Abstract 2393: Gene regulatory networks of enzalutamide resistance in prostate cancer

Abstract Introduction: Castration-resistant prostate cancer (CPRC) is typically managed with antiandrogens, such as enzalutamide (ENZA), which can delay disease progression but are not curative, as resistance to these treatments eventually develops. This resistance is likely a consequence of significant remodeling of gene regulatory landscape of cells adapting to an androgen-deprived, stressful environment. Understanding the aberrancies in gene regulation underlying ENZA resistance is essential for improving the therapeutic strategies for CRPC. Methods: Using single-cell chromatin accessibility (ATAC) and transcriptome sequencing data sourced from the parental and ENZA-resistant LNCaP prostate cancer cells, we have applied knowledge graph-based neural networks to model transcription factor (TF) regulons and their associated molecular processes underlying the cell states from initial ENZA response towards ENZA resistance. Results: We have identified TF regulons associated with stress responses, cell cycle progression and androgen signaling, altered in ENZA-resistant cells. Specifically, the ENZA-resistant cells are characterized by the gain of SOX4 regulon, likely to contribute to the metabolic and proliferative reprogramming of the resistant cells. Cell cycle analysis revealed that while the cell proportion is largest in G1 phase in each treatment, the proportion of cells in S phase is increased in resistant samples, suggesting enhanced S-phase transition in resistant cells in contrast to G1 arrest caused by ENZA in treatment-responsive cells. We validate our findings in independent transcriptomic studies of ENZA-resistant VCaP and DuCaP cell lines indicating the robustness of the results. Moreover, utilizing spatial transcriptomic data from a longitudinal patient cohort, we pinpoint that the SOX4 regulon target genes are enriched in the epithelium of CRPC patients, compared to treatment-naïve and neoadjuvant-treated disease states. Conclusion: In summary, we determine gene regulatory alterations associated with ENZA resistance in preclinical models, providing valuable insights into uncovering the mechanisms of resistance to antiandrogens in CRPC. Citation Format: Sini Hakkola, Anni Perämäki, Karishma Sajnani, Antti Kiviaho, Alfonso Urbanucci, Matti Nykter, Mikael Marttinen. Gene regulatory networks of enzalutamide resistance in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2393.