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Integrated virus-host methylome analysis in head and neck squamous cell carcinoma

Wilson, GA; Lechner, M; Köferle, A; Carén, H; Butcher, LM; Feber, A; Fenton, T; ... Beck, S; + view all (2013) Integrated virus-host methylome analysis in head and neck squamous cell carcinoma. Epigenetics , 8 (9) pp. 953-961. 10.4161/epi.25614. Green open access

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Abstract

One in six cancers worldwide is caused by infection and human papillomavirus (HPV) is one of the main culprits. To better understand the dynamics of HPV integration and its effect on both the viral and host methylomes, we conducted whole-genome DNA methylation analysis using MeDIP-seq of HPV+ and HPV- head and neck squamous cell carcinoma (HNSCC). We determined the viral subtype to be HPV-16 in all cases and show that HPV-16 integrates into the host genome at multiple random sites and that this process predominantly involves the transcriptional repressor gene (E2) in the viral genome. Comparative analysis identified 453 (FDR ≤ 0.01) differentially methylated regions (DMRs) in the HPV+ host methylome. Bioinformatics characterization of these DMRs confirmed the previously reported cadherin genes to be affected but also revealed new targets for HPV-mediated methylation changes at regions not covered by array-based platforms, including the recently identified super-enhancers.

Type: Article
Title: Integrated virus-host methylome analysis in head and neck squamous cell carcinoma
Open access status: An open access version is available from UCL Discovery
DOI: 10.4161/epi.25614
Publisher version: http://dx.doi.org/10.4161/epi.25614
Language: English
Additional information: © 2013 Landes Bioscience. under the Creative Commons Attribution-NonCommercial 3.0 Unported License (http://creativecommons.org/licenses/by-nc/3.0).
Keywords: DNA methylation, Epigenome, Head and neck squamous cell cancer (HNSCC), Human papillomavirus (HPV), Methylome
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci
URI: https://discovery.ucl.ac.uk/id/eprint/1401784
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