Structural patterns and transcriptional effects of integrated Epstein-Barr virus revealed by long-read sequencing and RNA-sequencing in Nasopharyngeal Carcinoma

Integration of Epstein-Barr virus (EBV) DNA into the human genome is a critical event in nasopharyngeal carcinogenesis. Here, we comprehensively characterize large-scale virus-human integration events in four EBV-positive nasopharyngeal carcinoma (NPC) cell lines and tumors using Nanopore long-read sequencing technology. We identified four distinct integration types, with Type I being particularly notable, characterized by continuous long reads covering nearly the entire EBV genome. Our findings reveal the involvement of multiple integration events in inducing inter-chromosomal translocations, leading to significant genomic disruption through chromosomal rearrangements. Additionally, we explore the relationship between EBV integration sites and structural variations, further supporting the role of EBV integration in driving genomic instability. By integrating RNA-seq data, we demonstrate the potential for EBV integration to disrupt gene expression, highlighting several integration sites within cancer-associated genes such as CD96, ARHGAP27, ASH1L, KDM3B, ZMYM2, and PIK3C2A. Notably, EBV-human fusion events were prevalent in EBV-associated NPCs, including fusion transcripts such as LRRC8C-RPMS1 and LINC00486-RPMS1, supporting the oncogenic potential of EBV integration. Taken together, this study uncovers EBV integration patterns in nasopharyngeal carcinogenesis using long-read sequencing technology.

EB病毒（Epstein-Barr virus, EBV）DNA整合进入人类基因组，是鼻咽癌发生过程中的关键事件。本研究借助纳米孔长读长测序技术，对4株EB病毒阳性鼻咽癌细胞系及肿瘤样本中的大规模病毒-人类整合事件进行了全面表征。我们鉴定出4种不同的整合类型，其中I型尤为显著，其特征为存在覆盖几乎完整EB病毒基因组的连续长读长序列。研究结果揭示，多重整合事件可诱导染色体间易位，通过染色体重排造成严重的基因组破坏。此外，本研究探讨了EBV整合位点与结构变异之间的关联，进一步支持EBV整合在驱动基因组不稳定性中的作用。通过整合RNA测序（RNA-seq）数据，我们证实EBV整合具有干扰基因表达的潜能，并在CD96、ARHGAP27、ASH1L、KDM3B、ZMYM2及PIK3C2A等癌症相关基因中发现了多个整合位点。值得注意的是，EB病毒-人类融合事件在EB病毒相关鼻咽癌中普遍存在，包括LRRC8C-RPMS1、LINC00486-RPMS1等融合转录本，这为EBV整合的致瘤潜能提供了佐证。综上，本研究借助长读长测序技术，阐明了鼻咽癌发生过程中的EBV整合模式。