Abstract 4116: A multi-omics study reveals an epigenomic subtype shapes a pro-metastatic niche in Epstein-Barr virus-associated nasopharyngeal carcinoma

Abstract Nasopharyngeal carcinoma (NPC) is a unique form of cancer that originates in the epithelial lining of the nasopharynx. It is often associated with Epstein-Barr virus (EBV) infection. NPC's etiology involves various factors, including genetic predispositions, environmental influences and particularly, epigenetic dysregulation. In an earlier study, it was discovered that there are two methylation subtypes with global hypermethylation (HyperNPC) and hypomethylation (HypoNPC) in NPC, representing 80% and 20% of patients, respectively. This study further investigates HypoNPC to characterize its biological features, association with EBV life cycles and to evaluate its clinical impact. Whole exome sequencing (WES), RNA-sequencing (RNAseq), and targeted bisulfite sequencing (BS) using the customized panel targeting the EBV genome and 23 selected human regions were performed for the tumor biopsies from 82 NPC patients. Patients were characterized as the HypoNPC subtype based on their methylation ratios across 13 selected regions using linear discriminant analysis (LDA). The WES data was utilized to evaluate the mutational profiles of the subtypes, while the RNAseq data was used to identify differentially expressed genes in both host and EBV. Chromosome instability (CIN) was quantified based on the extent of allelic imbalances in NPC tumors. The patients were stratified as metastatic (MET) NPC if they developed distant metastasis within 3 years post-treatment, and as non-metastatic (nonMET) NPC if they did not develop distant metastasis within the same time period. This multi-omics study revealed that HypoNPC patients are more likely to develop metastasis within 3 years post-treatment (OR=5.60, 95% CI=1.29-38.89) compared to HyperNPC patients. HypoNPC is enriched for loss-of-function mutations of KDM6A, which could lead to the hyperactivation of the mTORC1 signaling pathway. These patients also display elevated CIN, heightened DNA damage responses, replication stress and mitotic spindle assembly, alongside increased MYC activation. We found that pro-metastatic genes like SKP2 and PHF8 are upregulated, while anti-metastatic genes like PTPRD and ZNF154 are suppressed in these patients. Interestingly, the EBV genome in HypoNPC has a larger variation of DNA methylation levels, suggesting less stringent control of EBV gene transcription through DNA methylation. In addition, HypoNPC has a distinctive immunosuppressive tumor microenvironment, marked by a significant reduction in plasma B cells and suppressed complement function through macrophages. HypoNPC exhibits distinctive cancer cell features and the tumor microenvironment, which may form a pro-metastatic niche leading to early development of distant metastasis in these patients. This study highlights the needs for molecular subtyping in NPC to improve patient management and treatment. Citation Format: Kazi Anisha Islam, Larry Ka-Yue Chow, Kiu Wai Cheng, Dittman Lai-Shun Chung, Zhaozheng Hou, Yingpei Zhang, Anne Wing-Mui Lee, Wai Tong Ng, Roger Kai-Cheong Ngan, Dora Lai-Wan Kwong, Wei Dai. A multi-omics study reveals an epigenomic subtype shapes a pro-metastatic niche in Epstein-Barr virus-associated nasopharyngeal carcinoma [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 4116.