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

Wu, Liang, Zhang, Xiaolong, Zhao, Zhikun, Wang, Ling, Li, Bo, Li, Guibo, Dean, Michael, Yu, Qichao, Wang, Yanhui, Lin, Xinxin, Rao, Weijian, Mei, Zhanlong, Li, Yang, Jiang, Runze, Yang, Huan, Li, Fuqiang, Xie, Guoyun, Xu, Liqin, Wu, Kui, Zhang, Jie, Chen, Jianghao, Wang, Ting, Kristiansen, Karsten, Zhang, Xiuqing, Li, Yingrui, Yang, Huanming, Wang, Jian, Hou, Yong and Xu, Xun (2015) Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells. GigaScience, 4 51: 1-17. doi:10.1186/s13742-015-0091-4


Author Wu, Liang
Zhang, Xiaolong
Zhao, Zhikun
Wang, Ling
Li, Bo
Li, Guibo
Dean, Michael
Yu, Qichao
Wang, Yanhui
Lin, Xinxin
Rao, Weijian
Mei, Zhanlong
Li, Yang
Jiang, Runze
Yang, Huan
Li, Fuqiang
Xie, Guoyun
Xu, Liqin
Wu, Kui
Zhang, Jie
Chen, Jianghao
Wang, Ting
Kristiansen, Karsten
Zhang, Xiuqing
Li, Yingrui
Yang, Huanming
Wang, Jian
Hou, Yong
Xu, Xun
Title Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
Journal name GigaScience   Check publisher's open access policy
ISSN 2047-217X
Publication date 2015-11-05
Year available 2015
Sub-type Article (original research)
DOI 10.1186/s13742-015-0091-4
Open Access Status DOI
Volume 4
Issue 51
Start page 1
End page 17
Total pages 17
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2016
Language eng
Formatted 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.

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.
Keyword Single-cell transcriptome
HeLa
HPV
Virus
Tumor heterogeneity
Cancer
RNA splicing
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2016 Collection
Institute for Molecular Bioscience - Publications
 
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