Epigenetic Regulation of Chromosomal Instability by EZH2 Methyltransferase

Abstract Chromosomal instability (CIN) and epigenetic reprogramming are central drivers of breast cancer progression, yet the mechanisms connecting them remain elusive. Here, we uncover a direct role for EZH2 histone methyltransferase in promoting CIN in triple-negative breast cancer. Across breast cancers, EZH2 expression correlates with copy-number alterations, and its catalytic activity is associated with increased CIN in metastasis-initiating cells. Pharmacologic EZH2 inhibition suppresses CIN, revealing an unexpected vulnerability. Integrated chromatin and transcriptome profiling identified tankyrase (TNKS), a PARP, as a direct transcriptional target of EZH2. Mechanistically, EZH2-mediated TNKS suppression disrupts centrosomal P4.1–associated protein (CPAP), driving centrosome overduplication, multipolar mitosis, and exacerbated CIN. In vivo, CIN suppression is a critical mechanism underlying the antimetastatic effects of EZH2 inhibition. These findings delineate a previously unrecognized epigenetic mechanism governing CIN and establish EZH2 inhibitors as the first therapeutic agents capable of directly suppressing CIN, underscoring the need for trials with metastasis-focused endpoints. Significance: We elucidate epigenetic regulation of CIN through EZH2–TNKS–CPAP-axis and show that CIN suppression is important for the efficacy of EZH2 inhibition on metastasis. These mechanistic insights are informative for developing CIN-suppressing therapies.