Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator.

Transcription factors (TFs) are aspirational therapeutic targets, as their dysregulation drives altered cell states. Yet many disease-relevant TFs are disordered and lack canonical binding pockets, frustrating direct small-molecule inhibition. Indirectly targeting the effector molecules that modulate TF function is a promising, underexplored alternative. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. With an intein-based method for catalyst conjugation in biochemically intact nuclei, we capture unique c-Myc interactomes in healthy and cancerous prostate cells and mine them for druggable vulnerabilities. We identify STE20-like kinase (SLK), a cancer-specific interactor that stabilizes c-Myc, drives epithelial morphology and is essential for tumorigenesis. Mechanistically, SLK phosphorylates c-Myc at serine 329, antagonizing GSK3β-dependent phosphodegron phosphorylation. This interaction is associated with a splicing change promoting nuclear localization of the long SLK isoform. Patient data link this isoform to c-Myc target expression across tumor types; the interaction validates across diverse tissues.