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Gigascience. 2015 Nov 5;4:51. doi: 10.1186/s13742-015-0091-4. eCollection 2015.

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

Author information

1
BGI-Shenzhen, Shenzhen, 518083 China.
2
BGI-Shenzhen, Shenzhen, 518083 China ; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China.
3
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.
4
Department of Vascular and Endocrine Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032 China.
5
BGI-Shenzhen, Shenzhen, 518083 China ; Department of Biology, University of Copenhagen, Copenhagen, 1599 Denmark.
6
Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick, MD 21702 USA.
7
BGI-Shenzhen, Shenzhen, 518083 China ; BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 China.
8
Department of Biology, University of Copenhagen, Copenhagen, 1599 Denmark.
9
The Guangdong Enterprise Key Laboratory of Human Disease Genomics, BGI-Shenzhen, Shenzhen, 518083 China.
10
BGI-Shenzhen, Shenzhen, 518083 China ; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072 Australia.
11
BGI-Shenzhen, Shenzhen, 518083 China ; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, 310058 China.

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.

KEYWORDS:

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

PMID:
26550473
PMCID:
PMC4635585
DOI:
10.1186/s13742-015-0091-4
[Indexed for MEDLINE]
Free PMC Article

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