Abstract Introduction: The mechanisms linking Epstein-Barr virus (EBV) infection to mutagenesis in nasopharyngeal carcinoma (NPC) remain poorly understood. Methods: By integrating whole-genome sequencing of 216 NPC tumors with multi-omics profiling, including chromatin isolation by RNA purification (ChIRP)-seq for lncBARTs binding sites, CUT0.0001). Crucially, the viral lncBART does not increase mutation rates but fundamentally reshapes their distribution, randomizing mutations into a stochastic, Poisson-distributed pattern within KDM5B-bound domains (p=0.3665), which otherwise exhibit clustered, non-random mutagenesis (p0.001). Furthermore, the lncBART binding sites enriches specific mutation signatures, namely GT transversions (2.1-fold increase, p=0.005) and GA transitions (1.3-fold increase, p=0.05), indicative of oxidative damage and replication stress, without altering the overall mutation density. We developed a computational model that predicts mutation patterns based on CTCF, KDM5B, and lncBART binding together with enhancer status and chromatin accessibility, demonstrating that these factors partially define the landscape of genomic instability. Incorporation of the data from ChIRP-seq and Capture RNA-Protein interactions (CARPID) following mass spectrometry analysis revealed that lncBARTs may act as a central scaffold that directly co-recruits key members of NuRD complex to create chromatin states against large processive mutagens and blockade of the base excision repair (BER) machinery. Conclusions: Our work establishes a novel paradigm in which a virus co-opts and modulates host epigenetic machinery to create a context-dependent mutagenic environment, providing a new framework for understanding virus-driven cancer evolution. Acknowledgement: This work was supported by General Research Fund (17101122) and Theme-based Research Scheme (T12-703/22-R; T123-70323-N) from Research Grant Council and Health@InnoHK from Innovation and Technology Commission in the government of Hong Kong (SAR), P. R. China Citation Format: Wei Dai, Lai Shun Dittman Chung, Jiayan Liu, Kiu-Wai Cheng, Kazi Anisha Islam, Zhonghua Liu, Honglin Chen. Stochastic mutagenesis at lncBART-KDM5B-bound genomic loci in Epstein-Barr virus-associated nasopharyngeal carcinoma abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 226.
Dai et al. (2026) studied this question.