Genome-wide profiling of BK polyomavirus integration in bladder cancer of kidney transplant recipients reveals mechanisms of the integration at the nucleotide level

Authors：Jin, Yu; Zhou, Yi; Deng, Wenfeng; Wang, Yuchen; Lee, Richard J.; Liu, Yanna; Elias, Nahel; Hu, Yangcheng; Luo, Min-Hua; Liu, Rumin; Guan, Bowen; Geng, Jian; Xu, Jian; Ma, Junfeng; Zhou, Jiapeng; Liu, Na; Blute, Michael L.; Colvin, Robert B.; Wu, Chin-Lee^*; Miao, Yun^*

Source：Oncogene, 2021, 40(1): 46-54.

DOI：10.1038/s41388-020-01502-w

• INFECTION
• VIRUS
• MICROHOMOLOGY
• REPLICATION
• BLOOD

Chronic BK polyomavirus (BKPyV) infection is recognized as a potential oncogenic factor of urothelial carcinoma (UC) in renal transplant recipients. Recent studies have reported a positive correlation among BKPyV integration, persistent overexpression of viral large T antigen (TAg), and malignancy, yet little is known about the specific integration mechanisms and the impacts of viral integration. Here, we performed whole-genome sequencing (WGS) and viral capture-based sequencing on high-grade immunohistochemically TAg-positive UCs in two renal transplant recipients. A total of 181 integration sites, including the three found by WGS, were identified by viral capture-based sequencing, indicating its enhanced sensitivity and ability in identifying low-read integration sites in subpopulations of the tumor cells. The microhomologies between human and BKPyV genomes were significantly enriched in the flanking regions of 84.5% the integration sites, with a median length of 7 bp. Notably, 75 human genes formed fusion sequences due to viral insertional integration. Among them, the expression of 15 genes were statistically associated with UC based on GEO2R expression analysis. Our results indicated a multisite and multifragment linear integration pattern and a potential microhomology or nonhomologous end joining integration mechanism at the single-nucleotide level. We put forward a potential selection mechanism driven by immunity and centered on viral integration in the carcinogenesis of BKPyV.

• Institution
  y; 南方医科大学; 中国科学院