HeLa S3 single-cell RNA-seq. Homo sapiens

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 pipeline to prepare single cell RNA at 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 cell gene expression, alternative splicing and gene 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. Not only provide a transcriptome characterization of HeLa S3 cells at the single cell level, but are a demonstration of the power of single cell RNA-seq analysis of virally infected cells and cancers.