Abstract 2668: Spatial-temporal diversity of extrachromosomal DNA shapes urothelial carcinoma evolution and tumor-immune microenvironment
Authors: Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Jens Luebeck, Huiying Tao, Yanfen Zhu, Xiaolong Sui, Yue Li, Shiqi Jiang, Qingqing Gao, Elias Rodriguez Fos, Gino Prasad, Yuanmei Wang, Run Zhou, Zhe Xu, Xiaoguang Pan, Linlin Chen, Xiang Xi, Huajing Teng, Chaoyang Sun, Tianyu Qin, Wei Dong, Yongwei Li, Xun Lan, Xuesong Li, Lin Lin, Lars Bolund, Huanming Yang, Roel G. Verhaak, Bishoy M. Faltas, Jacob B. Hansen, Sihan Wu, Paul S. Mischel, Anton G. Henssen, Vineet Bafna, Birgitte Regenberg, Yonglun Luo, Chunhua Lin, Peng Han
Journal: Cancer Research (2025)

Abstract Extrachromosomal DNA (ecDNA) presents a promising target for cancer therapy; however, its spatial-temporal diversity and influence on tumor evolution and the immune microenvironment remain largely unclear. Here, we apply computational methods to detect and reconstruct ecDNA from whole-genome sequencing data from 595 patients prospectively recruited into the Chinese Urothelial Carcinoma Genome Atlas (CUGA) study. We demonstrate that ecDNA contributes to clonal evolution through structural rearrangements and copy number variation during malignant transformation and recurrence of urothelial carcinoma (UC). This supports a model wherein tumors evolve via the selective expansion of ecDNA-bearing cells. Through multi-regional sampling of tumors, we demonstrate ubiquitous ecDNA presence across clones in multi-focal cancers, directly linking ecDNA to the evolution of multifocality. Notably, we observe highly variable levels of ecDNA across multiple foci within the same tumor, and ecDNA contributes to increased intratumoral heterogeneity and serves as a substrate for natural selection and evolution. EcDNA is present in 36% of UC tumors and correlates with an unstable cancer genome, an immunosuppressive phenotype, and significantly reduced 5-year survival. Single-cell RNA sequencing analyses reveal that ecDNA+ malignant cells exhibit diminished expression of major histocompatibility complex class I molecules, enabling them to evade T-cell mediated immune responses. Finally, we show that sequencing of urinary sediment-derived DNA has excellent specificity in detecting ecDNA, underscoring its diagnostic potential. This study delineates the evolutionary trajectory of ecDNA during tumor progression and provides further insights into immune evasion mechanisms associated with ecDNA. Citation Format: Wei Lv, Yuchen Zeng, Conghui Li, Yuan Liang, Jens Luebeck, Huiying Tao, Yanfen Zhu, Xiaolong Sui, Yue Li, Shiqi Jiang, Qingqing Gao, Elias Rodriguez Fos, Gino Prasad, Yuanmei Wang, Run Zhou, Zhe Xu, Xiaoguang Pan, Linlin Chen, Xiang Xi, Huajing Teng, Chaoyang Sun, Tianyu Qin, Wei Dong, Yongwei Li, Xun Lan, Xuesong Li, Lin Lin, Lars Bolund, Huanming Yang, Roel G. Verhaak, Bishoy M. Faltas, Jacob B. Hansen, Sihan Wu, Paul S. Mischel, Anton G. Henssen, Vineet Bafna, Birgitte Regenberg, Yonglun Luo, Chunhua Lin, Peng Han. Spatial-temporal diversity of extrachromosomal DNA shapes urothelial carcinoma evolution and tumor-immune microenvironment [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 2668.