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Taguchi A, Yoshimoto D, Kusakabe M, Baba S, Kawata A, Miyamoto Y, Mori M, Sone K, Hirota Y, Osuga Y. Impact of human papillomavirus types on uterine cervical neoplasia. J Obstet Gynaecol Res 2024. [PMID: 38852606 DOI: 10.1111/jog.15995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 05/23/2024] [Indexed: 06/11/2024]
Abstract
Human papillomavirus (HPV) is a major cause of cervical cancer. As the natural history of HPV-associated cervical lesions is HPV genotype-dependent, it is important to understand the characteristics of these genotypes and to manage them accordingly. Among high-risk HPVs, HPV16 and 18 are particularly aggressive, together accounting for 70% of HPV genotypes detected in cervical cancer. Other than HPV16 and 18, HPV31, 33, 35, 45, 52, and 58 are also at a high risk of progression to cervical intraepithelial neoplasia (CIN)3 or higher. Recent studies have shown that the natural history of HPV16, 18, 52, and 58, which are frequently detected in Japan, depends on the HPV genotype. For example, HPV16 tends to progress in a stepwise fashion from CIN1 to CIN3, while HPV52 and 58 are more likely to persist in the CIN1 to CIN2 state. Among the high-risk HPVs, HPV18 has some peculiar characteristics different from those of other high-risk HPV types; the detection rate in precancerous lesions is much lower than those of other high-risk HPVs, and it is frequently detected in highly malignant adenocarcinoma and small cell carcinoma. Recent findings demonstrate that HPV18 may be characterized by latent infection and carcinogenesis in stem cell-like cells. In this context, this review outlines the natural history of HPV-infected cervical lesions and the characteristics of each HPV genotype.
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Affiliation(s)
- Ayumi Taguchi
- Laboratory of Human Single Cell Immunology, WPI Immunology Frontier Research Center Osaka University, Osaka, Japan
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Yoshimoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Misako Kusakabe
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Baba
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Kawata
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuichiro Miyamoto
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mayuyo Mori
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasushi Hirota
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Guo C, Ran Z, Li D, Zhu J, Peng Y, Zhao W, Song L, Lyv Y, Tian Z, Wang J, Ding L. Effects of CpG sites methylation modification of HPV16 integration essential gene on the proliferation of cervical cancer cells. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023:10.1007/s12094-023-03088-7. [PMID: 36694079 DOI: 10.1007/s12094-023-03088-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
PURPOSE The mechanism of methylation of HPV CpG sites in the occurrence and prognosis of cervical carcinogenesis remains unclear. We investigated the effects of demethylation of the CpG sites of E2 and E6, essential genes of HPV16 integration, on cervical cancer cell expression, integration, and proliferation. MATERIALS AND METHODS HPV16-positive (Caski) cells were treated with different concentrations of the demethylation compound 5-aza-dc (0, 5, 10, 20 μmol/l) in vitro. After the intervention, the methylation statuses of HPV16 E2 and E6 were detected by TBS, the expression levels of E2 and E6 mRNA and protein were detected by real-time PCR and western blot, cell proliferation activity was detected by CCK8, and cell cycle and apoptosis were determined by FCM. GraphPad Prism version 8.4.2 and R version 4.2.3 were used for relevant data analyses. RESULTS The methylation levels of HPV16 E2 and E6 CpG sites decreased gradually with increasing 5-aza-dc intervention concentrations. With decreasing E2 and E6 methylation rates, E2 expression increased, the E2/E6 ratio increased, E6 expression decreased, and the growth inhibition rate of Caski cells increased. E2 and E6 expression were negatively and positively correlated with their degrees of methylation respectively, while the E2/E6 mRNA to protein ratio was negatively correlated with the methylation degrees of E2 and E6. CONCLUSION Demethylation can be used as a prospective treatment to affect HPV expression and persistent infection, providing a new theoretical basis for the clinical treatment of viral infections.
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Affiliation(s)
- Chongyu Guo
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Zhaoxia Ran
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Decheng Li
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Jingjing Zhu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Yushu Peng
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Weihong Zhao
- Department of Obstetrics and Gynecology, Second Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Li Song
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Yuanjing Lyv
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Zhiqiang Tian
- Shanxi Bethune Hospital (Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital), The Third Hospital of Shanxi Medical University, Taiyuan, 030032, China
| | - Jintao Wang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China.
| | - Ling Ding
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China.
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Zhang L, Tan W, Yang H, Zhang S, Dai Y. Detection of Host Cell Gene/HPV DNA Methylation Markers: A Promising Triage Approach for Cervical Cancer. Front Oncol 2022; 12:831949. [PMID: 35402283 PMCID: PMC8990922 DOI: 10.3389/fonc.2022.831949] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 02/05/2023] Open
Abstract
Cervical cancer is the most prevalent gynecologic malignancy, especially in women of low- and middle-income countries (LMICs). With a better understanding of the etiology and pathogenesis of cervical cancer, it has been well accepted that this type of cancer can be prevented and treated via early screening. Due to its higher sensitivity than cytology to identify precursor lesions of cervical cancer, detection of high-risk human papillomavirus (HR-HPV) DNA has been implemented as the primary screening approach. However, a high referral rate for colposcopy after HR-HPV DNA detection due to its low specificity in HR-HPV screening often leads to overtreatment and thus increases the healthcare burden. Emerging evidence has demonstrated that detection of host cell gene and/or HPV DNA methylation represents a promising approach for the early triage of cervical cancer in HR-HPV-positive women owing to its convenience and comparable performance to cytology, particularly in LMICs with limited healthcare resources. While numerous potential markers involving DNA methylation of host cell genes and the HPV genome have been identified thus far, it is crucial to define which genes or panels involving host and/or HPV are feasible and appropriate for large-scale screening and triage. An ideal approach for screening and triage of CIN/ICC requires high sensitivity and adequate specificity and is suitable for self-sampling and inexpensive to allow population-based screening, particularly in LMICs. In this review, we summarize the markers of host cell gene/HR-HPV DNA methylation and discuss their triage performance and feasibility for high-grade precancerous cervical intraepithelial neoplasia or worse (CIN2+ and CIN3+) in HR-HPV-positive women.
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Affiliation(s)
- Lingyi Zhang
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Wenxi Tan
- Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, China
| | - Hongmei Yang
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China.,Department of Critical Care Medicine, The First Hospital of Jilin University, Changchun, China
| | - Songling Zhang
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, China
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, The First Hospital of Jilin University, Changchun, China
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Bowden SJ, Kalliala I, Veroniki AA, Arbyn M, Mitra A, Lathouras K, Mirabello L, Chadeau-Hyam M, Paraskevaidis E, Flanagan JM, Kyrgiou M. The use of human papillomavirus DNA methylation in cervical intraepithelial neoplasia: A systematic review and meta-analysis. EBioMedicine 2019; 50:246-259. [PMID: 31732479 PMCID: PMC6921230 DOI: 10.1016/j.ebiom.2019.10.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Methylation of viral DNA has been proposed as a novel biomarker for triage of human papillomavirus (HPV) positive women at screening. This systematic review and meta-analysis aims to assess how methylation levels change with disease severity and to determine diagnostic test accuracy (DTA) in detecting high-grade cervical intra-epithelial neoplasia (CIN). METHODS We performed searches in MEDLINE, EMBASE and CENTRAL from inception to October 2019. Studies were eligible if they explored HPV methylation levels in HPV positive women. Data were extracted in duplicate and requested from authors where necessary. Random-effects models and a bivariate mixed-effects binary regression model were applied to determine pooled effect estimates. FINDINGS 44 studies with 8819 high-risk HPV positive women were eligible. The pooled estimates for positive methylation rate in HPV16 L1 gene were higher for high-grade CIN (≥CIN2/high-grade squamous intra-epithelial lesion (HSIL) (95% confidence interval (95%CI:72·7% (47·8-92·2))) vs. low-grade CIN (≤CIN1/low-grade squamous intra-epithelial lesion (LSIL) (44·4% (95%CI:16·0-74·1))). Pooled difference in mean methylation level was significantly higher in ≥CIN2/HSIL vs. ≤CIN1/LSIL for HPV16 L1 (11·3% (95%CI:6·5-16·1)). Pooled odds ratio of HPV16 L1 methylation was 5·5 (95%CI:3·5-8·5) for ≥CIN2/HSIL vs. ≤CIN1/LSIL (p < 0·0001). HPV16 L1/L2 genes performed best in predicting CIN2 or worse (pooled sensitivity 77% (95%CI:63-87), specificity 64% (95%CI:55-71), area under the curve (0·73 (95%CI:0·69-0·77)). INTERPRETATION Higher HPV methylation is associated with increased disease severity, whilst HPV16 L1/L2 genes demonstrated high diagnostic accuracy to detect high-grade CIN in HPV16 positive women. Direct clinical use is limited by the need for a multi-genotype and standardised assays. Next-generation multiplex HPV sequencing assays are under development and allow potential for rapid, automated and low-cost methylation testing. FUNDING NIHR, Genesis Research Trust, Imperial Healthcare Charity, Wellcome Trust NIHR Imperial BRC, European Union's Horizon 2020.
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Affiliation(s)
- Sarah J Bowden
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK; West London Gynaecology Cancer Centre, Hammersmith Hospital, Imperial Healthcare NHS Trust, UK
| | - Ilkka Kalliala
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK; Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Finland
| | - Areti A Veroniki
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK; Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Department of Primary Education, School of Education, University of Ioannina, Ioannina, Greece
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Scientific Institute of Public Health, Brussels, Belgium
| | - Anita Mitra
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK; West London Gynaecology Cancer Centre, Hammersmith Hospital, Imperial Healthcare NHS Trust, UK
| | - Kostas Lathouras
- West London Gynaecology Cancer Centre, Hammersmith Hospital, Imperial Healthcare NHS Trust, UK
| | - Lisa Mirabello
- Department of Clinical Genetics, National Institute of Health (NIH), Bethesda, MD, USA
| | - Marc Chadeau-Hyam
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK
| | | | - James M Flanagan
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK
| | - Maria Kyrgiou
- Department of Surgery and Cancer, 3rd Floor IRDB, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 ONN, London, UK; West London Gynaecology Cancer Centre, Hammersmith Hospital, Imperial Healthcare NHS Trust, UK.
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Zhang X, Zhi Y, Li Y, Fan T, Li H, Du P, Cheng G, Li X. Study on the relationship between methylation status of HPV 16 E2 binding sites and cervical lesions. Clin Chim Acta 2019; 493:98-103. [DOI: 10.1016/j.cca.2019.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 11/15/2022]
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Schmitz M, Eichelkraut K, Schmidt D, Zeiser I, Hilal Z, Tettenborn Z, Hansel A, Ikenberg H. Performance of a DNA methylation marker panel using liquid-based cervical scrapes to detect cervical cancer and its precancerous stages. BMC Cancer 2018; 18:1197. [PMID: 30509219 PMCID: PMC6276155 DOI: 10.1186/s12885-018-5125-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/22/2018] [Indexed: 01/30/2023] Open
Abstract
Background A change of cervical cancer screening algorithms to an HPV-based screening setting is discussed in many countries, due to higher sensitivity of HPV testing compared to cytology. Reliable triage methods are, however, an essential prerequisite in such a setting to avoid overtreatment and higher screening costs. Results In this study, a series of cervical scrapes collected in PreservCyt liquid-based cytology (LBC) medium from women with cervical cancer (n = 5), cervical intraepithelial neoplasia grade 1–3 (n = 74), and normal cytology (n = 201; further n = 352 collected in SureThin®) were assessed for methylation of the marker regions ASTN1, DLX1, ITGA4, RXFP3, SOX17, and ZNF671 using the GynTect assay and compared to cobas® HPV and CINtec Plus® biomarker results. All samples from women with cervical cancer, 61.2% of CIN3, 44.4% of CIN2 and 20.0% of CIN1 cases were scored positive for the GynTect methylation assay. In contrast, all CIN, irrespective of severity grade, and carcinomas were positive by both, CINtec Plus and cobas HPV. The specificity of GynTect for CIN3+ was 94.6% compared to 69.9% for CINtec Plus and 82.6% for cobas HPV (all HPV types) and 90.6% for cobas HPV 16/18. DNA methylation analysis of this methylation marker panel (GynTect assay) in cervical scrapes consistently detects cervical cancer and the majority of CIN3 as well as a subset of CIN1/2 lesions. The detection rate among cytologically normal samples is extraordinarily low (1.5%). Conclusion GynTect shows excellent performance when using cervical scrape material collected in liquid-based cytology media, a prerequisite for employing such a test as a triage in screening programs. Compared to the other test systems used in this work, GynTect showed higher specificity while still detecting all cancer cases.
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Affiliation(s)
| | | | - Dana Schmidt
- oncgnostics GmbH, Winzerlaer Strasse 2, Jena, Germany
| | | | - Ziad Hilal
- ZyDoLab, Institute for Cytology and Immune Cytochemistry, Markt 10, Dortmund, Germany
| | - Zena Tettenborn
- ZyDoLab, Institute for Cytology and Immune Cytochemistry, Markt 10, Dortmund, Germany
| | - Alfred Hansel
- oncgnostics GmbH, Winzerlaer Strasse 2, Jena, Germany
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Liu L, Ying C, Zhao Z, Sui L, Zhang X, Qian C, Wang Q, Chen L, Guo Q, Wu J. Identification of reliable biomarkers of human papillomavirus 16 methylation in cervical lesions based on integration status using high-resolution melting analysis. Clin Epigenetics 2018; 10:10. [PMID: 29410710 PMCID: PMC5781301 DOI: 10.1186/s13148-018-0445-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 01/11/2018] [Indexed: 01/13/2023] Open
Abstract
Background The dynamic methylation of human papillomavirus (HPV) 16 DNA is thought to be associated with the progression of cervical lesions. Previous studies that did not consider the physical status of HPV 16 may have incorrectly mapped HPV 16 methylomes. In order to identify reliable biomarkers for squamous cervical cancer (SCC), we comprehensively evaluated the methylation of HPV 16 depending on the integration incidence of each sample. Methods Based on the integration status of 115 HPV 16-infected patients (50 SCC, 30 high-grade squamous intraepithelial lesion [HSIL], and 35 low-grade squamous intraepithelial lesion [LSIL]) and HPV 16-infected Caski cell lines by PCR detection of integrated papillomavirus sequences, we designed a series of primers that would not be influenced by breakpoints for a high-resolution melting (HRM) PCR method to detect the genome methylation. Results A few regions with recurrent interruptions were identified in E1, E2/E4, L1, and L2 despite scattering of breakpoints throughout all eight genes of HPV 16. Frequent integration sites often occurred concomitantly with methylated CpG sites. The HRM PCR method showed 100% agreement with pyrosequencing when 3% was set as the cutoff value. A panel of CpG sites such as nt5606, nt5609, nt5615, and nt5378 can be combined in reweighing calculations to distinguish SCC from HSIL and LSIL patients which have high sensitivity and specificity (88% and 92.31%, respectively). Conclusions Our research shows that combination of CpG sites nt5606, nt5609, nt5615, and nt5378 can be used as potential diagnosis biomarkers for SCC, and the HRM PCR method is suitable for clinical methylation analysis. Electronic supplementary material The online version of this article (10.1186/s13148-018-0445-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lu Liu
- 1Department of Clinical Laboratory, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Chunmei Ying
- 1Department of Clinical Laboratory, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Zhen Zhao
- 2Department of Clinical Laboratory, Minhang District Central Hospital, Shanghai, China
| | - Long Sui
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Xinyan Zhang
- 4The Research Institute of Obstetrics and Gynecology, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunyan Qian
- 5Yuhang Branch, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Qing Wang
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Limei Chen
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Qisang Guo
- 3Medical Center of Diagnosis and Treatment for Cervical Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Fangxie Road No. 419, Huangpu District, Shanghai, 200001 China
| | - Jiangnan Wu
- 6Department of Clinical Statistics, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Epigenetic Alterations in Human Papillomavirus-Associated Cancers. Viruses 2017; 9:v9090248. [PMID: 28862667 PMCID: PMC5618014 DOI: 10.3390/v9090248] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
Approximately 15–20% of human cancers are caused by viruses, including human papillomaviruses (HPVs). Viruses are obligatory intracellular parasites and encode proteins that reprogram the regulatory networks governing host cellular signaling pathways that control recognition by the immune system, proliferation, differentiation, genomic integrity, and cell death. Given that key proteins in these regulatory networks are also subject to mutation in non-virally associated diseases and cancers, the study of oncogenic viruses has also been instrumental to the discovery and analysis of many fundamental cellular processes, including messenger RNA (mRNA) splicing, transcriptional enhancers, oncogenes and tumor suppressors, signal transduction, immune regulation, and cell cycle control. More recently, tumor viruses, in particular HPV, have proven themselves invaluable in the study of the cancer epigenome. Epigenetic silencing or de-silencing of genes can have cellular consequences that are akin to genetic mutations, i.e., the loss and gain of expression of genes that are not usually expressed in a certain cell type and/or genes that have tumor suppressive or oncogenic activities, respectively. Unlike genetic mutations, the reversible nature of epigenetic modifications affords an opportunity of epigenetic therapy for cancer. This review summarizes the current knowledge on epigenetic regulation in HPV-infected cells with a focus on those elements with relevance to carcinogenesis.
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Liu P, Iden M, Fye S, Huang YW, Hopp E, Chu C, Lu Y, Rader JS. Targeted, Deep Sequencing Reveals Full Methylation Profiles of Multiple HPV Types and Potential Biomarkers for Cervical Cancer Progression. Cancer Epidemiol Biomarkers Prev 2017; 26:642-650. [PMID: 28069683 DOI: 10.1158/1055-9965.epi-16-0368] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/15/2016] [Accepted: 12/15/2016] [Indexed: 11/16/2022] Open
Abstract
Background: Invasive cervical cancer (ICC) and its premalignant phase (cervical intraepithelial neoplasia; CIN1-3) are distinguished by gynecologic and pathologic examination, yet no current methodologies can predict precancerous lesions that are destined to progress to ICC. Thus, development of reliable assays to assess patient prognosis is much needed.Methods: Human papillomavirus (HPV) DNA methylation is significantly altered in cervical disease. Using an HPV enrichment approach and next-generation DNA sequencing, methylation status was characterized in a case-case comparison of CIN (n = 2 CIN1; n = 2 CIN2; n = 20 CIN3) and ICC (n = 37) samples. Pyrosequencing validated methylation changes at CpGs of interest in a larger sample cohort (n = 61 CIN3; 50 ICC).Results: Global viral methylation, across HPV types, was significantly higher in ICC than CIN3. Average L1 gene methylation in 13 different HPV types best distinguished CIN3 from ICC. Methylation levels at individual CpG sites as a quantitative classifier achieved a sensitivity and specificity of >95% for detecting ICC in HPV 16 samples. Pyrosequencing confirmed significantly higher methylation of these CpGs in E1 of HPV 16 in ICC compared with CIN3.Conclusions: Global HPV methylation is significantly higher in ICC than CIN3, with L1 gene methylation levels performing best for distinguishing CIN3 from ICC. Methylation levels at CpGs in the E1 gene of HPV 16 (972, 978, 1870, and 1958) can distinguish between CIN3 and ICC.Impact: Higher methylation at specific E1 CpGs may associate with increased likelihood of progression to ICC in HPV 16-positive CIN3 lesions. Cancer Epidemiol Biomarkers Prev; 26(4); 642-50. ©2017 AACR.
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Affiliation(s)
- Pengyuan Liu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
- Sir Run Run Shaw Hospital and Institute for Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Marissa Iden
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Samantha Fye
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Elizabeth Hopp
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Chen Chu
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yan Lu
- Department of Gynecologic Oncology, The Affiliated Women's Hospital and Institute for Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Janet S Rader
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin.
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Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis. Clin Chim Acta 2016; 461:156-64. [DOI: 10.1016/j.cca.2016.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/06/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
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11
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Durzynska J, Lesniewicz K, Poreba E. Human papillomaviruses in epigenetic regulations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 772:36-50. [PMID: 28528689 DOI: 10.1016/j.mrrev.2016.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/01/2016] [Accepted: 09/17/2016] [Indexed: 12/12/2022]
Abstract
Human Papillomaviruses (HPVs) are double-stranded DNA viruses, that infect epithelial cells and are etiologically involved in the development of human cancer. Today, over 200 types of human papillomaviruses are known. They are divided into low-risk and high-risk HPVs depending on their potential to induce carcinogenesis, driven by two major viral oncoproteins, E6 and E7. By interacting with cellular partners, these proteins are involved in interdependent viral and cell cycles in stratified differentiating epithelium, and concomitantly induce epigenetic changes in infected cells and those undergoing malignant transformation. E6 and E7 oncoproteins interact with and/or modulate expression of many proteins involved in epigenetic regulation, including DNA methyltransferases, histone-modifying enzymes and subunits of chromatin remodeling complexes, thereby influencing host cell transcription program. Furthermore, HPV oncoproteins modulate expression of cellular micro RNAs. Most of these epigenetic actions in a complex dynamic interplay participate in the maintenance of persistent infection, cell transformation, and development of invasive cancer by a considerable deregulation of tumor suppressor and oncogenes. In this study, we have undertaken to discuss a number of studies concerning epigenetic regulations in HPV-dependent cells and to focus on those that have biological relevance to cancer progression.
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Affiliation(s)
- Julia Durzynska
- Department of Molecular Virology, Institute of Experimental Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Elzbieta Poreba
- Department of Molecular Virology, Institute of Experimental Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland.
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12
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Molano M, Tabrizi SN, Garland SM, Roberts JM, Machalek DA, Phillips S, Chandler D, Hillman RJ, Grulich AE, Jin F, Poynten IM, Templeton DJ, Cornall AM. CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker. PLoS One 2016; 11:e0160673. [PMID: 27529629 PMCID: PMC4987059 DOI: 10.1371/journal.pone.0160673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/22/2016] [Indexed: 11/18/2022] Open
Abstract
Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC) are associated with human papillomavirus (HPV). Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS) and laser capture microdissected (LCM) tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL.
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Affiliation(s)
- Monica Molano
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Sepehr N. Tabrizi
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne and Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Suzanne M. Garland
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne and Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | | | - Dorothy A. Machalek
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Samuel Phillips
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | | | - Richard J. Hillman
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, Parramatta, New South Wales, Australia
- Sydney Medical School, Westmead, University of Sydney, Sydney, New South Wales, Australia
| | - Andrew E. Grulich
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Fengyi Jin
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - I. Mary Poynten
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - David J. Templeton
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
- RPA Sexual Health, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Alyssa M. Cornall
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Victoria, Australia
- * E-mail:
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13
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Luttmer R, De Strooper LMA, Steenbergen RDM, Berkhof J, Snijders PJF, Heideman DAM, Meijer CJLM. Management of high-risk HPV-positive women for detection of cervical (pre)cancer. Expert Rev Mol Diagn 2016; 16:961-74. [PMID: 27459506 DOI: 10.1080/14737159.2016.1217157] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Primary HPV-testing has been shown to provide a superior detection of women at risk of cervical (pre)cancer compared to cytology-based screening. However, as most high-risk HPV infections are harmless, additional triage testing of HPV-positive women is necessary to identify those with cervical (pre)cancer. In this paper, we compare the performance, advantages and limitations of clinically relevant available triage strategies for HPV-positive women. AREAS COVERED Many different colposcopy triage strategies, comprising both microscopy-based and molecular (virus/host-related) markers, have been suggested: Pap cytology, p16/Ki-67 dual-stained cytology, HPV16/18 genotyping, viral DNA methylation and host cell DNA methylation. Literature search was limited to triage strategies that have achieved at least phase 2 of the five-phase framework for biomarker development and studies including large cohorts (≥100 hrHPV-positive women). Triage markers were stratified by sample type (cervical scrape, self-collected sample) and by study population (screening, non-attendee, referral). Expert commentary: At present, repeat Pap cytology and Pap cytology combined with HPV16/18 genotyping are the only triage strategies that have been robustly shown to be ready for implementation. Other strategies such as p16/Ki-67 dual-stained cytology and host cell DNA methylation analysis, with or without additional HPV16/18 genotyping, are attractive options for the near future.
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Affiliation(s)
- Roosmarijn Luttmer
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands.,b Department of Obstetrics & Gynecology , Diakonessenhuis , Utrecht , the Netherlands
| | - Lise M A De Strooper
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | | | - Johannes Berkhof
- c Department of Epidemiology & Biostatistics , VU University Medical Center , Amsterdam , the Netherlands
| | - Peter J F Snijders
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | - Daniëlle A M Heideman
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
| | - Chris J L M Meijer
- a Department of Pathology , VU University Medical Center , Amsterdam , the Netherlands
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14
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Abstract
Human papillomaviruses are the causative agents of cervical, anal as well as many oropharyngeal cancers. While prophylactic vaccines have been developed, uptake is low in the US and other Western countries, and access is limited in less developed countries. A number of areas are emerging as critical for future study. These include investigation of the mechanisms regulating infection and progression to cancer at both cervical and oropharyngeal sites as these appear to be distinct. HPV-induced cancers also may be susceptible to immune therapy, revealing opportunities for treating advanced cervical disease and reducing the morbidity of treatments for oropharyngeal cancers. We believe these areas are critical focal points for HPV cancer research in the next decade.
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Affiliation(s)
- Erika Langsfeld
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laimonis A Laimins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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15
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Zhang C, Deng Z, Pan X, Uehara T, Suzuki M, Xie M. Effects of Methylation Status of CpG Sites within the HPV16 Long Control Region on HPV16-Positive Head and Neck Cancer Cells. PLoS One 2015; 10:e0141245. [PMID: 26509736 PMCID: PMC4625038 DOI: 10.1371/journal.pone.0141245] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/05/2015] [Indexed: 12/31/2022] Open
Abstract
Objective To map comprehensively the methylation status of the CpG sites within the HPV16 long control region (LCR) in HPV-positive cancer cells, and to explore further the effects of methylation status of HPV16 LCR on cell bioactivity and E6 and E7 expression. In addition, to analyze the methylation status of the LCR in HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) patients. Methods and Materials Methylation patterns of HPV16 LCR in UM-SCC47, CaSki, and SiHa cells and HPV16-positiive OPSCC specimens were detected by bisulfite-sequencing PCR and TA cloning. For cells treated with 5-aza-2′-deoxycytidine and E6 and E7 knockdown, MTS and trypan blue staining, annexin-V and 7-AAD staining, and prodidium iodide were used to evaluate cell growth and cell proliferation, cell apoptosis, and cell cycle arrest, respectively. E6 and E7 mRNA and protein expression were analyzed by quantitative real-time PCR and immunocytochemistry, respectively. Results Hypermethylation status of the LCR in UM-SCC47 (79.8%) and CaSki cells (90.0%) and unmethylation status of the LCR in SiHa cells (0%) were observed. Upon demethylation, the cells with different methylation levels responded differently during growth, apoptosis, and cell cycle arrest, as well as in terms of their E6 and E7 expression. In HPV16-positive OPSCC patients, the methylation rates were 9.5% in the entire LCR region, 13.9% in the 5′-LCR, 6.0% in the E6 enhancer, and 9.5% in the p97 promoter, and hypermethylation of p97 promoter was found in a subset of cases (20.0%, 2/10). Conclusions Our study revealed two different methylation levels of the LCR in HPV16-positive cancer cells and OPSCC patients, which may represent different carcinogenesis mechanisms of HPV-positive cancers cells. Demethylating the meCpGs in HPV16 LCR might be a potential target for a subgroup of HPV16-positive patients with head and neck squamous cell carcinoma.
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Affiliation(s)
- Chunlin Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Otorhinolaryngology, Head and Neck Surgery, University of the Ryukyus, Okinawa, Japan
- Department of Otorhinolaryngology, Head and Neck Surgery, Affiliated hospital of Zunyi Medical University, Zunyi, China
| | - Zeyi Deng
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Otorhinolaryngology, Head and Neck Surgery, University of the Ryukyus, Okinawa, Japan
| | - Xiaoli Pan
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Department of Otorhinolaryngology, Head and Neck Surgery, University of the Ryukyus, Okinawa, Japan
- Department of Otorhinolaryngology, Head and Neck Surgery, The First People’s Hospital of Guangzhou, Guangzhou, China
| | - Takayuki Uehara
- Department of Otorhinolaryngology, Head and Neck Surgery, University of the Ryukyus, Okinawa, Japan
| | - Mikio Suzuki
- Department of Otorhinolaryngology, Head and Neck Surgery, University of the Ryukyus, Okinawa, Japan
- * E-mail: (MX); (MS)
| | - Minqiang Xie
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- * E-mail: (MX); (MS)
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16
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Simanaviciene V, Popendikyte V, Gudleviciene Z, Zvirbliene A. Different DNA methylation pattern of HPV16, HPV18 and HPV51 genomes in asymptomatic HPV infection as compared to cervical neoplasia. Virology 2015; 484:227-233. [PMID: 26119875 DOI: 10.1016/j.virol.2015.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/04/2015] [Indexed: 12/29/2022]
Abstract
Epigenetic alterations of human papillomavirus (HPV) genome play an important role in virus life cycle and carcinogenic progression. The aim of the current study was to investigate the correlation between the grade of cervical pathology and DNA methylation status within the L1 gene and the long control region (LCR) of HPV16, HPV18 and HPV51. HPV genomes were analyzed using bisulfite DNA modification procedure with the subsequent amplification of target DNA regions and sequencing. A collection of 202 cervical specimens was analyzed: 157 HPV16-positive specimens, 21 HPV18-positive specimens and 24 HPV51-positive specimens. This study revealed that methylation of CpG was significantly more prevalent in L1 gene as compared to LCR region of all three studied HPV types and the degree of DNA methylation level correlated with the severity of cervical neoplasia. An increased DNA methylation level of HPV16 promoter region in case of cervical cancer was determined.
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Affiliation(s)
- Vaida Simanaviciene
- Institute of Biotechnology, Vilnius University, Graiciuno Str.8, LT-02241 Vilnius, Lithuania.
| | - Violeta Popendikyte
- Thermo Fischer Scientific Baltic, Graiciuno Str.8, LT-02241 Vilnius, Lithuania
| | - Zivile Gudleviciene
- National Cancer Institute, Santariskiu Str.1, LT-08660 Vilnius, Lithuania; Faculty of Medicine, Vilnius University, M.K. Ciurlionio Str.21, LT-03101 Vilnius, Lithuania
| | - Aurelija Zvirbliene
- Institute of Biotechnology, Vilnius University, Graiciuno Str.8, LT-02241 Vilnius, Lithuania
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Mirabello L, Frimer M, Harari A, McAndrew T, Smith B, Chen Z, Wentzensen N, Wacholder S, Castle PE, Raine-Bennett T, Schiffman M, Burk RD. HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. Int J Cancer 2015; 136:E146-53. [PMID: 25081507 PMCID: PMC4262737 DOI: 10.1002/ijc.29119] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/03/2014] [Indexed: 01/02/2023]
Abstract
We have developed and evaluated a next-generation bisulfite sequencing (NGS) assay to distinguish HPV16 cervical precancer (CIN2-3; N=59) from HPV16-positive transient infections (N=40). Cervical DNA was isolated and treated with bisulfite and HPV16 methylation was quantified by (i) amplification with barcoded primers and massively parallel single molecule sequencing and (ii) site-specific pyrosequencing. Assays were evaluated for agreement using intraclass correlation coefficients (ICC). Odds ratios (OR) for high methylation vs. low methylation were calculated. Single site pyrosequencing and NGS data were correlated (ICC=0.61) and both indicated hypermethylation was associated with precancer (ORs of 2-37). Concordant NGS and pyrosequencing results yieled ORs that were stronger when compared with using either assay separately. Within the L1 region, the ORs for CIN2-3 were 14.3 and 22.4 using pyrosequencing and NGS assays, respectively; when both methods agreed the OR was 153. NGS assays provide methylation haplotypes, termed methyl-haplotypes from single molecule reads: cases had increased methyl-haplotypes with ≥1 methylated CpG site(s) per fragment compared with controls, particularly in L1 (p=3.0×10(-8)). The maximum discrimination of cases from controls for a L1 methyl-haplotype had an AUC of 0.89 corresponding to a sensitivity of 92.5% and a specificity of 73.1%. The strengthening of the OR when the two assays were concordant suggests the true association of CpG methylation with precancer is stronger than with either assay. As cervical cancer prevention moves to DNA testing methods, DNA based biomarkers, such as HPV methylation could serve as a reflex strategy to identify women at high risk for cervix cancer.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Marina Frimer
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Ariana Harari
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Thomas McAndrew
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Benjamin Smith
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Zigui Chen
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Tina Raine-Bennett
- Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Robert D. Burk
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY
- Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY
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18
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Bryant D, Onions T, Raybould R, Jones S, Tristram A, Hibbitts S, Fiander A, Powell N. Increased methylation of Human Papillomavirus type 16 DNA correlates with viral integration in Vulval Intraepithelial Neoplasia. J Clin Virol 2014; 61:393-9. [PMID: 25218242 DOI: 10.1016/j.jcv.2014.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/25/2014] [Accepted: 08/08/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Methylation of HPV16 DNA is a promising biomarker for triage of HPV positive cervical screening samples but the biological basis for the association between HPV-associated neoplasia and increased methylation is unclear. OBJECTIVES To determine whether HPV16 DNA methylation was associated with viral integration, and investigate the relationships between viral DNA methylation, integration and gene expression. STUDY DESIGN HPV16 DNA methylation, integration and gene expression were assessed using pyrosequencing, ligation-mediated PCR and QPCR, in biopsies from 25 patients attending a specialist vulval neoplasia clinic and in short-term clonal cell lines derived from vulval and vaginal neoplasia. RESULTS Increased methylation of the HPV16 L1/L2 and E2 regions was associated with integration of viral DNA into the host genome. This relationship was observed both in vivo and in vitro. Increased methylation of E2 binding sites did not appear to be associated with greater expression of viral early genes. Expression of HPV E6 and E7 did not correlate with either integration state or increased L1/L2 methylation. CONCLUSIONS The data suggest that increased HPV DNA methylation may be partly attributable to viral integration, and provide a biological rationale for quantification of L1/L2 methylation in triage of HPV positive cervical screening samples.
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Affiliation(s)
- Dean Bryant
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Tiffany Onions
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Rachel Raybould
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Sadie Jones
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Amanda Tristram
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Samantha Hibbitts
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Alison Fiander
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
| | - Ned Powell
- HPV Research Group, Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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19
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Marongiu L, Godi A, Parry JV, Beddows S. Human Papillomavirus 16, 18, 31 and 45 viral load, integration and methylation status stratified by cervical disease stage. BMC Cancer 2014; 14:384. [PMID: 24885011 PMCID: PMC4053304 DOI: 10.1186/1471-2407-14-384] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/27/2014] [Indexed: 11/30/2022] Open
Abstract
Background Persistent infection with oncogenic Human Papillomavirus (HPV) is associated with the development of cervical cancer with each genotype differing in their relative contribution to the prevalence of cervical disease. HPV DNA testing offers improved sensitivity over cytology testing alone but is accompanied by a generally low specificity. Potential molecular markers of cervical disease include type-specific viral load (VL), integration of HPV DNA into the host genome and methylation of the HPV genome. The aim of this study was to evaluate the relationship between HPV type-specific viral load, integration and methylation status and cervical disease stage in samples harboring HPV16, HPV18, HPV31 or HPV45. Methods Samples singly infected with HPV16 (n = 226), HPV18 (n = 32), HPV31 (n = 75) or HPV45 (n = 29) were selected from a cohort of 4,719 women attending cervical screening in England. Viral load and integration status were determined by real-time PCR while 3’L1-URR methylation status was determined by pyrosequencing or sequencing of multiple clones derived from each sample. Results Viral load could differentiate between normal and abnormal cytology with a sensitivity of 75% and a specificity of 80% (odds ratio [OR] 12.4, 95% CI 6.2–26.1; p < 0.001) with some variation between genotypes. Viral integration was poorly associated with cervical disease. Few samples had fully integrated genomes and these could be found throughout the course of disease. Overall, integration status could distinguish between normal and abnormal cytology with a sensitivity of 72% and a specificity of 50% (OR 2.6, 95% CI 1.0–6.8; p = 0.054). Methylation levels were able to differentiate normal and low grade cytology from high grade cytology with a sensitivity of 64% and a specificity of 82% (OR 8.2, 95% CI 3.8–18.0; p < 0.001). However, methylation varied widely between genotypes with HPV18 and HPV45 exhibiting a broader degree and higher magnitude of methylated CpG sites than HPV16 and HPV31. Conclusions This study lends support for HPV viral load and CpG methylation status, but not integration status, to be considered as potential biomarkers of cervical disease.
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Affiliation(s)
| | | | | | - Simon Beddows
- Virus Reference Department, Public Health England, 61 Colindale Avenue, London NW9 5EQ, U,K.
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20
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Hesselink AT, Heideman DAM, Steenbergen RDM, Gök M, van Kemenade FJ, Wilting SM, Berkhof J, Meijer CJLM, Snijders PJF. Methylation marker analysis of self-sampled cervico-vaginal lavage specimens to triage high-risk HPV-positive women for colposcopy. Int J Cancer 2014; 135:880-6. [PMID: 24474183 DOI: 10.1002/ijc.28723] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/17/2013] [Accepted: 12/20/2013] [Indexed: 01/23/2023]
Abstract
Methylation markers were studied for their suitability to triage human papillomavirus (HPV)-positive women by testing self-collected cervico-vaginal lavage specimens. For this purpose, we analyzed 355 hrHPV-positive self-collected specimens with three methylation markers, that is, CADM1-m18, MAL-m1 and miR-124-2 by quantitative methylation-specific PCR. The areas under the receiver-operating characteristic (ROC) curve for end-point cervical intraepithelial neoplasia grade 3 or worse (CIN3+) were 0.637 for CADM1-m18, 0.767 for MAL-m1 and 0.762 for miR-124-2. This indicates that CADM1-m18 is not suitable as single marker. By varying the thresholds of both markers in the bi-marker panels CADM1-m18/MAL-m1, CADM1-m18/miR-124-2 and MAL-m1/miR-124-2 upper and lower ROC curves were obtained, depicting the maximum and minimum CIN3+ sensitivity, respectively, at given specificity. For all these bi-marker combinations, the upper curves were similar. However, for the MAL-m1/miR-124-2 panel, the distance between upper and lower ROC curves was closest and this panel displayed the highest assay thresholds, indicating that this combination was most robust. At clinical specificities of 50 and 70%, the MAL-m1/miR-124-2 sensitivity for detection of CIN3+ ranged from 77.0 to 87.8% and from 64.9 to 71.6%, respectively. At 70% specificity thresholds no carcinomas were missed. By comparison, the CIN3+ sensitivity of HPV16/18 genotyping on the self-sampled lavage specimens was 58.1% (95%CI: 46.6-68.8) at a specificity of 87.7% (95%CI: 83.2-91.2). In conclusion, methylation analysis is a promising triage tool that in combination with HPV-DNA testing offers feasible, full molecular screening on self-collected cervico-vaginal lavage specimens.
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Affiliation(s)
- A T Hesselink
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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21
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Uyar D, Rader J. Genomics of cervical cancer and the role of human papillomavirus pathobiology. Clin Chem 2013; 60:144-6. [PMID: 24046199 DOI: 10.1373/clinchem.2013.212985] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Denise Uyar
- Awardee, 2013 Best Doctors of America, Medical College of Wisconsin, Milwaukee, WI
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22
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Abstract
Human papilllomaviruses (HPVs) are common human pathogens that infect cutaneous or mucosal epithelia in which they cause warts, self-contained benign lesions that commonly regress. The HPV life cycle is intricately tied to the differentiation of the host epithelium it infects. Mucosotropic HPVs are the most common sexually transmitted pathogen known to mankind. A subset of the mucosotropic HPVs, so-called high risk HPVs, is etiologically associated with numerous cancers of the anogenital tract, most notably the cervix, as well as a growing fraction of head and neck cancers. In these cancers, the HPV genome, which normally exists an a double stranded, circular, nuclear plasmid, is commonly found integrated into the host genome and expresses two viral oncogenes, E6 and E7, that are implicated in the development and maintainance of the cancers caused by these high risk HPVs. Numerous studies, primarily on the high risk HPV16, have documented that the methylation status of the viral genome changes not only in the context of the viral life cycle but also in the context of the progressive neoplastic disease that culminates in cancer. In this article, we summarize the knowledge gained from those studies. We also provide the first analysis of available ChIP-seq data on the occupancy of both epigentically modified histones as well as transcription factors on the high risk HPV18 genome in the context of HeLa cells, a cervical cancer-derived cell line that has been the subject of extensive analyses using this technique.
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23
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Methylation of human papillomavirus Type 16 CpG sites at E2-binding site 1 (E2BS1), E2BS2, and the Sp1-binding site in cervical cancer samples as determined by high-resolution melting analysis-PCR. J Clin Microbiol 2013; 51:3207-15. [PMID: 23863566 DOI: 10.1128/jcm.01106-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
High-risk (HR) human papillomavirus (HPV)-associated carcinogenesis is driven mainly by the overexpression of E7 and E6 oncoproteins following viral DNA integration and the concomitant loss of the E2 open reading frame (ORF). However, the integration of HR-HPV DNA is not systematically observed in cervical cancers. The E2 protein acts as a transcription factor that governs viral oncogene expression. The methylation of CpGs in the E2-binding sites (E2BSs) in the viral long control region abrogates E2 binding, thus impairing the E2-mediated regulation of E7/E6 transcription. Here, high-resolution melting (HRM)-PCR was developed to quantitatively analyze the methylation statuses of E2BS1, E2BS2, and the specificity protein 1 (Sp1)-binding site in 119 HPV16-positive cervical smears. This is a rapid assay that is suitable for the analysis of cervical samples. The proportion of cancer samples with methylated E2BS1, E2BS2, and Sp1-binding site CpGs was 47%, whereas the vast majority of samples diagnosed as being within normal limits, low-grade squamous intraepithelial lesions (LSIL), or high-grade squamous intraepithelial lesions (HSIL) harbored unmethylated CpGs. Methylation levels varied widely, since some cancer samples harbored up to 60% of methylated HPV16 genomes. A pyrosequencing approach was used as a confirmation test and highlighted that quantitative measurement of methylation can be achieved by HRM-PCR. Its prognostic value deserves to be investigated alone or in association with other biomarkers. The reliability of this single-tube assay offers great opportunities for the investigation of HPV16 methylation in other HPV-related cancers, such as head and neck cancers, which are a major public health burden.
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Steenbergen RDM, Ongenaert M, Snellenberg S, Trooskens G, van der Meide WF, Pandey D, Bloushtain-Qimron N, Polyak K, Meijer CJLM, Snijders PJF, Van Criekinge W. Methylation-specific digital karyotyping of HPV16E6E7-expressing human keratinocytes identifies novel methylation events in cervical carcinogenesis. J Pathol 2013; 231:53-62. [DOI: 10.1002/path.4210] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/17/2013] [Accepted: 05/07/2013] [Indexed: 12/12/2022]
Affiliation(s)
| | - Maté Ongenaert
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
- Centre for Medical Genetics; Ghent University; Belgium
| | - Suzanne Snellenberg
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Geert Trooskens
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
| | | | - Deeksha Pandey
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Noga Bloushtain-Qimron
- Department of Medical Oncology; Dana-Farber Cancer Institute, Harvard Medical School; Boston MA USA
| | - Kornelia Polyak
- Department of Medical Oncology; Dana-Farber Cancer Institute, Harvard Medical School; Boston MA USA
| | - Chris JLM Meijer
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Peter JF Snijders
- Department of Pathology; VU University Medical Centre; Amsterdam The Netherlands
| | - Wim Van Criekinge
- BioBix, Department of Mathematical Modelling, Statistics and Bioinformatics; Ghent University; Belgium
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Chaiwongkot A, Vinokurova S, Pientong C, Ekalaksananan T, Kongyingyoes B, Kleebkaow P, Chumworathayi B, Patarapadungkit N, Reuschenbach M, von Knebel Doeberitz M. Differential methylation of E2 binding sites in episomal and integrated HPV 16 genomes in preinvasive and invasive cervical lesions. Int J Cancer 2012; 132:2087-94. [PMID: 23065631 DOI: 10.1002/ijc.27906] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/01/2012] [Indexed: 12/17/2022]
Abstract
Enhanced expression of the HPV 16 E6-E7 oncogenes may trigger neoplastic transformation of the squamous epithelial cells at the uterine cervix. The HPV E2 protein is a key transcriptional regulator of the E6-E7 genes. It binds to four E2 binding sites (E2BSs 1-4) in the viral upstream regulatory region (URR). Modification of E2 functions, for example, by methylation of E2BSs is hypothesized to trigger enhanced expression of the viral E6-E7 oncogenes. In the majority of HPV-transformed premalignant lesions and about half of cervical carcinomas HPV genomes persist in an extra-chromosomal, episomal state, whereas they are integrated into host cells chromosomes in the remaining lesions. Here we compared the methylation profile of E2BSs 1-4 of the HPV 16 URR in a series of 18 HPV16-positive premalignant lesions and 33 invasive cervical cancers. CpGs within the E2BSs 1, 3, and 4 were higher methylated in all lesions with only episomal HPV16 genomes compared with lesions displaying single integrated copies. Samples with multiple HPV16 integrated copies displayed high methylation levels for all CpGs suggesting that the majority of multiple copies were silenced by extensive methylation. These data support the hypothesis that differential methylation of the E2BSs 1, 3 and 4 is related to the activation of viral oncogene expression in cervical lesions as long as the viral genome remains in the episomal state. Once the virus becomes integrated into host cell chromosomes these methylation patterns may be substantially altered due to complex epigenetic changes of integrated HPV genomes.
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Affiliation(s)
- Arkom Chaiwongkot
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Clarke MA, Wentzensen N, Mirabello L, Ghosh A, Wacholder S, Harari A, Lorincz A, Schiffman M, Burk RD. Human papillomavirus DNA methylation as a potential biomarker for cervical cancer. Cancer Epidemiol Biomarkers Prev 2012; 21:2125-37. [PMID: 23035178 DOI: 10.1158/1055-9965.epi-12-0905] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sexually transmitted carcinogenic human papillomavirus (HPV) infections are extraordinarily prevalent worldwide. However, most incident HPV infections clear within a few years, whereas a small minority persists to invasive cancer. Recent studies indicate that detection of methylated viral DNA may distinguish women with cervical intraepithelial neoplasia grade 2+ (CIN2+) from those with a carcinogenic HPV-type infection that shows no evidence of CIN2+. Several studies have reported a positive association between methylation of CpG sites in the L1 gene and CIN2+, although there are inconclusive results about methylation of CpG sites in the upstream regulatory region (URR). In this review, we summarize the current state of knowledge on HPV DNA methylation in cervical carcinogenesis, and discuss the merits of different methods used to measure HPV DNA methylation. To follow the promising leads, we suggest future studies to validate the use of methylated carcinogenic HPV DNA as a predictive and/or diagnostic biomarker for risk of cervical cancer among HPV-positive women.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
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