Nanoscale photoproximity labeling of c-Myc predicts cancer specific therapeutic targets

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 alternative strategy. Here we report a unified strategy for capturing cancer-specific protein-protein interactions using µMap photoproximity labeling. Using a recently reported intein-based strategy for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in androgen receptor dependent and independent prostate cancer cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a PC-3 specific Myc interactor, SLK, selectively promotes Myc stabilization and drives epithelial morphology only in androgen receptor negative prostate cancer. RNA-seq profiling of total mRNA in WPMY-1, LNCaP, and PC-3 wild-type cells. The goal of this experiment is to evaluate alternative splicing of SLK in each cell line. Additionally, PC-3 cells transfected with 0.75µg c-Myc-CfaN or c-Myc-V5-6xHis plasmids are compared against PC-3 wild-type mRNA profiles to validate that c-Myc target gene transcription is increased after transient transfection of both constructs.