Although single-gene perturbation screens have revealed a number of new targets, vulnerabilities specific to frequently altered drivers have not been uncovered. An important question is whether the compensatory relationship between functionally redundant genes masks potential therapeutic targets in single-gene perturbation studies. To identify digenic dependencies, we developed a CRISPR paralog targeting library to investigate the viability effects of disrupting 3,284 genes, 5,065 paralog pairs and 815 paralog families. We identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells through the hyperactivation of MAPK signaling. Furthermore, cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations such that the mechanisms of resistance to the inhibitors reinforce this mechanism of vulnerability. Together, multigene perturbation technologies unveil previously unrecognized digenic vulnerabilities that may be leveraged as new therapeutic targets in cancer.

尽管单基因扰动筛选已经揭示了许多新目标，但尚未发现针对频繁改变的驱动程序的特定漏洞。一个重要的问题是功能冗余基因之间的代偿关系是否掩盖了单基因扰动研究中的潜在治疗靶点。为了识别双基因依赖性，我们开发了一个 CRISPR 旁系同源靶向库，以研究破坏 3,284 个基因、5,065 个旁系同源对和 815 个旁系同源家族的生存能力影响。我们发现DUSP4和DUSP6的双重失活会选择性地损害NRAS和BRAF的生长突变细胞通过 MAPK 信号的过度激活。此外，对 MAPK 通路治疗剂具有抗性的细胞对DUSP4和DUSP6扰动变得交叉敏感，因此对抑制剂的抗性机制加强了这种脆弱性机制。总之，多基因扰动技术揭示了以前未被认识到的双基因漏洞，这些漏洞可能被用作癌症的新治疗靶点。