Abstract 4716: Characterization of 3D genome in nasopharyngeal carcinoma (NPC)

Abstract Background: Epstein-Barr virus (EBV) can be detected in more than 90% of NPC patients in Hong Kong. It has been shown that EBV infection could hijack the human epigenome in B cell lymphoma and EBV+ gastric cancer, however, the role of EBV in epigenetic dysregulation remains largely unknown in NPC. Recently, our epigenomic landscape study demonstrated EBV was associated with changes of chromatin accessibility in NPC, which were largely involved in the binding sites of CTCF, a master regulator of chromosome organization. Therefore, we aim to further characterize the 3D chromatin structure in NPC. Methods: We used the Hi-C (Omni-C Seq) to profile the chromatin interactions in the EBV-positive (EBV+) NPC, EBV-negative (EBV-) NPC, and normal immortalized epithelial (NPE) cell lines. The Omni-C Seq data were integrated with the ATAC-Seq, RNA-Seq, and CUT&RUN-Seq data. The histone markers including H3K4me3, H3K27ac, and H3K27me3, were applied to classify the active and inactive status of the chromatins. The chromatin looping and topologically associated domains (TADs) were defined by the CTCF binding sites. Results: We observed a much larger compartmentalization size in EBV+ NPC with a consistent increase of active to inactive (A to B) compartments, compared to NPE and EBV- NPC. Pathway enrichment analysis showed that these changes potentially influenced immune response, cell differentiation and development, metabolism, ERBB pathway, and calcium signaling transduction. In addition to the changes in compartmentalization, we observed a reduction of CTCF binding signals at the TADs boundaries and the loss of chromatin looping at the 10kb resolution. Consistently, the aggregate peak analysis has shown a significant reduction of the CTCF anchor, indicating the abandonment of architectural CTCF in EBV+ NPC. More importantly, we found EBV tethering to the host chromatins. In the EBV genome, the tethering sites were often located at the regions associated with OriP, EBNA1, and BARTs. In the human genome, the tethering sites were dramatically enriched in the inactive to active (B to A) compartments, which were highly associated with the enhancer regions with H3K27ac. We identified a specific target gene CD74 with EBV tethering at the nearby super-enhancer region. Our results suggest the upregulation of CD74 could be controlled via remodulating the host 3D genome in EBV+ NPC. The spatial transcriptome analysis indicated that the expression of CD74 was highly correlated with HLA-DRA. The spatial analysis further showed that the NPC patients with upregulated HLA-DRA often had de novo distant metastasis after treatment (p=0.007). Conclusions: The EBV tethering to the host genome has a significant impact on host 3D genome organization, affecting chromatin accessibility and gene regulation, providing survival advantages of cancer cell growth and potentially contributing to immune suppression and metastasis. Citation Format: Dittman Lai-Shun Chung, Larry Ka-Yue Chow, Wei Dai. Characterization of 3D genome in nasopharyngeal carcinoma (NPC). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4716.