Department of Clinical Oncology, University of Hong Kong, Hong Kong (SAR), PR China.
Department of Clinical Pathology, Tuen Mun Hospital, Hong Kong (SAR), PR China.
EBioMedicine. 2022 Dec;86:104357. doi: 10.1016/j.ebiom.2022.104357. Epub 2022 Nov 11.
Epstein-Barr virus (EBV) latent infection is associated with genome-wide epigenomic changes in several malignancies, but its role in epigenetic dysregulation remains unclear in nasopharyngeal carcinoma (NPC).
To investigate EBV-associated epigenetic dysregulation, we performed a multi-omics study by integrating whole-genome bisulfite sequencing (WGBS), assay for transposase-accessible chromatin using sequencing (ATAC-Seq), whole-exome sequencing (WES), and single-cell RNA sequencing (scRNA-Seq) data.
In addition to the known global DNA hypermethylated subtype, we discovered a novel subtype with global hypomethylation in EBV + NPC. The consistent EBV-specific differentially methylated regions (EBV-DMRs) in the human genome were identified from both subtypes and associated with loss of CTCF binding (P < 2.2e-16). Importantly, CTCF is a master chromatin regulator and CTCF protein was reduced in 45% of NPC cases, especially in those with advanced NPC (Stage IV vs. others: 62% vs. 38%, P = 0.034). This result links EBV with chromatin changes. The ATAC-Seq data suggest regulatory epigenome reprogramming through chromatin accessibility changes in EBV + NPC with altered CTCF binding and the switch of transcription factor binding from differentiation-associated KLF/SP family to the innate and adaptive immunity-related NF-ĸB and IRF families. Detailed chromatin accessibility analysis identified a potential EBV target gene CD74, which mediated EBV-specific cell-cell communications in the tumor microenvironment (TME) and was strongly correlated with T cell exhaustion (r = 0.55).
Our study reveals the unexpected epigenetic heterogeneity, providing insights into NPC pathogenesis and highlighting the involvement of host factors in virus-associated epigenetic changes. EBV infection is associated with epigenome reprogramming and may promote immune evasion.
This study was funded by the Hong Kong Research Grants Council grant (AoE/M-06/08) to MLL, General Research Fund (17103218 and 17102619) and seed funding for basic research (201611159158) to WD, and General Research Fund (17119618) to HC.
爱泼斯坦-巴尔病毒（EBV）潜伏感染与多种恶性肿瘤的全基因组表观基因组变化有关，但在鼻咽癌（NPC）中，其在表观遗传失调中的作用仍不清楚。
为了研究 EBV 相关的表观遗传失调，我们通过整合全基因组亚硫酸氢盐测序（WGBS）、测序的转座酶可及染色质分析（ATAC-Seq）、全外显子测序（WES）和单细胞 RNA 测序（scRNA-Seq）数据进行了多组学研究。
除了已知的全基因组 DNA 高甲基化亚型外，我们还在 EBV+NPC 中发现了一种新的全基因组低甲基化亚型。从两个亚型中都鉴定到了 EBV 特异性差异甲基化区域（EBV-DMRs），这些区域与 CTCF 结合的丧失有关（P<2.2e-16）。重要的是，CTCF 是一个主要的染色质调节因子，在 45%的 NPC 病例中发现 CTCF 蛋白减少，尤其是在晚期 NPC 病例中（IV 期与其他期：62%与 38%，P=0.034）。这一结果将 EBV 与染色质变化联系起来。ATAC-Seq 数据表明，通过改变 CTCF 结合和转录因子结合从分化相关的 KLF/SP 家族向先天和适应性免疫相关的 NF-ĸB 和 IRF 家族的转换，调节了 EBV+NPC 的调控表观基因组重编程。详细的染色质可及性分析鉴定出一个潜在的 EBV 靶基因 CD74，它在肿瘤微环境（TME）中介导 EBV 特异性细胞间通讯，并与 T 细胞耗竭呈强相关性（r=0.55）。
我们的研究揭示了意想不到的表观遗传异质性，为 NPC 的发病机制提供了深入的了解，并强调了宿主因素在病毒相关表观遗传变化中的参与。EBV 感染与表观基因组重编程有关，并可能促进免疫逃逸。
本研究由香港研究资助局拨款（AoE/M-06/08）给 MLL、研究基金（17103218 和 17102619）和基础研究种子基金（201611159158）给 WD，以及研究基金（17119618）给 HC。
