Table_2_Multiple HPV integration mode in the cell lines based on long-reads sequencing.XLS

BackgroundThe integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome.
MethodsIn this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines.
ResultsWe found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines.
ConclusionElucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.

背景 人乳头瘤病毒（human papillomavirus, HPV）的整合与宫颈癌的发生密切相关，但目前对HPV整合进入宿主基因组的完整状态仍知之甚少。
方法 本研究选取3株HPV阳性细胞系HeLa、SiHa及CaSki，采用纳米孔长读长测序（Nanopore long-read sequencing）技术检测HPV整合情况；通过自主开发的软件（HPV-TSD）分析病毒整合模式，最终获得了这3株HPV细胞系的多种完整整合模式。
结果 本研究发现HPV18与HPV16的整合模式存在显著差异；即便同为HPV16整合，不同病毒的整合特征也存在显著区别。CaSki细胞中的HPV整合情况相对复杂，HeLa细胞中HPV18整合状态占主导地位，而SiHa与CaSki细胞中整合型HPV16的占比显著更低。此外，HeLa细胞中的病毒序列并不完整，且以整合状态存在；本研究还在HPV16与HPV18的整合区域中鉴定出大量串联重复序列。本研究不仅明确了高通量长读长测序应用于HPV整合研究的可行性，还探索了多种HPV整合模式，并证实病毒整合是细胞系中HPV存在的重要形式。
结论 阐明HPV整合模式将为HPV整合检测算法的开发，以及病毒整合技术在临床实践与药物研发中的应用提供重要指导。