Table_1_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（HPV）的整合与子宫颈癌的发生密切相关。然而，关于HPV完整整合至宿主基因组的状态，目前所知甚少。方法：在本研究中，对三种HPV阳性细胞系HeLa、SiHa和CaSki进行了NANOPORE长读长测序，以检测HPV整合。利用自主研发的软件（HPV-TSD）对病毒整合模式进行分析，为三种HPV细胞系揭示了多种完整的整合模式。结果：我们发现HPV18和HPV16的整合模式存在显著差异。此外，尽管它们均属于HPV16整合，但病毒的整合特征存在显著差异。CaSki细胞中的HPV整合相对复杂。HeLa细胞中HPV18整合状态为主，而SiHa和CaSki细胞中整合的HPV16百分比显著较低。此外，HeLa细胞中的病毒序列不完整，且处于整合状态。我们还发现了大量HPV16和HPV18整合中的串联重复序列。本研究不仅阐明了高通量长读长测序在HPV整合研究中的可行性，而且探索了多种HPV整合模型，并证实病毒整合是细胞系中HPV的重要形式。结论：阐明HPV整合模式将为开发HPV整合检测算法提供关键指导，并有助于病毒整合在临床实践和药物研发中的应用。