Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator [total RNA-seq]

Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancer-specific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.