Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers

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. A CRISPR paralog targeting library profiling 815 paralog families across 11 cell lines identifies DUSP4 and DUSP6 as paralog pairs whose combined inactivation confers sensitivity to cells resistant to MAPK inhibitors or cells harboring NRAS or BRAF mutations.

Automated summary

Research using a CRISPR paralog targeting library identified that dual inactivation of DUSP4 and DUSP6 selectively impairs growth in NRAS and BRAF mutant cells. Cells resistant to MAPK pathway therapeutics become cross-sensitized to DUSP4 and DUSP6 perturbations, reinforcing the mechanisms of resistance to the inhibitors.