Long non-coding RNA FAM83H-AS1 is regulated by human papillomavirus 16 E6 independently of p53 in cervical cancer cells

Global long non-coding RNA (lncRNA) expression profile in primary human keratinocytes post-expression of high-risk HPV-16 E6 oncoprotein Purpose: The goal of this study is to utlize high-throughput RNA sequencing (RNA-seq) to identify differentially expressed host lncRNAs with the presence of the high-risk HPV-16 E6 oncoprotein in primary human foreskin keratinocytes. Methods: Primary human foreskin keratinocytes (HEKa) stably expressing HPV-16 E6 compared to GFP control were analyzed, in triplicates, by RNA-seq (Illumina). qRT-PCR validation was performed using SYBR Green assays. Results: 151 up- and 100 down-regulated host lncRNAs were altered greater than 1.5-fold change in HEKa expressing HPV-16 E6 compared to GFP control cells. Altered expression of 16 genes (8 up- and 8 down-regulated) were confirmed by qRT-PCR, demonstrating the high-degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first global screening of host lncRNAs altered specifically by HPV-16 E6 oncoprotein expression. Host lncRNA profiles of HEKa stably expressing HPV-16 E6 compared to control cells were generated, in triplicate, and analyzed by RNA-seq (Illumina).