PO.IM03.01 · 免疫学
EB病毒相关鼻咽癌中lncBART-KDM5B结合基因组位点处的随机诱变
Stochastic mutagenesis at lncBART-KDM5B-bound genomic loci in Epstein-Barr virus-associated nasopharyngeal carcinoma
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
引言：将EB病毒（Epstein-Barr virus, EBV）感染与鼻咽癌（NPC）诱变相联系的机制仍知之甚少。
方法：通过将216例NPC肿瘤的全基因组测序与多组学分析相整合——包括用于检测lncBART结合位点的RNA纯化染色质分离（ChIRP）-seq、用于检测KDM5B和CTCF结合位点及组蛋白标记H3K27ac的CUT&RUN、用于检测病毒-宿主染色质相互作用的4C-seq，以及用于检测染色质可及性的ATAC-seq——我们揭示了一个多层次的病毒驱动诱变模型。
结果：我们首先表明，细胞表观遗传调控因子CTCF和KDM5B独立地界定了突变负荷显著升高的基因组结构域（比匹配对照高2倍，P<0.0001）。关键的是，病毒lncBART并不增加突变率，而是从根本上重塑了突变分布，在KDM5B结合的结构域内将突变随机化为一种随机的、泊松分布模式（p=0.3665），而这些结构域在其他情况下表现为聚集性、非随机的诱变（p<0.001）。此外，lncBART结合位点富集特定的突变特征，即G>T颠换（增加2.1倍，p=0.005）和G>A转换（增加1.3倍，p=0.05），提示氧化损伤和复制应激，而不改变总体突变密度。我们建立了一个计算模型，基于CTCF、KDM5B和lncBART的结合以及增强子状态和染色质可及性来预测突变模式，表明这些因素部分界定了基因组不稳定性的格局。结合ChIRP-seq数据以及经质谱分析的捕获RNA-蛋白相互作用（CARPID）数据，揭示lncBART可能作为一个中心支架，直接共募集NuRD复合物的关键成员，从而形成针对大型持续性诱变剂并阻断碱基切除修复（BER）机制的染色质状态。
结论：我们的工作确立了一种新的范式，即病毒挪用并调控宿主表观遗传机制以创造一种依赖情境的诱变环境，为理解病毒驱动的癌症演化提供了新框架。
致谢：本工作得到中国香港（特别行政区）政府研究资助局的一般研究基金（17101122）和主题研究计划（T12-703/22-R；T123-70323-N），以及创新科技署的Health@InnoHK的支持。
查看英文原文 English 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, CUT&RUN for the binding sites of KDM5B and CTCF and histone mark H3K27ac, 4C-seq for virus-host chromatin interactions, and ATAC-seq for chromatin accessibility, we uncover a multi-layered model of virus-driven mutagenesis.
Results: We first show that cellular epigenetic regulators CTCF and KDM5B independently define genomic domains of significantly elevated mutation burden (2-fold more than matched controls, P<0.0001). 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 (p<0.001). Furthermore, the lncBART binding sites enriches specific mutation signatures, namely G>T transversions (2.1-fold increase, p=0.005) and G>A 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
利益披露 Disclosure
W. Dai, None..
J. Liu, None..
K. Cheng, None..
Z. Liu, None.