitive cell lines (A549, NCIH1437, MDAMB231, PC9, CALU1).