SETDB1-mediated repression of RhoB promotes EMT and metastatic progression in prostate cancer [CUT&Run]

Metastatic castration-resistant prostate cancer (CRPC) remains a clinical challenge, and epithelial–mesenchymal transition (EMT) contributes to metastatic progression and reduced response to therapy. However, the upstream epigenetic mechanisms that sustain EMT programs in advanced prostate cancer (PCa) are not fully defined. We identify the histone H3 lysine 9 (H3K9) methyltransferase SET domain bifurcated 1 (SETDB1) as a key regulator of EMT and metastasis through direct repression of the small GTPase RhoB. SETDB1 is genomically amplified and transcriptionally upregulated in metastatic CRPC, and SETDB1 depletion reduces cell migration, invasion, and metastatic dissemination. Integrated chromatin profiling and transcriptomic analyses demonstrate that SETDB1 occupies the RhoB promoter and mediates its transcriptional silencing through H3K9 methylation. Restoration of RhoB reverses EMT gene expression and suppresses invasive behavior, whereas RhoB knockdown rescues the effects of SETDB1 depletion, establishing RhoB as a critical downstream effector of SETDB1 function. Androgen signaling inhibitor-resistant PCa models exhibit RhoB loss and EMT activation, linking this axis to therapy-resistant phenotypes. Finally, antisense oligonucleotide-mediated SETDB1 silencing restores RhoB expression and suppresses EMT and invasion in CRPC cell models. Together, these findings define a SETDB1-RhoB epigenetic pathway that promotes EMT and metastatic progression in PCa and may be therapeutically targeted in advanced disease.