BET BD2 inhibition facilitates SPOP-mediated degradation of chromatin-associated BRD4/BRD4-NUT, a therapeutic vulnerability in NUT carcinoma

Abstract

BET bromodomain inhibitors block binding of BET family bromodomains 1 and 2 (BD1, BD2) to chromatin and have demonstrated clinical activity in NUT carcinoma (NC), a BRD-NUT fusion-driven cancer, but toxicity from BD1 inhibition has limited their effectiveness. We investigated whether selective inhibition of BRD4 bromodomain 2 (BD2) could retain antitumor activity while reducing toxicity. NC cells were uniquely sensitive to the novel BRD4-BD2 inhibitor DC-9476 and other BD2-selective inhibitors, which induced differentiation and growth arrest. A CRISPR knockout screen identified the BRD4-targeting E3 ligase SPOP as the top resistance hit. BD2 inhibition, but not BD1-selective or pan-BET inhibition, triggered SPOP-dependent proteasomal degradation of BRD4 and BRD4-NUT; SPOP loss prevented degradation and largely rescued BD2 inhibitor-induced differentiation and growth arrest. Unexpectedly, BRD4 and BRD4-NUT remained chromatin-associated during BD2 inhibition, whereas BD1 or pan-BET inhibition displaced them. Together with evidence that ectopic BRD4-NUT expression sensitizes BRD4 to degradation, these findings support a model in which BRD4-NUT megadomains create a high-density, degradation-competent SPOP substrate pool of BRD4 and BRD4-NUT upon BD2 inhibition, whereas pan-BET inhibition disperses this substrate and limits efficient degradation. In preclinical NC models, BD2-selective inhibition achieved greater tumor growth inhibition and survival benefit than pan-BET inhibition, revealing a therapeutic vulnerability.