title: Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells.
abstract: 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Liang
authors.initials: L
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China.
authors.forename: Xiaolong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China ; School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China.
authors.forename: Zhikun
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032 China.
authors.forename: Ling
authors.initials: L
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, Copenhagen, 1599 Denmark.
authors.forename: Guibo
authors.initials: G
authors.lastname: Li
authors.affiliation: Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick, MD 21702 USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Dean
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Yu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: Lin
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Weijian
authors.initials: W
authors.lastname: Rao
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Zhanlong
authors.initials: Z
authors.lastname: Mei
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Runze
authors.initials: R
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Huan
authors.initials: H
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Fuqiang
authors.initials: F
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Guoyun
authors.initials: G
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Liqin
authors.initials: L
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Kui
authors.initials: K
authors.lastname: Wu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032 China.
authors.forename: Jianghao
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032 China.
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, 1599 Denmark.
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.affiliation: The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, 310058 China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, 310058 China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, Copenhagen, 1599 Denmark.
authors.forename: Yong
authors.initials: Y
authors.lastname: Hou
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083 China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
mesh_terms: D052685:Alphapapillomavirus / Q000235:genetics / Q000302:isolation & purification*; D018740:Genetic Heterogeneity; D006367:HeLa Cells; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000821:virology*; D012326:RNA Splicing; D017423:Sequence Analysis, RNA
keywords: Cancer; HPV; HeLa; RNA splicing; Single-cell transcriptome; Tumor heterogeneity; Virus