Identification of downstream targets of the human papillomavirus E6 and E7 oncoproteins by RNA interference

Specific types of human papillomaviruses (HPVs) cause cervical cancer, the second most common tumor in females worldwide. Both cellular transformation and the maintenance of the oncogenic phenotype of HPV-positive tumor cells are linked to the expression of the viral E6 and E7 oncogenes. In order to identify downstream cellular target genes for the viral oncoproteins, we silenced endogenous E6 and E7 expression in HPV-positive HeLa cells by RNA interference (RNAi). Subsequently, we assessed changes of the cellular transcriptome by genome-wide microarray analysis. We identified, 648 genes wich were either downregulated (360 genes) or upregulated (288 genes) upon inhibition of E6/E7 expression. A large fraction of these genes is involved in tumour-relevant processes, such as apoptosis control, cell cycle regulation, or spindle formation. Others may represent novel cellular targets for the HPV oncogenes, such as a large group of C-MYC-associated genes involved in RNA splicing. Keywords: siRNA mediated knockdown Hybridizations were performed on RZPD Unigene 3.1 cDNA microarrays (37.5K). Gene expression was analyzed by performing 6 microarray hybridizations, using three cell culture replicates treated with siRNA 18E7-3.5 or control siRNA siControl. Each replicate of the 18E7-3.5 experiments was hybridized against a replicate of the siControl experiment, including a technical dye swap.