Plasticity of the Cullin-RING Ligase Repertoire Shapes Sensitivity to Ligand-Induced Protein Degradation

Inducing protein degradation via small molecules is a transformative therapeutic paradigm. Although structural requirements of target degradation are emerging, mechanisms determining the cellular response to small-molecule degraders remain poorly understood. To systematically delineate effectors required for targeted protein degradation, we applied genome-scale CRISPR/Cas9 screens for five drugs that hijack different substrate receptors (SRs) of cullin RING ligases (CRLs) to induce target proteolysis. We found that sensitivity to small-molecule degraders is dictated by shared and drug-specific modulator networks, including the COP9 signalosome and the SR exchange factor CAND1. Genetic or pharmacologic perturbation of these effectors impairs CRL plasticity and arrests a wide array of ligases in a constitutively active state. Resulting defects in CRL decommissioning prompt widespread CRL auto-degradation that confers resistance to multiple degraders. Collectively, our study informs on regulation and architecture of CRLs amenable for targeted protein degradation and outlines biomarkers and putative resistance mechanisms for upcoming clinical investigation. [Display omitted] •Unbiased survey reveals global and specific effectors for target degradation•CRL dependency on CAND1/CSN is ligase and context specific•Perturbing CAND1/CSN abrogates CRL plasticity and prompts ligase auto-degradation•CSN inactivation blocks substrate-driven CRL assembly Mayor-Ruiz et al. combine functional genomics and quantitative proteomics to identify cellular modulators of ligand-induced targeted protein degradation. Several regulators, such as CAND1 and the COP9 signalosome, maintain context-specific ligase plasticity to enable substrate-driven ligase assembly and protect substrate receptors from auto-degradation.