Plasticity of the cullin-RING ligase repertoire shapes sensitivity to ligand-induced protein degradation

Inducing protein degradation via small-molecules is a novel and transformative therapeutic paradigm. While 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 target protein degradation, we applied genome-scale CRISPR/Cas9 screens for five drugs that hijack different substrate receptors (SRs) of cullin RING ligases (CRLs) for target protein degradation. We find 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 target protein degradation, and outlines biomarkers and putative resistance mechanisms for upcoming clinical investigation.

通过小分子诱导蛋白质降解是一种全新且具有变革性的治疗范式。尽管靶标降解的结构要求正逐步明晰，但决定细胞对小分子降解剂产生应答的分子机制仍有待深入探究。为系统阐明靶标蛋白质降解所需的效应因子，我们针对五种劫持不同Cullin环指连接酶（cullin RING ligases, CRLs）底物受体（substrate receptors, SRs）以实现靶标蛋白降解的药物，开展了全基因组CRISPR/Cas9筛选。研究发现，小分子降解剂的细胞敏感性由共享的以及药物特异性的调控网络共同决定，其中包括COP9信号小体（COP9 signalosome）以及底物受体交换因子CAND1。对这些效应因子进行遗传或药理学扰动，会损害CRL的可塑性，并使大量连接酶持续处于激活状态。由此引发的CRL失活周转缺陷会触发广泛的CRL自身降解，进而使细胞对多种降解剂产生耐药性。综上，本研究揭示了可用于靶标蛋白质降解的CRLs的调控机制与结构特征，并为后续临床研究明确了生物标志物及潜在的耐药机制。