Abstract Background: Castration-resistant prostate cancer (CRPC) remains a lethal disease largely due to its ability to rapidly adapt to therapeutic pressure. Genome instability, including mutational processes and structural genome alterations, is increasingly recognized as a key driver of tumor heterogeneity, drug resistance, and immune evasion. APOBEC family cytidine deaminases are prominent sources of cancer-associated mutagenesis, yet how APOBEC-driven genome instability intersects with extrachromosomal DNA (ecDNA) formation and immune regulation in CRPC remains poorly understood. Objective: This study aims to define how dysregulated mutagenesis promotes genome instability and ecDNA amplification in CRPC and to investigate how these processes collectively contribute to drug resistance and modulation of antitumor immune signaling. Methods: We integrated functional genomics, whole-genome and whole-exome sequencing, single-cell and spatial transcriptomics, and epigenomic profiling across CRPC cell lines, patient-derived organoids, and genetically engineered mouse models. Perturbation studies targeting regulators of APOBEC activity and genome maintenance were combined with ecDNA detection, chromatin profiling, and immune signaling analyses to assess the impact of mutagenesis on therapeutic response and tumor-immune interactions. Results: We identify dysregulated APOBEC activity as a major driver of mutational burden and intratumoral heterogeneity in therapy-resistant CRPC. Elevated APOBEC activity is associated with increased DNA damage, chromosomal rearrangements, and the emergence of ecDNA-mediated oncogene amplification. Single-cell analyses reveal that mutagenesis-driven genome instability promotes divergent tumor cell states with enhanced survival under androgen receptor-targeted therapy. Importantly, tumors with high mutational and ecDNA burden exhibit altered innate immune signaling, including perturbations in DNA sensing pathways, suggesting a mechanistic link between genome instability and immune modulation. Conclusion: Our findings establish mutagenesis as a unifying force that connects genome instability, ecDNA amplification, drug resistance, and immune regulation in CRPC. This work highlights how cancer cells exploit mutational processes not only to adapt to therapy but also to reshape immune signaling. Targeting the interplay between mutagenesis, ecDNA maintenance, and immune pathways represents a promising therapeutic strategy for overcoming resistance in advanced prostate cancer. Citation Format: Xiaoling Li. Mutagenesis-driven genome instability links ecDNA amplification to drug resistance and immune modulation in prostate cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts) ; 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86 (8Suppl): Abstract nr LB188.
Xiaoling Li (Fri,) studied this question.