Degradome analysis to identify direct substrates of small-molecule protein degraders

ABSTRACT: Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach that combines stable isotope labeling and click-chemistry for selective quantification of protein degradation by mass spectrometry, excluding confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the time scale of TPD (hours) and we demonstrate its utility by analyzing the Cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply it to characterize compound 1, a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target.

INSTRUMENT(S): Orbitrap Fusion, Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell

DISEASE(S): Acute Leukemia,Chronic Myeloid Leukemia

SUBMITTER: Lina-Marie Wagner  

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD048931 | Pride | 2024-10-14

REPOSITORIES: Pride