The impact of HPV16 and HPV18 E6/E7 oncogenes on gene expression in non-tumorigenic keratinocytes transcriptome

This analysis aimed to identify differentially expressed genes in non-tumorigenic keratinocytes transduced with E6E7 oncogenes of HPV16 and 18. The working cell models were named HaCaT E6E7 HPV16, HaCaT E6E7 HPV18, and HaCaT pLVX empty lentiviral vector as controls. mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model.Methodology: The bioinformatics pipeline analysis was executed as described below: Rstudio v2023.06.1 and Galaxy open-source platforms were used to analyze the Illumina raw data. The Quality Check was performed through the FastQC tool v0.12.1; afterward, all the reads were processed by the Rsubread package v2.14.2; at that point, the reads were trimmed and aligned to the Human Genome Reference GRCh38.p14 v43. The resulting output was the BAM files, of which the number of reads was counted by the featureCounts tool v2.0.3; at the final step, the Differential Expression Analysis was settled by DESeq2 tool v2.11.40.8. The differential gene expression measurements were normalized by DESeq2 median of ratios method. All chemokine genes with an adjusted p-value more than 0.05 and fold change over 1 .5 or less than -1.5 were selected as differentially expressed genes. Some genes from the resulting outputs were validated through qPCR.Conclusions: Our study found 3296 differentially expressed genes in HaCaT E6E7 HPV16 and 1943 in HaCaT E6E7 HPV18. These results suggest that E6E7 oncogenes from HPV16 and 18 can broadly modify transcriptomic expression.