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Identification of cellular targets for the human papillomavirus E6 and E7 oncogenes by RNA interference and transcriptome analyses

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Abstract

Specific types of human papillomaviruses (HPVs) cause cervical cancer, the second most common tumor in women 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. To identify downstream cellular target genes for the viral oncogenes, 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, which were either downregulated (360 genes) or upregulated (288 genes), upon inhibition of E6/E7 expression. A large fraction of these genes is involved in tumor-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 processing and splicing. Comparison with published microarray data revealed a substantial concordance between the genes repressed by RNAi-mediated E6/E7 silencing in HeLa cells and genes reported to be upregulated in HPV-positive cervical cancer biopsies.

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Acknowledgements

This work was supported by the Landesstiftung Baden-Württemberg (P-LS-RNS/18) and by a grant from the German National Genome Research Network NGFN-2 (01GR0418). We thank Sabrina Balaguer and Gabi Rottsahl for excellent technical assistance. Ruprecht Kuner and Markus Vogt contributed equally to the work.

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Authors and Affiliations

  1. Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany

    Ruprecht Kuner, Holger Sultmann, Andreas Buness, Mark Fellmann & Annemarie Poustka

  2. Molecular Therapy of Virus-Associated Cancers, German Cancer Research Center, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany

    Markus Vogt, Susanne Dymalla, Julia Bulkescher, Karin Butz & Felix Hoppe-Seyler

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  1. Ruprecht Kuner
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  2. Markus Vogt
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Correspondence to Felix Hoppe-Seyler.

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Supplementary Table 1

Microarray analysis (LIMMA) revealed 648 genes which were affected by siRNA-mediated inhibition of E6/E7 expression in HeLa cells. All genes fulfill the cut-off criteria of an FDR < 5% and a linear fold change ±1.5. Some genes were marked “yes” for their presence in previously published studies [6, 7, 11–13, 30,]. (PDF 428 kb)

Supplementary Table 2

Functional annotation of potential E6/E7 target genes which were identified in the present and in previously published studies [6, 7, 11–13, 30,]. Analysis was performed using the GO software GOstat. GO results were filtered with respect to the category “biological process,” as detailed in the text. Every GO category includes GO identifier, GO name, presence of the genes in the analyzed signatures (Groupcount) in comparison to the total amount of genes annotated in this GO category (Totalcount), and the statistical significance as p value. (PDF 214 kb)

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Kuner, R., Vogt, M., Sultmann, H. et al. Identification of cellular targets for the human papillomavirus E6 and E7 oncogenes by RNA interference and transcriptome analyses. J Mol Med 85, 1253–1262 (2007). https://doi.org/10.1007/s00109-007-0230-1

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  • DOI: https://doi.org/10.1007/s00109-007-0230-1

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