Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

GigaScience

Xun Xu⁸  Yong Hou³  Jian Wang⁶  Huanming Yang⁶  Yingrui Li²  Xiuqing Zhang⁷  Karsten Kristiansen³  Ting Wang¹  Jianghao Chen¹  Jie Zhang⁸  Kui Wu⁸  Liqin Xu⁸  Guoyun Xie⁸  Fuqiang Li⁸  Huan Yang⁸  Runze Jiang⁸  Yang Li⁸  Zhanlong Mei⁸  Weijian Rao⁸  Xinxin Lin⁸  Yanhui Wang⁸  Qichao Yu^1,10  Michael Dean⁵  Guibo Li³  Bo Li⁸  Ling Wang¹  Zhikun Zhao⁹  Xiaolong Zhang⁴  Liang Wu⁸ 

[1] Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an 710032, China;Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, QLD, Australia;Department of Biology, University of Copenhagen, Copenhagen 1599, Denmark;College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick 21702, MD, USA;James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China;The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen 518083, China;BGI-Shenzhen, Shenzhen 518083, China;School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China;BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China

关键词: RNA splicing;    Cancer;    Tumor heterogeneity;    Virus;    HPV;    HeLa;    Single-cell transcriptome;   

Others  :  1231999
DOI  :  10.1186/s13742-015-0091-4

 received in 2015-07-20, accepted in 2015-10-21,  发布年份 2015

【 摘 要 】

Background

Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cancers, but virally induced tumors have not been studied. HeLa is a well characterized HPV+ cervical cancer cell line.

Result

We developed a new high throughput platform to prepare single-cell RNA on a nanoliter scale based on a customized microwell chip. Using this method, we successfully amplified full-length transcripts of 669 single HeLa S3 cells and 40 of them were randomly selected to perform single-cell RNA sequencing. Based on these data, we obtained a comprehensive understanding of the heterogeneity of HeLa S3 cells in gene expression, alternative splicing and fusions. Furthermore, we identified a high diversity of HPV-18 expression and splicing at the single-cell level. By co-expression analysis we identified 283 E6, E7 co-regulated genes, including CDC25, PCNA, PLK4, BUB1B and IRF1 known to interact with HPV viral proteins.

Conclusion

Our results reveal the heterogeneity of a virus-infected cell line. It not only provides a transcriptome characterization of HeLa S3 cells at the single cell level, but is a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.

【 授权许可】

   
2015 Wu et al.

【 图 表 】

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