Abstract 211: Epstein-Barr virus (EBV)‒human host chromatin interactions rearrange spatial DNA genome organisation and hijack KDM5B to distant metastasis proneness in EBV-associated nasopharyngeal carcinoma (NPC)
Authors: Lai Shun Dittman Chung, Zhaozheng Hou, Ying Wang, Kazi Anisha Islam, Songran Liu, Jiayan Liu, Larry Ka-Yue Chow, Cyrus Pakk-Ting Chak, Yingpei Zhang, Lanqi Gong, Karl Kui-Wai Cheng, Zhuoyou Yu, Ping Feng, Zilu Huang, Roger Kai-Cheong Ngan, Xinyuan Guan, Wai-Tong Ng, Zhonghua Liu, Anna Chi-Man Tsang, Dora Lai-Wan Kwong, Annie Wing-Mui Lee, Victor Ho-Fun Lee, Honglin Chen, Yunfei Xia, Wei Dai
Journal: Cancer Research (2025)

Abstract Introduction: Epstein-Barr virus (EBV), the first identified human DNA tumour virus, has been detected in nasopharyngeal carcinoma (NPC) over 40 years and over 90% of NPC is strongly associated with EBV infection in the endemic regions. However, the detailed roles of EBV in NPC pathogenesis and disease progression remain inconclusive. We hypothesise that EBV‒human chromatin interactions induce the spatial reorganisation of compartments and chromatin loops facilitating NPC tumour progression. Methods: Chromosome conformation capture sequencing (Hi-C), transposase-accessible chromatin with sequencing (ATAC-seq), and Cleavage Under Targets and Release Using Nuclease with sequencing (CUT&amp;RUN-seq) were performed in EBV-positive (EBV+) and EBV-negative NPC cell lines, EBV+ patient-derived xenografts (PDXs) and EBV+ clinical samples, followed by single-cell RNA sequencing (scRNA-seq), GeoMx Digital Spatial Profiler, and Spatial Molecular Imaging platform using the clinical samples. To evaluate the clinical impact of the high-order epigenomic changes associated with EBV, whole exome sequencing (WES) and bulk RNA sequencing (RNA-seq) were conducted for NPC biopsies in the multi-center multi-omics study. Results: EBV modulates 3D human genome by cross-species chromatin interactions. Two paired NPC cell lines demonstrated EBV infection causes 3D genome reorganisation. The PDXs and one clinical sample showed distinctive compartmentalisation compared to normal epithelial (NPE) cells. We discovered that the EBV episomes could tether to the human genome through EBV-interacting regions (EBVIRs), particularly related to inactive-to-active compartment transition. These regions have shown an increase in H3K27-acetylation, suggesting enhancer infestation by the EBV-host chromatin interactions, resulting in aberrant upregulation of KDM5B and its targets (EBVIR-enhancer-KDM5B signature). The spatial transcriptome data revealed that the cancer cells with higher expression of EBV latent genes had increased EBVIR-enahncer-KDM5B signature with metastatic potential. Similarly, the bulk RNA-seq data indicated this signature was highly associated with development of distant metastasis in two independent patient cohorts. The combination of KDM5B pathway activity with plasma EBV DNA level at baseline or after treatment suggests this can be a promising predictor of metastatic risk, achieving AUC = 0.77 and AUC = 0.82, respectively. Conclusion: EBV, as episomes, tethers to the human genome to reorganise 3D genome and epigenome. Through this mechanism, it regulates cancer-related genes and promotes distant metastasis in NPC. Our discovery of EBVIR-enhancer-KDM5B signature can be used as a promising metastatic predictor in the future. Citation Format: Lai Shun Dittman Chung, Zhaozheng Hou, Ying Wang, Kazi Anisha Islam, Songran Liu, Jiayan Liu, Larry Ka-Yue Chow, Cyrus Pakk-Ting Chak, Yingpei Zhang, Lanqi Gong, Karl Kui-Wai Cheng, Zhuoyou Yu, Ping Feng, Zilu Huang, Roger Kai-Cheong Ngan, Xinyuan Guan, Wai-Tong Ng, Zhonghua Liu, Anna Chi-Man Tsang, Dora Lai-Wan Kwong, Annie Wing-Mui Lee, Victor Ho-Fun Lee, Honglin Chen, Yunfei Xia, Wei Dai. Epstein-Barr virus (EBV)‒human host chromatin interactions rearrange spatial DNA genome organisation and hijack KDM5B to distant metastasis proneness in EBV-associated nasopharyngeal carcinoma (NPC) [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 211.