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This study analyzes the epigenetic landscape of HPV16, focusing on the L1 gene and untranslated region (UTR), using pyrosequencing, and evaluates HPV16 physical status in HPV16-positive HNSCC FFPE biopsies via E2/E6 ratio analysis. Methylation is detected across six L1 sites and seven UTR sites, with L1 CpG sites 7136 and 7145 associated with tumor histological grade (p \u003C 0.01). Viral physical status shows no correlation with methylation or tumor characteristics.",{"@graph":14,"@context":76},[15,34,55],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & 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Cancer Cases  \nIoannis Zygouras 1,†, Danai Leventakou 2,†, Abraham Pouliakis 2, Styliana Panagiotou 1, Dimitris Tsakogiannis 3, *, Georgios Konstantopoulos 1, Eirini Logotheti 1, Menelaos Samaras 2, Zaharoula Kyriakopoulou 4, Apostolos Beloukas 5,6, Ioannis S. Pateras 2, Alexandros Delides 7, Amanda Psyrri 8, Ioannis G. Panayiotides 2, Minas Yiangou 1 and Christine Kottaridi 1, *  \nCitation: Zygouras, I.; Leventakou, D.; Pouliakis, A.; Panagiotou, S.; Tsakogiannis, D.; Konstantopoulos, G.; Logotheti, E.; Samaras, M.;  \nKyriakopoulou, Z.; Beloukas, A.; et al. Human Papillomavirus 16 DNA Methylation Patterns and Investigation of Integration Status in Head and Neck Cancer Cases. Int. J. Mol. Sci. 2023, 24, 14593. [https://](https://)[ ](https://)[doi.org/10.3390/ijms241914593](doi.org/10.3390/ijms241914593)  \nAcademic Editor: Shinichi Fukushige  \nReceived: 31 August 2023  \nRevised: 26 September 2023  \nAccepted: 26 September 2023  \nPublished: 26 September 2023  \nCopyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) .  \n1 Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; [izygouras@bio.auth.gr](izygouras@bio.auth.gr) (I.Z.); [stylianap@bio.auth.gr](stylianap@bio.auth.gr) (S.P.); [konstanto@bio.auth.gr](konstanto@bio.auth.gr) (G.K.); [eirinilg@bio.auth.gr](eirinilg@bio.auth.gr) (E.L.); [yiangou@bio.auth.gr](yiangou@bio.auth.gr) (M.Y.)  \n2 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; [dleventakou@med.uoa.gr](dleventakou@med.uoa.gr) (D.L.); [apouliak@med.uoa.gr](apouliak@med.uoa.gr) (A.P.); [menelaos.g.samaras@gmail.com](menelaos.g.samaras@gmail.com) (M.S.); [ispasath2004@yahoo.com](ispasath2004@yahoo.com) (I.S.P.); [ioagpan@med.uoa.gr](ioagpan@med.uoa.gr) (I.G.P.)  \n3 Research Center, Hellenic Anticancer Institute, 10680 Athens, Greece  \n4 Department of Environment, School of Technology, University of Thessaly, Gaiopolis Campus,  \n41500 Larissa, Greece; [zahkyr@uth.gr](zahkyr@uth.gr)  \n5 Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece; [abeloukas@uniwa.gr](abeloukas@uniwa.gr)  \n6 National AIDS Reference Centre of Southern Greece, School of Public Health, University of West Attica, 11521 Athens, Greece  \n7 2nd Department of Otolaryngology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; [adelidis@med.uoa.gr](adelidis@med.uoa.gr)  \n8 2nd Department of Internal Medicine-Propaedeutic, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; [psyrri237@yahoo.com](psyrri237@yahoo.com)  \n* Correspondence: [dtsakogiannis@gmail.com](dtsakogiannis@gmail.com) (D.T.); [ckottaridi@bio.auth.gr](ckottaridi@bio.auth.gr) (C.K.)† These authors contributed equally to this work.  \nAbstract: Persistent high-risk human papillomavirus (HPV) infection is a pivotal factor in the progression of cervical cancer. In recent years, an increasing interest has emerged in comprehending the influence of HPV on head and neck squamous cell carcinoma (HNSCC) . Notably, it is well established that HPV-associated HNSCC show cases with distinct molecular and clinical attributes compared to HPV-negative cases. The present study delves into the epigenetic landscape of HPV16, specifically its L1 gene and untranslated region (UTR), through pyrosequencing, while the HPV16 DNA physic","cbCaitPhhdYQENY1","https://ap.wps.com/l/cbCaitPhhdYQENY1","pdf",1026926,11,"English","# Introduction\n## Background on head and neck cancers\n## HPV association with HNSCC\n# Methods and Epigenetic Analysis\n## Pyrosequencing of HPV16 L1 and UTR\n## Assessment of HPV16 physical status using E2/E6 ratio\n# Results\n## Site-specific methylation patterns\n## Links between methylation and tumor histological grade\n## Relationship between physical status and methylation or tumor traits\n# Conclusion","[{\"question\":\"What epigenetic regions of HPV16 were investigated in this study?\",\"answer\":\"The study examined the HPV16 L1 gene and the untranslated region (UTR) using pyrosequencing.\"},{\"question\":\"How was HPV16 DNA physical status measured in the HNSCC samples?\",\"answer\":\"HPV16 DNA physical status was evaluated using E2/E6 ratio analysis in HPV16-positive HNSCC FFPE biopsies.\"},{\"question\":\"Which methylation sites were associated with tumor histological grade?\",\"answer\":\"Two L1 CpG sites (7136 and 7145) showed significant associations with tumor histological grade (p \\u003c 0.01).\"},{\"question\":\"Did HPV16 DNA physical status correlate with methylation or tumor characteristics?\",\"answer\":\"No correlation was found between HPV16 DNA physical status and methylation of the viral genome or tumor characteristics.\"}]","Human Papillomavirus 16 DNA Methylation Patterns and Investigation of Integration Status in Head and Neck Cancer Cases | PDF",1790261282,28]