Abstract Epigenetic reprogramming is a major contributor to therapy resistance in prostate cancer (PCa). Indeed, chromatin accessibility profiling classified PCa into distinct subtypes, predictive of clinical outcome. Histone modifications influence nucleosome positioning, ultimately dictating chromatin compactness. The histone methyltransferase G9a, frequently upregulated in advanced PCa, catalyzes a repressive histone modification (di-methylation of histone H3 lysine 9) that signals for gene transcriptional repression. CM-272 is a reversible and highly selective inhibitor against G9a activity, and we have previously shown in cell line models of PCa that it depicted strong anti-tumoral effects. However, fundamental aspects of altered transcriptomic programs remain unexplored. Here, we validated, in vivo, the CM-272 effects in advanced PCa, and explored the molecular mechanisms underscoring G9a inhibition-mediated effects. Specifically, the PCa patient-derived xenograft model BM18 was used to assess the mode of action of CM-272 in vivo. Moreover, RNA sequencing of tumor tissues was performed to further explore the underlying gene expression signature. Finally, chromatin immunoprecipitation followed by qPCR was used to investigate the underlying functional consequence of epigenetic targeting. Our results showed that CM-272 significantly delayed BM18 tumor growth, specifically impairing tumor cell G9a activity and proliferation. Transcriptomic profiling revealed 119 significantly upregulated and 99 downregulated genes in response to G9a inhibition. Notably, by integrating our gene expression dataset with published chromatin accessibility data, an increase in the androgen receptor (AR) signature and a concomitant decrease in the neuroendocrine (NE) features were observed in CM-272-treated samples. Additionally, pathway enrichment and master regulator analysis pinpointed both the androgen receptor and TP53 networks as significantly upregulated in treated tissues. In line with the reduction of the NE score, the MYC/MYCN were the most significantly downregulated transcription factors. Moreover, under the androgen pathway, upregulation of AZGP1, STK39, and DPP4 was observed. At the promoter level, a significant reduction in H3K9me2 levels was detected in treated samples, allowing, in turn, an increase in AR binding. Additionally, upon treatment, higher p53 binding was detected at the promoter of the p53-repressed genes AURKA, CDC25B, and CD44, whose expression was downregulated. Overall, targeting G9a with CM-272 might hold promising therapeutic potential for the management of advanced disease by modulating relevant tumoral transcriptional programs associated with core vulnerabilities in PCa. Citation Format: Filipa Moreira-Silva, Mark Zimmerli, Panagiotis Chouvardas, Beat Roth, Carmen Jerónimo, Marianna Kruithof-de Julio. G9a blockade uncovers therapeutic vulnerabilities in advanced prostate cancer, leading to tumor growth delay abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr A045.
Moreira-Silva et al. (Tue,) studied this question.