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

The pleiotropic cytokine interferon-gamma (IFN?) is known to be associated with cytostatic, anti-proliferation, and pro-apoptosis functions in cancer cells. However, cancer cells can become resistant to IFN?, and the underlying mechanism is not fully understood. To investigate the potential IFN? resistant mechanisms, we performed IFN? 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 IFN? sensitive and resistant cells, we discovered that activation of double-strand break (DSB) repair genes could result in IFN? resistance in cancer cells. In addition, suppression of single-strand break (SSB) repair genes increased the essentiality of DSB repair genes after IFN? treatment. The relationship between the activation of DSB repair genes and IFN? 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 IFN? resistance in cancer and has the potential to inform combinational therapeutic strategies to overcome immunotherapy resistance. Overall design: To further validate the molecular mechanisms related to IFN? resistance, we performed CRISPR knockout (KO) screens on four IFN? resistant cell lines (MCF7, 786O, HCT116, HUH6) and five sensitive cell lines (A549, NCIH1437, MDAMB231, PC9, CALU1).

多效性细胞因子干扰素-γ（interferon-gamma, IFN?）已知可在癌细胞中发挥细胞生长抑制、抗增殖以及促凋亡功能。然而癌细胞可对IFN?产生耐药性，其潜在具体机制尚未完全阐明。为探究IFN?耐药的潜在机制，我们对40余株癌细胞系开展了IFN?敏感性筛选，并对敏感株与耐药株进行了特征鉴定。通过对IFN?敏感细胞与耐药细胞开展CRISPR筛选与转录组谱分析，我们发现双链断裂（double-strand break, DSB）修复基因的激活可导致癌细胞产生IFN?耐药性。此外，在IFN?处理后，单链断裂（single-strand break, SSB）修复基因的抑制会增强DSB修复基因的必需性。我们进一步在癌症基因组图谱（The Cancer Genome Atlas, TCGA）与免疫检查点阻断（immune checkpoint blockade, ICB）队列的临床肿瘤谱数据中验证了DSB修复基因激活与IFN?耐药性之间的关联。本研究为阐明癌细胞IFN?耐药性提供了全面的研究资源，并有望为克服免疫治疗耐药的联合治疗策略提供理论指导。实验整体设计：为进一步验证与IFN?耐药相关的分子机制，我们对4株IFN?耐药细胞系（MCF7、786O、HCT116、HUH6）与5株敏感细胞系（A549、NCIH1437、MDAMB231、PC9、CALU1）开展了CRISPR敲除（CRISPR knockout, KO）筛选。