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Assessment of viral methylation levels for high risk HPV types by newly designed consensus primers PCR and pyrosequencing. PLoS One 2018; 13:e0194619. [PMID: 29579066 PMCID: PMC5868804 DOI: 10.1371/journal.pone.0194619] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/06/2018] [Indexed: 12/05/2022] Open
Abstract
Background Measuring viral DNA methylation in human papillomavirus (HPV) infected women showed promise for accurate detection of high-grade cervical lesions and cancer. Methylation status has been widely investigated for HPV16, sporadically for other HPV types. Methods Objective of this methodological study was to set up molecular methods to test the methylation levels in the twelve oncogenic HPV types by pyrosequencing, minimizing the number of HPV type-specific PCR protocols. Target CpGs were selected on the HPV L1 (two regions, L1 I and L1 II) and L2 genes. Study samples included DNA stored at Turin, Italy, purified by cervical cells collected in Standard Transport Medium or PreservCyt from women who participated in two studies (N = 126 and 140) nested within the regional organized screening programme. PCR consensus primers were designed by PyroMark Assay Design software to be suitable for amplification of many different oncogenic HPV types. Results Generation of consensus primers was successful for L1 I and II regions, unsuccessful for L2 region, for which HPV type-specific primers remained necessary. The difference between replicated tests on the same sample was ≤4% in 88%, 77% and 91% of cases when targeting the L1 I, L1 II and L2 regions, respectively. The corresponding intra-class correlation coefficients (ICC) were 0.94, 0.87 and 0.97 respectively. When comparing methylation measures based on consensus and type-specific primers, ICC was 0.97 for the L1 I region and 0.99 the for L1 II region. Conclusions The proposed protocols, applying consensus primers suitable to amplify the oncogenic HPV types and minimize the number of PCR reactions, represent a promising tool to quantify viral methylation in women positive for any high risk HPV type. Impact Potential application of these methylation protocols in screening settings can be explored to identify women with high probability of progression to high grade lesions.
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Clarke MA, Gradissimo A, Schiffman M, Lam J, Sollecito CC, Fetterman B, Lorey T, Poitras N, Raine-Bennett TR, Castle PE, Wentzensen N, Burk RD. Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women. Clin Cancer Res 2018; 24:2194-2202. [PMID: 29420222 DOI: 10.1158/1078-0432.ccr-17-3251] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/28/2017] [Accepted: 01/29/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Human papillomavirus (HPV) DNA methylation testing is a promising triage option for women testing HPV positive during cervical cancer screening. However, the extent to which methylation indicates precancer for all 12 carcinogenic HPV types has not been evaluated.Experimental Design: In this nested case-control study, we tested up to 30 cases of precancer [cervical intraepithelial neoplasia grade 3 (CIN3)/adenocarcinoma in situ (AIS)] and 30 normal controls for each carcinogenic type (single infections with 16/18/31/33/35/39/45/51/52/56/58/59). Next-generation bisulfite sequencing was performed on CpG sites within the L1 and L2 genes. We calculated differences in methylation, ORs, and AUC. Using a fixed sensitivity of 80%, we evaluated the specificity and the risk of CIN3/AIS for best performing CpG sites, and compared the performance of an explorative multi-type methylation assay with current triage strategies.Results: Methylation was positively associated with CIN3/AIS across all 12 types. AUCs for the top sites ranged from 0.71 (HPV51 and HPV56) to 0.86 (HPV18). A combined 12-type methylation assay had the highest Youden index (0.46), compared with cytology (0.31) and a 5-type methylation assay, including only previously described types (0.26). The 12-type methylation assay had higher sensitivity (80% vs. 76.6%) and lower test positivity compared with cytology (38.5% vs. 48.7%). The risk of CIN3/AIS was highest for methylation positives and lowest for cytology or HPV16/18 positives.Conclusions: HPV DNA methylation is a general phenomenon marking the transition from HPV infection to precancer for all 12 carcinogenic types. Development of a combined multitype methylation assay may serve as a triage test for HPV-positive women. Clin Cancer Res; 24(9); 2194-202. ©2018 AACR.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, MD, USA.
| | - Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, NCI, Rockville, MD, USA
| | - Jessica Lam
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York
| | | | - Barbara Fetterman
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | - Thomas Lorey
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | - Nancy Poitras
- Regional Laboratory, The Permanente Medical Group, Oakland, California
| | | | - Philip E Castle
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York
| | | | - Robert D Burk
- Departments of Epidemiology and Population Health, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York
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de Sanjosé S, Brotons M, Pavón MA. The natural history of human papillomavirus infection. Best Pract Res Clin Obstet Gynaecol 2018; 47:2-13. [DOI: 10.1016/j.bpobgyn.2017.08.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 01/14/2023]
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54
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Laengsri V, Kerdpin U, Plabplueng C, Treeratanapiboon L, Nuchnoi P. Cervical Cancer Markers: Epigenetics and microRNAs. Lab Med 2018; 49:97-111. [DOI: 10.1093/labmed/lmx080] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Vishuda Laengsri
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
| | - Usanee Kerdpin
- Department of Chemistry, Faculty of Science, Naresuan University, Phitsanulok, Thailand
| | - Chotiros Plabplueng
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
| | - Lertyot Treeratanapiboon
- Department of Community Medical Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Pornlada Nuchnoi
- Center for Research & Innovation, Mahidol University, Bangkok, Thailand
- Department of Clinical Microscopy, Mahidol University, Bangkok, Thailand
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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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Escobar-Escamilla N, Ramírez-González JE, Castro-Escarpulli G, Díaz-Quiñonez JA. Utility of high-throughput DNA sequencing in the study of the human papillomaviruses. Virus Genes 2017; 54:17-24. [PMID: 29282656 DOI: 10.1007/s11262-017-1530-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 12/19/2017] [Indexed: 11/28/2022]
Abstract
The Papillomaviridae family is probably the most diverse group of viruses that affect vertebrates. The study of the relationship between infection by certain types of human papillomavirus (HPV) and the development of neoplastic epithelial lesions is of particular interest because of the high prevalence of HPV-related carcinomas in populations of developing countries. To understand the mechanisms of infection and their association with different clinical manifestations, molecular tools play an important role in the description of new types of HPV, the characterization of effector properties of the viral factors, the specific diagnosis and monitoring of HPV types, and the alteration patterns at genetic level in the host. Technological advances in the field of DNA sequencing have led to the development of different next-generation sequencing systems, allowing obtaining a large amount of data and broadening the applications to study viral diseases. In this review, we summarize the main approaches and their perspectives where the use of massively parallel sequencing has been proved as a useful tool in the research of the HPV infection.
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Affiliation(s)
- Noé Escobar-Escamilla
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico.,Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | | | - José Alberto Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico.,División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Torres-Rojas FI, Alarcón-Romero LDC, Leyva-Vázquez MA, Ortiz-Ortiz J, Mendoza-Catalán MÁ, Hernández-Sotelo D, Del Moral-Hernández O, Rodríguez-Ruiz HA, Leyva-Illades D, Flores-Alfaro E, Illades-Aguiar B. Methylation of the L1 gene and integration of human papillomavirus 16 and 18 in cervical carcinoma and premalignant lesions. Oncol Lett 2017; 15:2278-2286. [PMID: 29434935 PMCID: PMC5776931 DOI: 10.3892/ol.2017.7596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 09/13/2017] [Indexed: 11/06/2022] Open
Abstract
High-risk human papillomavirus (HPV) is the primary cause of cervical carcinoma (CC). Viral integration into the host chromosomes is associated with neoplastic progression, and epigenetic changes may occur as a result. The objective of the present study was to analyze HPV L1 gene methylation and to compare the use of quantitative polymerase chain reaction (qPCR), in situ hybridization (ISH) and L1 methylation analysis as methods for detecting HPV integration. Cervical scrapes or biopsy samples positive for HPV 16 or 18, from 187 female patients with CC, squamous intraepithelial lesions (SILs) or no intraepithelial lesion (non-IL) were analyzed. Methylation of the L1 gene was determined using bisulfite modification followed by PCR, and HPV integration was subsequently analyzed. HPV 16 L1 gene methylation was revealed to increase with histological grade, with statistically significant differences observed as follows: Low-grade SIL vs. CC, P<0.0001 and non-IL vs. CC, P<0.0001. HPV 18 L1 gene methylation also increased according to histological grade, however, no statistically significant differences were observed. Methylation at CpG site 5608 of the HPV 16 L1 gene was associated with all grades of cervical lesions, whereas methylation at CpG site 5617 demonstrated the strongest association with CC (odds ratio, 42.5; 95% confidence interval, 4.7-1861; P<0.0001). The concordance rates between the various methods for the detection of the physical status of HPV 16 and HPV 18 were 96.1% for qPCR and ISH, 76.7% for qPCR and L1 gene methylation, and 84.8% for ISH and L1 gene methylation. In conclusion, methylation of the HPV 16 L1 gene increases significantly according to the grade of the cervical lesion, and methylation at CpG sites 5608 and 5617 of this gene may be used as prognostic biomarkers. ISH and L1 gene methylation have good concordance with qPCR with regards to the detection of HPV integration. Therefore, these are useful methods in determining the physical state of HPV.
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Affiliation(s)
- Francisco Israel Torres-Rojas
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Luz Del Carmen Alarcón-Romero
- Laboratory of Cytopathology and Histochemistry, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Marco Antonio Leyva-Vázquez
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Julio Ortiz-Ortiz
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Miguel Ángel Mendoza-Catalán
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Daniel Hernández-Sotelo
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Oscar Del Moral-Hernández
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Hugo Alberto Rodríguez-Ruiz
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Dinorah Leyva-Illades
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Eugenia Flores-Alfaro
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
| | - Berenice Illades-Aguiar
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero 39090, Mexico
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Yoshida W, Baba Y, Banzawa K, Karube I. A quantitative homogeneous assay for global DNA methylation levels using CpG-binding domain- and methyl-CpG-binding domain-fused luciferase. Anal Chim Acta 2017; 990:168-173. [PMID: 29029740 DOI: 10.1016/j.aca.2017.07.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/14/2017] [Accepted: 07/21/2017] [Indexed: 02/01/2023]
Abstract
Global DNA methylation levels have been considered as biomarkers for cancer diagnostics because transposable elements that constitute approximately 45% of the human genome are hypomethylated in cancer cells. We have previously reported a homogeneous assay for measuring methylated CpG content of genomic DNA based on bioluminescence resonance energy transfer (BRET) using methyl-CpG-binding domain (MBD)-fused luciferase (MBD-luciferase). In this study, a homogeneous assay for measuring unmethylated CpG content of genomic DNA in the same platform was developed using CXXC domain-fused luciferase (CXXC-luciferase) that specifically recognizes unmethylated CpG. In this assay, CXXC-luciferase recognizes unmethylated CpG on genomic DNA, whereby BRET between luciferase and the fluorescent DNA intercalating dye is detected. We demonstrated that the BRET signal depended on the genomic DNA concentration (R2 = 0.99) and unmethylated CpG content determined by the bisulfite method (R2 = 0.97). There was a significant negative correlation between the BRET signal of the CXXC-luciferase-based assay and that of the MBD-luciferase-based assay (R2 = 0.92). Moreover, we demonstrated that the global DNA methylation level determined using the bisulfite method was dependent on the ratio of the BRET signal in the MBD-luciferase-based assay to the total BRET signal in the MBD-luciferase- and CXXC-luciferase-based assays (R2 = 0.99, relative standard deviation < 2.2%, and analysis speed < 35 min). These results demonstrated that global DNA methylation levels can be quantified by calculating the BRET signal ratio without any calibration curve.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Yuji Baba
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Kyoko Banzawa
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo 192-0982, Japan.
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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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Highlights in nanocarriers for the treatment against cervical cancer. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 80:748-759. [PMID: 28866224 DOI: 10.1016/j.msec.2017.07.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/10/2017] [Accepted: 07/13/2017] [Indexed: 01/16/2023]
Abstract
Cervical cancer is the second most common malignant tumor in women worldwide and has a high mortality rate, especially when it is associated with human papillomavirus (HPV). In US, an estimated 12,820 cases of invasive cervical cancer and an estimated 4210 deaths from this cancer will occur in 2017. With rare and very aggressive conventional treatments, one sees in the real need of new alternatives of therapy as the delivery of chemotherapeutic agents by nanocarriers using nanotechnology. This review covers different drug delivery systems applied in the treatment of cervical cancer, such as solid lipid nanoparticles (SNLs), liposomes, nanoemulsions and polymeric nanoparticles (PNPs). The main advantages of drug delivery thus improving pharmacological activity, improving solubility, bioavailability to bioavailability reducing toxicity in the target tissue by targeting of ligands, thus facilitating new innovative therapeutic technologies in a too much needed area. Among the main disadvantage is the still high cost of production of these nanocarriers. Therefore, the aim this paper is review the nanotechnology based drug delivery systems in the treatment of cervical cancer.
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Van Keer S, Pattyn J, Tjalma WAA, Van Ostade X, Ieven M, Van Damme P, Vorsters A. First-void urine: A potential biomarker source for triage of high-risk human papillomavirus infected women. Eur J Obstet Gynecol Reprod Biol 2017; 216:1-11. [PMID: 28689156 DOI: 10.1016/j.ejogrb.2017.06.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/18/2017] [Accepted: 06/24/2017] [Indexed: 12/14/2022]
Abstract
Great interest has been directed towards the use of first-void urine as a liquid biopsy for high-risk human papillomavirus DNA testing. Despite the high correlations established between urinary and cervical infections, human papillomavirus testing is unable to distinguish between productive and transforming high-risk infections that have the tendency to progress to cervical cancer. Thus far, investigations have been primarily confined to the identification of biomarkers for triage of high-risk human papillomavirus-positive women in cervicovaginal specimens and tissue biopsies. This paper reviews urinary biomarkers for cervical cancer and triage of high-risk human papillomavirus infections and elaborates on the opportunities and challenges that have emerged regarding the use of first-void urine as a liquid biopsy for the analysis of both morphological- (conventional cytology and novel immunohistochemical techniques) and molecular-based (HPV16/18 genotyping, host/viral gene methylation, RNA, and proteins) biomarkers. A literature search was performed in PubMed and Web of Science for studies investigating the use of urine as a biomarker source for cervical cancer screening. Five studies were identified reporting on biomarkers that are still in preclinical exploratory or clinical assay development phases and on assessments of non-invasive (urine) samples. Although large-scale validation studies are still needed, we conclude that methylation of both host and viral genes in urine has been proven feasible for use as a molecular cervical cancer triage and screening biomarker in phase two studies. This is especially promising and underscores our hypothesis that human papillomavirus DNA and candidate human and viral biomarkers are washed away with the initial, first-void urine, together with exfoliated cells, debris and impurities that line the urethra opening. Similar to the limitations of self-collected cervicovaginal samples, first-void urine will likely not fulfil the high-quality cellularity standards required for morphological biomarkers. Molecular biomarkers will likely overcome this issue to yield high-throughput, objective, and reproducible results. When using proper sampling, transport, storage, preanalytical biomarker concentration techniques, and clinically validated assays, first-void urine is expected to be a valuable source of molecular biomarkers for cervical cancer screening. Furthermore, as first-void urine can be easily and non-invasively collected, it is a highly preferred technique among women and offers the ability to test both primary high-risk human papillomavirus and biomarkers in the same sample. In addition, the use of first-void urine confers opportunities to reduce loss-to follow-up and non-adherence to screening subjects.
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Affiliation(s)
- Severien Van Keer
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium
| | - Jade Pattyn
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium
| | - Wiebren A A Tjalma
- Multidisciplinary Breast Clinic, Unit Gynaecologic Oncology, Department of Obstetrics and Gynaecology, Molecular Imaging, Pathology, Radiotherapy, Oncology (MIPRO), Faculty of Medicine and Health Sciences, Antwerp University Hospital (UZA)-University of Antwerp, Belgium
| | - Xaveer Van Ostade
- Proteomics, Proteinscience, Proteomics & Epigenetic Signalling (PPES), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Belgium
| | - Margareta Ieven
- Laboratory of Medical Microbiology (LMM), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium
| | - Alex Vorsters
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), Faculty of Medicine and Health Sciences, University of Antwerp, Belgium.
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Adebamowo SN, Ma B, Zella D, Famooto A, Ravel J, Adebamowo C. Mycoplasma hominis and Mycoplasma genitalium in the Vaginal Microbiota and Persistent High-Risk Human Papillomavirus Infection. Front Public Health 2017; 5:140. [PMID: 28695118 PMCID: PMC5483445 DOI: 10.3389/fpubh.2017.00140] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/06/2017] [Indexed: 12/11/2022] Open
Abstract
Background Recent studies have suggested that the vaginal microenvironment plays a role in persistence of high-risk human papillomavirus (hrHPV) infection and thus cervical carcinogenesis. Furthermore, it has been shown that some mycoplasmas are efficient methylators and may facilitate carcinogenesis through methylation of hrHPV and cervical somatic cells. We examined associations between prevalence and persistence of Mycoplasma spp. in the vaginal microbiota, and prevalent as well as persistent hrHPV infections. Methods We examined 194 Nigerian women who were tested for hrHPV infection using SPF25/LiPA10 and we identified Mycoplasma genitalium and Mycoplasma hominis in their vaginal microbiota established by sequencing the V3–V4 hypervariable regions of the 16S rRNA gene. We defined the prevalence of M. genitalium, M. hominis, and hrHPV based on positive result of baseline tests, while persistence was defined as positive results from two consecutive tests. We used exact logistic regression models to estimate associations between Mycoplasma spp. and hrHPV infections. Results The mean (SD) age of the study participants was 38 (8) years, 71% were HIV positive, 30% M. genitalium positive, 45% M. hominis positive, and 40% hrHPV positive at baseline. At follow-up, 16% of the women remained positive for M. genitalium, 30% for M. hominis, and 31% for hrHPV. There was a significant association between persistent M. hominis and persistent hrHPV (OR 8.78, 95% CI 1.49–51.6, p 0.01). Women who were positive for HIV and had persistent M. hominis had threefold increase in the odds of having persistent hrHPV infection (OR 3.28, 95% CI 1.31–8.74, p 0.008), compared to women who were negative for both. Conclusion We found significant association between persistent M. hominis in the vaginal microbiota and persistent hrHPV in this study, but we could not rule out reverse causation. Our findings need to be replicated in larger, longitudinal studies and if confirmed, could have important diagnostic and therapeutic implications.
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Affiliation(s)
- Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States.,University of Maryland Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, United States.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Davide Zella
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, United States.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Clement Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, United States.,University of Maryland Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States.,Institute of Research Virology Nigeria, Abuja, Nigeria
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Clarke MA, Luhn P, Gage JC, Bodelon C, Dunn ST, Walker J, Zuna R, Hewitt S, Killian JK, Yan L, Miller A, Schiffman M, Wentzensen N. Discovery and validation of candidate host DNA methylation markers for detection of cervical precancer and cancer. Int J Cancer 2017; 141:701-710. [PMID: 28500655 DOI: 10.1002/ijc.30781] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/13/2017] [Indexed: 01/03/2023]
Abstract
Human papillomavirus (HPV) testing has been recently introduced as an alternative to cytology for cervical cancer screening. However, since most HPV infections clear without causing clinically relevant lesions, additional triage tests are required to identify women who are at high risk of developing cancer. We performed DNA methylation profiling on formalin-fixed, paraffin-embedded tissue specimens from women with benign HPV16 infection and histologically confirmed cervical intraepithelial neoplasia grade 3, and cancer using a bead-based microarray covering 1,500 CpG sites in over 800 genes. Methylation levels in individual CpG sites were compared using a t-test, and results were summarized by computing p-values. A total of 12 candidate genes (ADCYAP1, ASCL1, ATP10, CADM1, DCC, DBC1, HS3ST2, MOS, MYOD1, SOX1, SOX17 and TMEFF2) identified by DNA methylation profiling, plus an additional three genes identified from the literature (EPB41L3, MAL and miR-124) were chosen for validation in an independent set of 167 liquid-based cytology specimens using pyrosequencing and targeted, next-generation bisulfite sequencing. Of the 15 candidate gene markers, 10 had an area under the curve (AUC) of ≥ 0.75 for discrimination of high grade squamous intraepithelial lesions or worse (HSIL+) from <HSIL cytology using at least one assay. Overall, SOX1, DCC, and EPB41L3 showed the best discrimination with AUC values of ≥0.80, irrespective of methylation detection assay. In addition to verifying candidate markers from the literature (e.g., SOX1 and EPB41L3), we identified novel markers that may be considered for detection of cervical precancer and cancer and warrant further validation in prospective studies.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | - Julia C Gage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - S Terence Dunn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Joan Walker
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Rosemary Zuna
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Stephen Hewitt
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - J Keith Killian
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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Kottaridi C, Kyrgiou M, Pouliakis A, Magkana M, Aga E, Spathis A, Mitra A, Makris G, Chrelias C, Mpakou V, Paraskevaidis E, Panayiotides JG, Karakitsos P. Quantitative Measurement of L1 Human Papillomavirus Type 16 Methylation for the Prediction of Preinvasive and Invasive Cervical Disease. J Infect Dis 2017; 215:764-771. [PMID: 28170039 DOI: 10.1093/infdis/jiw645] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/28/2017] [Indexed: 11/15/2022] Open
Abstract
Background Methylation of the human papillomavirus (HPV) DNA has been proposed as a novel biomarker. Here, we correlated the mean methylation level of 12 CpG sites within the L1 gene, to the histological grade of cervical precancer and cancer. We assessed whether HPV L1 gene methylation can predict the presence of high-grade disease at histology in women testing positive for HPV16 genotype. Methods Pyrosequencing was used for DNA methylation quantification and 145 women were recruited. Results We found that the L1 HPV16 mean methylation (±SD) significantly increased with disease severity (cervical intraepithelial neoplasia [CIN] 3, 17.9% [±7.2] vs CIN2, 11.6% [±6.5], P < .001 or vs CIN1, 9.0% [±3.5], P < .001). Mean methylation was a good predictor of CIN3+ cases; the area under the curve was higher for sites 5611 in the prediction of CIN2+ and higher for position 7145 for CIN3+. The evaluation of different methylation thresholds for the prediction of CIN3+ showed that the optimal balance of sensitivity and specificity (75.7% and 77.5%, respectively) and positive and negative predictive values (74.7% and 78.5%, respectively) was achieved for a methylation of 14.0% with overall accuracy of 76.7%. Conclusions Elevated methylation level is associated with increased disease severity and has good ability to discriminate HPV16-positive women that have high-grade disease or worse.
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Affiliation(s)
- Christine Kottaridi
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Maria Kyrgiou
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Faculty of Medicine, Imperial College London, UK.,West London Gynaecological Cancer Center, Queen Charlotte's and Chelsea, Hammersmith Hospital, Imperial Healthcare NHS Trust, London, UK
| | - Abraham Pouliakis
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Maria Magkana
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Evangelia Aga
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Aris Spathis
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Anita Mitra
- Department of Surgery and Cancer, Institute of Reproductive and Developmental Biology, Faculty of Medicine, Imperial College London, UK.,West London Gynaecological Cancer Center, Queen Charlotte's and Chelsea, Hammersmith Hospital, Imperial Healthcare NHS Trust, London, UK
| | - George Makris
- Third Department of Obstetrics and Gynecology, University of Athens Medical School, "ATTIKON" University Hospital, Athens
| | - Charalampos Chrelias
- Third Department of Obstetrics and Gynecology, University of Athens Medical School, "ATTIKON" University Hospital, Athens
| | - Vassiliki Mpakou
- Second Department of Internal Medicine and Research Institute, University of Athens Medical School, "ATTIKON" University Hospital, Athens
| | | | - John G Panayiotides
- Second Department of Pathology, University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
| | - Petros Karakitsos
- Department of Cytopathology, National and Kapodistrian University of Athens Medical School, "ATTIKON" University Hospital, Athens, Greece
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Tota JE, Bentley J, Blake J, Coutlée F, Duggan MA, Ferenczy A, Franco EL, Fung-Kee-Fung M, Gotlieb W, Mayrand MH, McLachlin M, Murphy J, Ogilvie G, Ratnam S. Approaches for triaging women who test positive for human papillomavirus in cervical cancer screening. Prev Med 2017; 98:15-20. [PMID: 28279257 DOI: 10.1016/j.ypmed.2016.11.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/26/2016] [Indexed: 12/28/2022]
Abstract
Substantial evidence exists to support the introduction of molecular testing for human papillomavirus (HPV) as the primary technology in cervical cancer screening. While HPV testing is much more sensitive than cytology for detection of high-grade precancerous lesions, it is less specific. To improve efficiency, it is therefore recommended that a specific test (like cytology) be used in triaging HPV positive women to colposcopy. A number of studies have been conducted that support the use of cytology alone or in conjunction with HPV genotyping for triage. The decision to incorporate genotyping also depends on the commercial HPV test that is selected since not all tests provide results for certain individual high-risk types. Regardless of whether policy officials decide to adopt a triage approach that incorporates genotyping, the use of liquid based cytology (LBC) may also improve screening performance by reducing diagnostic delays. With LBC, the same cell suspension from a single collection may be used for HPV testing and a smear can be immediately prepared if HPV status is positive. This was a critical lesson from a community based demonstration project in Montreal (VASCAR study), where conventional cytology exists and specimen co-collection was not permitted for ethical reasons, requiring HPV positive women to return for an additional screening visit prior to colposcopy.
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Affiliation(s)
- Joseph E Tota
- Division of Cancer Epidemiology and Genetics, US National Cancer Institute, Rockville, MD, United States; Department of Oncology, McGill University, Montréal, Québec, Canada.
| | - James Bentley
- Department of Obstetrics & Gynecology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jennifer Blake
- Society of Obstetricians and Gynaecologists of Canada, Ottawa, Ontario, Canada
| | - François Coutlée
- Département de microbiologie et infectiologie, Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Máire A Duggan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Alex Ferenczy
- Departments of Pathology, Obstetrics & Gynecology, McGill University, Montréal, Québec, Canada
| | - Eduardo L Franco
- Department of Oncology, McGill University, Montréal, Québec, Canada; Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Michael Fung-Kee-Fung
- Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, Ontario, Canada
| | - Walter Gotlieb
- Departments of Oncology, Obstetrics & Gynecology, McGill University, Montréal, Québec, Canada
| | - Marie-Hélène Mayrand
- Département d'obstétrique-gynécologie et Médecine Sociale et Préventive, Université de Montréal, Montréal, Québec, Canada
| | - Meg McLachlin
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Joan Murphy
- Department of Obstetrics & Gynecology, University of Toronto, Toronto, Ontario, Canada
| | - Gina Ogilvie
- Departments of Family Practice, Obstetrics & Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sam Ratnam
- Department of Oncology, McGill University, Montréal, Québec, Canada; Division of Community Health and Humanities, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
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66
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Wang W, Sun Z, Liu J, Wang G, Lu Z, Zhou W, Qi T, Ruan Q. Increased methylation of human papillomavirus type 16 DNA is associated with the severity of cervical lesions in infected females from northeast China. Oncol Lett 2017; 13:3809-3816. [PMID: 28521481 DOI: 10.3892/ol.2017.5903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/26/2017] [Indexed: 02/03/2023] Open
Abstract
Hypermethylation of the cytosine-phosphate-guanine (CpG) sites located at the 3'-major capsid protein L1 (3'L1) and the long control region (LCR) of the human papillomavirus (HPV) genome may be associated with the progression of cervical cancer (CC). However, the methylation status of the LCR of HPV type 16 DNA remains to be elucidated in an infected Chinese population. The aim of the present study was to investigate the association between methylation of the HPV 16 L1 gene and LCR, and the severity of cervical lesions in infected female patients. Therefore, bisulfite modification, polymerase chain reaction amplification and sequencing were used to analyze 122 HPV 16-positive clinical cervical swabs obtained from patients in northeastern China. The proportion of methylated samples at each of the 7 CpG sites within the 3'-L1/5'-LCR and 5 CpG sites within the promoter region was significantly increased in patients with CC, compared with that observed in high-grade squamous intraepithelial lesions (HSIL) and normal tissue/low-grade intraepithelial lesions (LSIL) (χ2 test, P<0.01). The mean methylation frequencies of the CpG sites 7,089 and 7,143 exhibited an area under the curve value of 0.822 [95% confidence interval (CI)=0.733-0.911] for distinguishing CC from other lesions, 0.787 (95% CI=0.700-0.874) for distinguishing normal/LSIL from HSIL and CC, and 0.763 (95% CI=0.652-0.874) for distinguishing CC from HSIL. These results suggest that the methylation of CpG sites within the HPV 16 3'-L1 and LCR region is correlated with the severity of cervical lesions. Quantification of HPV DNA methylation in the L1 gene and promoter region appears to provide a promising novel marker for distinguishing between normal tissue/LSIL, HSIL and CC in a Chinese population.
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Affiliation(s)
- Wei Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Zhengrong Sun
- BioBank, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Jianhua Liu
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China.,Department of Clinical Laboratories, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Guili Wang
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Zhitao Lu
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Weiqiang Zhou
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Te Qi
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Qiang Ruan
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning 110004, P.R. China
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Huang J, Wang G, Tang J, Zhuang W, Wang LP, Liou YL, Liu YZ, Zhou HH, Zhu YS. DNA Methylation Status of PAX1 and ZNF582 in Esophageal Squamous Cell Carcinoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14020216. [PMID: 28241446 PMCID: PMC5334770 DOI: 10.3390/ijerph14020216] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 12/18/2022]
Abstract
Hypermethylation of specific gene promoters is an important mechanism of carcinogenesis. A high frequency of promoter methylation of PAX1 and ZNF582 genes has been detected in cervical cancer. In the present study, we investigated the methylation status of PAX1 and ZNF582 genes in esophageal squamous cell carcinoma (ESCC) tissues. Tumor and paracancerous tissues were obtained from 14 ESCC patients. Genomic DNA was extracted from both tumor and paracancerous tissues, and the concentration of DNA were determined. DNA methylation analysis of PAX1 and ZNF582 genes was carried out using quantitative methylation-specific PCR. To assess the diagnostic performance of the two methylated genes for cancer detection, receiver operating characteristic (ROC) curves were generated. Sensitivities and specificities were tested at cut-offs obtained from the ROC curves. The methylation levels of both PAX1 and ZNF582 genes were significantly higher in tumor tissues compared to non-tumor paracancerous tissues. The methylation rates of PAX1 and ZNF582 in ESCC tumor and paracancerous tissues were 100% and 21.4% (p = 0.006), 85.7% and 0% (p < 0.001), respectively. The sensitivities and specificities of PAX1 and ZNF582 methylation for the detection of cancer were 100% and 85.7%, and 78.6% and 100%, respectively. The DNA methylation levels and frequencies of PAX1 and ZNF582 genes were markedly higher in ESCC tumor tissues compared to those in paracancerous tissues. Moreover, the conclusions were verified by using The Cancer Genome Atlas (TCGA) datasets. DNA methylation status of these two genes showed a relatively good sensitivity and specificity for the detection of ESCC tumors. This data suggests that DNA methylation testing holds a great promise for ESCC screening and warrants further prospective population-based studies.
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Affiliation(s)
- Jin Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
| | - Wei Zhuang
- Department of Cardiovascular & Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Li-Ping Wang
- Department of Clinical Oncology, The First People's Hospital of Chenzhou, Chenzhou 423000, Hunan, China.
| | - Yu-Ligh Liou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
- iStat Biomedical Co. Ltd., Taipei 221, Taiwan.
| | - Ying-Zi Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
| | - Yuan-Shan Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China.
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, Hunan, China.
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Gradíssimo A, Burk RD. Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention. Expert Rev Mol Diagn 2017; 17:379-391. [PMID: 28277144 DOI: 10.1080/14737159.2017.1293525] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Human papillomavirus (HPV)-related cancers can be averted by type-specific vaccination (primary prevention) and/or through detection and ablation of precancerous cervical lesions (secondary prevention). This review presents current challenges to cervical cancer screening programs, focusing on recent molecular advances in HPV testing and potential improvements on risk stratification. Areas covered: High-risk (HR)-HPV DNA detection has been progressively incorporated into cervix cancer prevention programs based on its increased sensitivity. Advances in next-generation sequencing (NGS) are being rapidly applied to HPV typing. However, current HPV DNA tests lack specificity for identification of cervical precancer (CIN3). HPV typing methods were reviewed based on published literature, with a focus on these applications for screening and risk stratification in the emerging complex clinical scenario post-vaccine introduction. In addition, the potential for NGS technologies to increase specificity is discussed in regards to reflex testing of specimens for emerging biomarkers for cervix precancer/cancer. Expert commentary: Integrative multi-disciplinary molecular tests accurately triaging exfoliated cervical specimens will improve cervical cancer prevention programs while simplifying healthcare procedures in HPV-infected women. Hence, the concept of a 'liquid-biopsy' (i.e., 'molecular' Pap test) highly specific for early identification of cervical precancerous lesions is of critical importance in the years to come.
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Affiliation(s)
- Ana Gradíssimo
- a Department of Pediatrics (Division of Genetics) , Albert Einstein College of Medicine , Bronx , NY , USA
| | - Robert D Burk
- a Department of Pediatrics (Division of Genetics) , Albert Einstein College of Medicine , Bronx , NY , USA.,b Department of Microbiology & Immunology; Epidemiology & Population Health; and, Obstetrics, Gynecology & Women's Health , Albert Einstein College of Medicine , Bronx , NY , USA
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69
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Splicing and Polyadenylation of Human Papillomavirus Type 16 mRNAs. Int J Mol Sci 2017; 18:ijms18020366. [PMID: 28208770 PMCID: PMC5343901 DOI: 10.3390/ijms18020366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 01/29/2017] [Accepted: 02/03/2017] [Indexed: 12/24/2022] Open
Abstract
The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing. A number of cis-acting RNA elements on the HPV16 mRNAs and cellular and viral factors interacting with these elements are involved in the control of HPV16 gene expression. This review summarizes our knowledge of HPV16 cis-acting RNA elements and cellular and viral trans-acting factors that regulate HPV16 gene expression at the level of splicing and polyadenylation.
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70
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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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Senapati R, Senapati NN, Dwibedi B. Molecular mechanisms of HPV mediated neoplastic progression. Infect Agent Cancer 2016; 11:59. [PMID: 27933097 PMCID: PMC5123406 DOI: 10.1186/s13027-016-0107-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/05/2016] [Indexed: 12/15/2022] Open
Abstract
Human Papillomavirus is the major etiological agent in the development of cervical cancer but not a sufficient cause. Despite significant research, the underlying mechanisms of progression from a low-grade squamous intraepithelial lesion to high grade squamous intraepithelial lesion are yet to be understood. Deregulation of viral gene expression and host genomic instability play a central role in virus-mediated carcinogenesis. Key events such as viral integration and epigenetic modifications may lead to the deregulation of viral and host gene expression. This review has summarized the available literature to describe the possible mechanism and role of viral integration in mediating carcinogenesis. HPV integration begins with DNA damage or double strand break induced either by oxidative stress or HPV proteins and the subsequent steps are driven by the DNA damage responses. Inflammation and oxidative stress could be considered as cofactors in stimulating viral integration and deregulation of cellular and viral oncogenes during the progression of cervical carcinoma. All these events together with the host and viral genetic and epigenetic modifications in neoplastic progression have also been reviewed which may be relevant in identifying a new preventive therapeutic strategy. In the absence of therapeutic intervention for HPV-infected individuals, future research focus should be directed towards preventing and reversing of HPV integration. DNA damage response, knocking out integrated HPV sequences, siRNA approach, modulating the selection mechanism of cells harboring integrated genomes and epigenetic modifiers are the possible therapeutic targets.
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Affiliation(s)
- Rashmirani Senapati
- Virology Division, Regional Medical Research centre (ICMR), Nalco square, Chandrasekharpur, Bhubaneswar, 751023 Odisha India
| | | | - Bhagirathi Dwibedi
- Virology Division, Regional Medical Research centre (ICMR), Nalco square, Chandrasekharpur, Bhubaneswar, 751023 Odisha India
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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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73
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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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5-aza-2'-deoxycytidine (DAC) treatment downregulates the HPV E6 and E7 oncogene expression and blocks neoplastic growth of HPV-associated cancer cells. Oncotarget 2016; 8:52104-52117. [PMID: 28881717 PMCID: PMC5581016 DOI: 10.18632/oncotarget.10631] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/03/2016] [Indexed: 11/25/2022] Open
Abstract
High-risk human papillomaviruses (hr HPVs) may cause various human cancers and associated premalignant lesions. Transformation of the host cells is triggered by overexpression of the viral oncogenes E6 and E7 that deregulate the cell cycle and induce chromosomal instability. This process is accompanied by hypermethylation of distinct CpG sites resulting in silencing of tumor suppressor genes, inhibition of the viral E2 mediated control of E6 and E7 transcription as well as deregulated expression of host cell microRNAs. Therefore, we hypothesized that treatment with demethylating agents might restore those regulatory mechanisms. Here we show that treatment with 5-aza-2′-deoxycytidine (DAC) strongly decreases the expression of E6 and E7 in a panel of HPV-transformed cervical cancer and head and neck squamous cell carcinoma cell lines. Reduction of E6 and E7 further resulted in increased target protein levels including p53 and p21 reducing the proliferation rates and colony formation abilities of the treated cell lines. Moreover, DAC treatment led to enhanced expression of tumor the suppressive miRNA-375 that targets and degrades E6 and E7 transcripts. Therefore, we suggest that DAC treatment of HPV-associated cancers and respective precursor lesions may constitute a targeted approach to subvert HPV oncogene functions that deserves testing in clinical trials.
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Yoshida W, Yoshioka H, Bay DH, Iida K, Ikebukuro K, Nagasawa K, Karube I. Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction. Anal Chem 2016; 88:7101-7. [PMID: 27351368 DOI: 10.1021/acs.analchem.6b00982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA methylation has been proposed as one of the promising biomarkers for cancer diagnosis. In this study, we developed a DNA methylation detection system utilizing G-quadruplex and i-motif-forming sequences that requires neither sodium bisulfite treatment nor methylated DNA ligands. We hypothesized that G-quadruplex and i-motif structures would be stabilized by DNA methylation and arrest DNA polymerase activity during quantitative polymerase chain reaction (qPCR). The PCR products from VEGF, RET G-quadruplex, and i-motif-forming sequences were used as templates and analyzed by qPCR. Our results indicated that the initial elongation efficiency of PCR decreased with increasing DNA methylation levels in the G-quadruplex and i-motif-forming sequences. Moreover, we demonstrated that the initial elongation efficiency of PCR decreased with increased DNA methylation of the VEGF region on genomic DNA. These results indicated that DNA methylation of the G-quadruplex and i-motif-forming sequences on genomic DNA can be detected by qPCR.
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Affiliation(s)
- Wataru Yoshida
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Hitomi Yoshioka
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Daniyah Habiballah Bay
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.,Biology Department, Umm Al-Qura University , P.O. Box 715, Makkah, 21955, Kingdom of Saudi Arabia
| | - Keisuke Iida
- Graduate School of Science and Engineering, Saitama University , Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Isao Karube
- School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
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76
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Prigge ES, von Knebel Doeberitz M, Reuschenbach M. Clinical relevance and implications of HPV-induced neoplasia in different anatomical locations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 772:51-66. [PMID: 28528690 DOI: 10.1016/j.mrrev.2016.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/11/2016] [Accepted: 06/20/2016] [Indexed: 01/26/2023]
Abstract
Human papillomaviruses (HPV) are widespread DNA viruses that can infect epithelial cells of the skin and mucosa. Most HPV infections remain clinically unapparent and clear spontaneously. In few cases, however, HPV infections persist and can cause benign and malignant neoplasms at different anatomic locations. Malignant HPV-induced neoplasms are caused by distinct types of HPV (oncogenic or high-risk (HR) HPV types) and present in the anogenital (anus, penis, uterine cervix, vagina and vulva) and head and neck (particularly oropharynx) region. In the anogenital region defined precancerous stages precede invasive cancer. In the head and neck region there is clear evidence only for the invasive stage of HPV-induced neoplasia. In early infection stages the HPV oncogenes (E6/E7) are under tight control in the basal and parabasal cell layers. In more advanced precancerous stages increased expression of the HPV oncogenes E6 and E7 occurs (transforming infection) that may result in transformation of these cells. The defined carcinogenesis in the anogenital tract enables cancer early detection, particularly at the uterine cervix where cytologic and molecular tests contribute to early diagnosis and treatment at a non-invasive stage. Up to now, the treatment of HPV-related precancerous stages (high-grade intraepithelial neoplasia) and cancer is not specifically targeting molecular characteristics of the virus. This article reviews the current state and new developments in epidemiology, prevention, diagnosis and treatment of HPV-associated neoplasia in various anatomic locations.
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Affiliation(s)
- Elena Sophie Prigge
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, and Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, and Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miriam Reuschenbach
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, and Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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77
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Liu MY, Zhang H, Hu YJ, Chen YW, Zhao XN. Identification of key genes associated with cervical cancer by comprehensive analysis of transcriptome microarray and methylation microarray. Oncol Lett 2016; 12:473-478. [PMID: 27347167 PMCID: PMC4907103 DOI: 10.3892/ol.2016.4658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/17/2016] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is the second most commonly diagnosed type of cancer and the third leading cause of cancer-associated mortality in women. The current study aimed to determine the genes associated with cervical cancer development. Microarray data (GSE55940 and GSE46306) were downloaded from Gene Expression Omnibus. Overlapping genes between the differentially expressed genes (DEGs) in GSE55940 (identified by Limma package) and the differentially methylated genes were screened. Gene Ontology (GO) enrichment analysis was subsequently performed for these genes using the ToppGene database. In GSE55940, 91 downregulated and 151 upregulated DEGs were identified. In GSE46306, 561 overlapping differentially methylated genes were obtained through the differential methylation analysis at the CpG site level, CpG island level and gene level. A total of 5 overlapping genes [dipeptidyl peptidase 4 (DPP4); endothelin 3 (EDN3); fibroblast growth factor 14 (FGF14); tachykinin, precursor 1 (TAC1); and wingless-type MMTV integration site family, member 16 (WNT16)] between the 561 overlapping differentially methylated genes and the 242 DEGs were identified, which were downregulated and hypermethylated simultaneously in cervical cancer samples. Enriched GO terms were receptor binding (involving DPP4, EDN3, FGF14, TAC1 and WNT16), ameboidal-type cell migration (DPP4, EDN3 and TAC1), mitogen-activated protein kinase cascade (FGF14, EDN3 and WNT16) and cell proliferation (EDN3, WNT16, DPP4 and TAC1). These results indicate that DPP4, EDN3, FGF14, TAC1 and WNT16 may be involved in the pathogenesis of cervical cancer.
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Affiliation(s)
- Ming-Yan Liu
- Department of Gynecology and Oncology, Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin 300100, P.R. China
| | - Hong Zhang
- Department of Gynecology and Oncology, Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin 300100, P.R. China
| | - Yuan-Jing Hu
- Department of Gynecology and Oncology, Tianjin Central Hospital of Gynecology and Obstetrics, Tianjin 300100, P.R. China
| | - Yu-Wei Chen
- Department of Obstetrics and Gynecology, Graduate School of Tianjin Medical University, Tianjin 300100, P.R. China
| | - Xiao-Nan Zhao
- Department of Obstetrics and Gynecology, Graduate School of Tianjin Medical University, Tianjin 300100, P.R. China
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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79
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Curcumin Nanoformulation for Cervical Cancer Treatment. Sci Rep 2016; 6:20051. [PMID: 26837852 PMCID: PMC4738284 DOI: 10.1038/srep20051] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/23/2015] [Indexed: 12/12/2022] Open
Abstract
Cervical cancer is one of the most common cancers among women worldwide. Current standards of care for cervical cancer includes surgery, radiation, and chemotherapy. Conventional chemotherapy fails to elicit therapeutic responses and causes severe systemic toxicity. Thus, developing a natural product based, safe treatment modality would be a highly viable option. Curcumin (CUR) is a well-known natural compound, which exhibits excellent anti-cancer potential by regulating many proliferative, oncogenic, and chemo-resistance associated genes/proteins. However, due to rapid degradation and poor bioavailability, its translational and clinical use has been limited. To improve these clinically relevant parameters, we report a poly(lactic-co-glycolic acid) based curcumin nanoparticle formulation (Nano-CUR). This study demonstrates that in comparison to free CUR, Nano-CUR effectively inhibits cell growth, induces apoptosis, and arrests the cell cycle in cervical cancer cell lines. Nano-CUR treatment modulated entities such as miRNAs, transcription factors, and proteins associated with carcinogenesis. Moreover, Nano-CUR effectively reduced the tumor burden in a pre-clinical orthotopic mouse model of cervical cancer by decreasing oncogenic miRNA-21, suppressing nuclear β-catenin, and abrogating expression of E6/E7 HPV oncoproteins including smoking compound benzo[a]pyrene (BaP) induced E6/E7 and IL-6 expression. These superior pre-clinical data suggest that Nano-CUR may be an effective therapeutic modality for cervical cancer.
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80
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Bava SV, Thulasidasan AKT, Sreekanth CN, Anto RJ. Cervical cancer: A comprehensive approach towards extermination. Ann Med 2016; 48:149-61. [PMID: 26911282 DOI: 10.3109/07853890.2016.1145796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human Papilloma Virus (HPV) is one of the most common sexually transmitted pathogen, globally. Oncogenic types of HPV are the causative agents of many neoplastic diseases, including cervical cancer, which ranks as the most common cancer affecting females in developing countries. HPV infection of the cervical epithelium and the subsequent integration of viral DNA into the host genome are the major risk factors for cervical cancer. The scientific discovery of HPV as the causal agent of cervical cancer has led to the development of HPV-based diagnostic tools. Prophylactic vaccines, based on the oncogenic HPV type virus-like particles have been introduced in several developed countries as a preliminary preventive approach. Nevertheless, it remains a continuous threat to women in developing countries, where the prophylactic vaccines are unaffordable and organized screening programmes are lacking. This warrants implementation of prevention strategies that will reduce cervical cancer-related mortality. In this review, we have discussed molecular pathogenesis of HPV infection and the risk factors associated with it. The diagnosis, treatment and prevention strategies of HPV-related cervical cancer have also been discussed.
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Affiliation(s)
- Smitha V Bava
- a Department of Biotechnology , University of Calicut , Malappuram , Kerala , India
| | - Arun Kumar T Thulasidasan
- b Cancer Research Program, Division of Cancer Research , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - Chanickal N Sreekanth
- b Cancer Research Program, Division of Cancer Research , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
| | - Ruby John Anto
- b Cancer Research Program, Division of Cancer Research , Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram , Kerala , India
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81
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Cullen M, Boland JF, Schiffman M, Zhang X, Wentzensen N, Yang Q, Chen Z, Yu K, Mitchell J, Roberson D, Bass S, Burdette L, Machado M, Ravichandran S, Luke B, Machiela MJ, Andersen M, Osentoski M, Laptewicz M, Wacholder S, Feldman A, Raine-Bennett T, Lorey T, Castle PE, Yeager M, Burk RD, Mirabello L. Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2015; 1:3-11. [PMID: 26645052 PMCID: PMC4669577 DOI: 10.1016/j.pvr.2015.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 05/27/2015] [Indexed: 11/27/2022]
Abstract
For unknown reasons, there is huge variability in risk conferred by different HPV types and, remarkably, strong differences even between closely related variant lineages within each type. HPV16 is a uniquely powerful carcinogenic type, causing approximately half of cervical cancer and most other HPV-related cancers. To permit the large-scale study of HPV genome variability and precancer/cancer, starting with HPV16 and cervical cancer, we developed a high-throughput next-generation sequencing (NGS) whole-genome method. We designed a custom HPV16 AmpliSeq™ panel that generated 47 overlapping amplicons covering 99% of the genome sequenced on the Ion Torrent Proton platform. After validating with Sanger, the current "gold standard" of sequencing, in 89 specimens with concordance of 99.9%, we used our NGS method and custom annotation pipeline to sequence 796 HPV16-positive exfoliated cervical cell specimens. The median completion rate per sample was 98.0%. Our method enabled us to discover novel SNPs, large contiguous deletions suggestive of viral integration (OR of 27.3, 95% CI 3.3-222, P=0.002), and the sensitive detection of variant lineage coinfections. This method represents an innovative high-throughput, ultra-deep coverage technique for HPV genomic sequencing, which, in turn, enables the investigation of the role of genetic variation in HPV epidemiology and carcinogenesis.
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Affiliation(s)
- Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Xijun Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Zigui Chen
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Moara Machado
- Department de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sarangan Ravichandran
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
| | - Brian Luke
- Frederick National Laboratory for Cancer Research, Simulation, Analysis and Mathematical Modeling Group Advanced Biomedical Computing Center, Frederick, MD, USA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mark Andersen
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Matt Osentoski
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Michael Laptewicz
- Thermo Fisher Scientific (Formerly Life Technologies), Carlsbad, CA, USA
| | - Sholom Wacholder
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ashlie Feldman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Tina Raine-Bennett
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas Lorey
- Regional Laboratory and Women’s Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Philip E. Castle
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
- Global Coalition Against Cervical Cancer, Arlington, VA, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, At Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women’s Health, at Albert Einstein College of Medicine, Bronx, NY, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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82
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Triage of HPV positive women in cervical cancer screening. J Clin Virol 2015; 76 Suppl 1:S49-S55. [PMID: 26643050 DOI: 10.1016/j.jcv.2015.11.015] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/05/2015] [Accepted: 11/10/2015] [Indexed: 02/07/2023]
Abstract
Despite HPV vaccines, screening will remain central for decades to control cervical cancer. Recently, HPV testing alone or with cytology was introduced as an alternative to cytology screening. However, most HPV infections are harmless and additional tests are required to identify women with progressing infections or precancer. With three options for primary screening, and without clear strategies for triage of screen-positive women, there is great confusion about the best approach. Also, increasing HPV vaccination coverage will lead to lower disease prevalence, and force new screening approaches. Currently recommended triage strategies for primary HPV screening include HPV genotyping for HPV16 and HPV18 and cytology. Other alternatives that are currently evaluated include p16/Ki-67 dual stain cytology, host methylation, and viral methylation testing. Clinical management of women with cervical cancer screening results is moving to use risk thresholds rather than individual test results. Specific risk thresholds have been defined for return to primary screening, repeat testing, referral to colposcopy, and immediate treatment. Choice of test algorithms is based on comparison of absolute risk estimates from triage tests with established clinical thresholds. Importantly, triage tests need to be evaluated together with the primary screening test and the downstream clinical management. An optimal integrated screening and triage strategy should reassure the vast majority of women that they are at very low risk of cervical cancer, send the women at highest risk to colposcopy at the right time, when disease can be colposcopically detected, and minimize the intermediate risk group that requires continued surveillance.
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83
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Ma Y, Zhang H, Liu F, Wu Z, Lu S, Jin Q, Zhao J, Zhong X, Mao H. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method. NANOSCALE 2015; 7:17547-17555. [PMID: 26446775 DOI: 10.1039/c5nr04956c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers.
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Affiliation(s)
- Yunfei Ma
- Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, 200237, PR China.
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84
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Qiu C, Zhi Y, Shen Y, Gong J, Li Y, Rong S, Okunieff P, Zhang L, Li X. Performance of the HPV-16 L1 methylation assay and HPV E6/E7 mRNA test for the detection of squamous intraepithelial lesions in cervical cytological samples. J Virol Methods 2015; 224:35-41. [PMID: 26297960 DOI: 10.1016/j.jviromet.2015.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 08/07/2015] [Accepted: 08/14/2015] [Indexed: 01/19/2023]
Abstract
HPV-16 L1 methylation and E6/E7 mRNA have suggested that they had close relationship with cervical neoplastic progression. This study aimed to evaluate the clinical performance of the HPV-16 L1 methylation assay and E6/E7 mRNA test for detecting high-grade cervical lesions (CIN2+). A total of 81 women with liquid-based cytology (LBC) samples, histological results, and positive HPV-DNA test for HPV type 16 only were included in this study. HPV-16 L1 methylation and E6/E7 mRNA levels were measured using methylation-sensitive high resolution melting (MS-HRM) analysis and Quantivirus®HPV E6/E7 RNA 3.0 assay (bDNA), respectively, in the same residue of LBC samples. The current date showed a positive correlation between the HPV-16 L1 methylation and the E6/E7 mRNA levels. The L1 methylation and mRNA levels both increased with disease severity. The mRNA test method showed higher sensitivity and NPV (98.0 and 91.7% vs. 89.8 and 80.8%), while lower specificity and PPV (34.4 and 69.6% vs. 65.6 and 80.0%), than the L1 methylation assay for detecting histology-confirmed CIN2+. When using the detection method of mRNA test combined with L1 methylation assay, we obtained a sensitivity of 89.8% and a specificity of 71.9%. These findings suggest that assessment of HPV-16 L1 methylation testing combined with E6/E7 mRNA testing may be a promising method for the triage of women with HPV type 16 only.
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Affiliation(s)
- Cui Qiu
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yanfang Zhi
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yong Shen
- The Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Street, Jinshui District, Zhengzhou 450008, China
| | - Jiaomei Gong
- The Second Affiliated Hospital of Zhengzhou University, No. 2 Jingba Street, Guancheng Hui District, Zhengzhou 450014, China
| | - Ya Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Shouhua Rong
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Paul Okunieff
- University of Florida Shands Cancer Center, Gainesville, FL, USA
| | - Lulu Zhang
- Engineering Research Center of Microbial Tumer Marker and Drug Sensitive Test, Xinxiang, Henan, 453400, China
| | - Xiaofu Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China.
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85
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van Baars R, van der Marel J, Snijders PJF, Rodriquez-Manfredi A, ter Harmsel B, van den Munckhof HAM, Ordi J, del Pino M, van de Sandt MM, Wentzensen N, Meijer CJLM, Quint WGV. CADM1 and MAL methylation status in cervical scrapes is representative of the most severe underlying lesion in women with multiple cervical biopsies. Int J Cancer 2015. [PMID: 26219541 DOI: 10.1002/ijc.29706] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent studies have shown that CADM1/MAL methylation levels in cervical scrapes increase with severity and duration of the underlying cervical intraepithelial neoplasia (CIN) lesion. Multiple lesions of different histological grades and duration are frequently present on the cervix. To gain more insight into the possible epigenetic heterogeneity and its consequences for the methylation status in cervical scrapes, we performed an exploratory study of CADM1/MAL methylation in different grades of CIN lesions present in women with multiple cervical biopsies. CADM1-M18 and MAL-M1 methylation was assessed using a standardised, multiplex, quantitative methylation specific PCR on 178 biopsies with various grades of CIN in 65 women, and in their corresponding cervical scrapes. CADM1/MAL methylation positivity increased with disease severity, from 5.5% in normal biopsies to 63.3% and 100% in biopsies with CIN3 and cervical cancer, respectively. In the majority (8/9) of women where besides a CIN2/3 lesion a biopsy from normal cervical tissue was present, the CIN2/3 biopsy was CADM1/MAL methylation positive and the normal biopsy was CADM1/MAL methylation negative. A good concordance (78%) was found between CADM1/MAL methylation results on the scrapes and the biopsy with the worst diagnosis, particularly between samples of women with CIN3 and cervical cancer (92% and 100% concordance, respectively). Thus, in women with multiple cervical biopsies, CADM1/MAL methylation increases with severity of the lesion and is lesion-specific. CADM1/MAL methylation status in cervical scrapes appears to be representative of the worst underlying lesion, particularly for CIN3 and cervical cancer.
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Affiliation(s)
| | | | - Peter J F Snijders
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | | | | | - Jaume Ordi
- Department of Pathology, CRESIB (Centre De Recerca En Salut Internacional De Barcelona)-Hospital Clinic, Faculty of Medicine-University of Barcelona, Barcelona, Spain
| | - Marta del Pino
- Department of Obstetrics and Gynaecology, Hospital Clínic, Barcelona, Spain
| | | | - N Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Chris J L M Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Wim G V Quint
- DDL Diagnostic Laboratory, Rijswijk, The Netherlands
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86
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HPVbase--a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep 2015. [PMID: 26205472 PMCID: PMC4513345 DOI: 10.1038/srep12522] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human papillomaviruses (HPVs) are extremely associated with different carcinomas. Despite consequential accomplishments, there is still need to establish more promising biomarkers to discriminate cancerous progressions. Therefore, we have developed HPVbase (http://crdd.osdd.net/servers/hpvbase/), a comprehensive resource for three major efficacious cancer biomarkers i.e. integration and breakpoint events, HPVs methylation patterns and HPV mediated aberrant expression of distinct host microRNAs (miRNAs). It includes clinically important 1257 integrants and integration sites from different HPV types i.e. 16, 18, 31, 33 and 45 associated with distinct histological conditions. An inclusive HPV integrant and breakpoints browser was designed to provide easy browsing and straightforward analysis. Our study also provides 719 major quantitative HPV DNA methylation observations distributed in 5 distinct HPV genotypes from higher to lower in numbers namely HPV 16 (495), HPV 18 (113), HPV45 (66), HPV 31 (34) and HPV 33 (11). Additionally, we have curated and compiled clinically significant aberrant expression profile of 341 miRNAs including their target genes in distinct carcinomas, which can be utilized for miRNA therapeutics. A user-friendly web interface has been developed for easy data retrieval and analysis. We foresee that HPVbase an integrated and multi-comparative platform would facilitate reliable cancer diagnostics and prognosis.
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87
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Höfler D, Böhmer G, von Wasielewski R, Neumann H, Halec G, Holzinger D, Dondog B, Gissmann L, Pawlita M, Schmitt M. HPV16 RNA patterns defined by novel high-throughput RT-qPCR as triage marker in HPV-based cervical cancer precursor screening. Gynecol Oncol 2015; 138:676-82. [PMID: 26148764 DOI: 10.1016/j.ygyno.2015.06.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Cervical cancer precursor screening by HPV testing has a low positive predictive value for advanced lesion. HPV16 RNA patterns characteristic for HPV16-transformed cells but based on laborious, cost-intensive singleplex NASBA reactions promised high value in triaging HPV16 DNA-positive women. METHODS We developed two high-throughput reverse transcriptase quantitative (RT-q) PCR assays for the HPV16 transcripts E6*I, E1^E4 and E1C and the cellular transcript ubiquitin C and analysed RNA of 158 singly HPV16 DNA-positive cervical cell samples archived in PreservCyt buffer for the presence of transformation-associated HPV16 RNA patterns, i.e., upregulation of E6*I relative to E1^E4 and/or presence of E1C. RESULTS HPV16 RNA pattern analyses classified 85% of 58 samples diagnosed ≤CIN1 (no cytologically and histologically detectable cervical lesion or CIN grade 1) as negative and 90% of 59 samples diagnosed as ≥CIN3 (CIN grade 3 or invasive cancer) as positive. Among 41 CIN grade 2 samples representing an intermediate lesion group, 49% were HPV16 RNA patterns-positive. Interestingly, 3 of 4 HPV16 RNA patterns-positive lesions initially diagnosed as ≤CIN1 at follow-up 5-24 months later had progressed to ≥CIN2. CONCLUSIONS We successfully developed and validated a second generation of HPV16 RNA patterns assay by rapid RT-qPCR as triage marker for HPV16 DNA-positive women offering clinical utility to distinguish between the need for immediate colposcopy and continued observation. Limited follow-up data suggests that HPV16 RNA patterns-positivity in ≤CIN1 lesions can predict disease progression.
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Affiliation(s)
- Daniela Höfler
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Gerd Böhmer
- Deutsche Klinik Bad Münder, Zentrum für IVF und Reproduktionsmedizin, Hannoversche Straße 24, 31848 Bad Münder, Germany.
| | - Reinhard von Wasielewski
- Deutsche Klinik Bad Münder, Zentrum für IVF und Reproduktionsmedizin, Hannoversche Straße 24, 31848 Bad Münder, Germany.
| | - Heinrich Neumann
- Deutsche Klinik Bad Münder, Zentrum für IVF und Reproduktionsmedizin, Hannoversche Straße 24, 31848 Bad Münder, Germany.
| | - Gordana Halec
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Dana Holzinger
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Bolormaa Dondog
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Lutz Gissmann
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
| | - Markus Schmitt
- Division of Molecular Diagnostics of Oncogenic Infections, Research Program Infection and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
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Milutin Gašperov N, Sabol I, Planinić P, Grubišić G, Fistonić I, Ćorušić A, Grce M. Methylated Host Cell Gene Promoters and Human Papillomavirus Type 16 and 18 Predicting Cervical Lesions and Cancer. PLoS One 2015; 10:e0129452. [PMID: 26057381 PMCID: PMC4461273 DOI: 10.1371/journal.pone.0129452] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 05/08/2015] [Indexed: 12/18/2022] Open
Abstract
Change in the host and/or human papillomavirus (HPV) DNA methylation profile is probably one of the main factors responsible for the malignant progression of cervical lesions to cancer. To investigate those changes we studied 173 cervical samples with different grades of cervical lesion, from normal to cervical cancer. The methylation status of nine cellular gene promoters, CCNA1, CDH1, C13ORF18, DAPK1, HIC1, RARβ2, hTERT1, hTERT2 and TWIST1, was investigated by Methylation Specific Polymerase Chain Reaction (MSP). The methylation of HPV18 L1-gene was also investigated by MSP, while the methylated cytosines within four regions, L1, 5’LCR, enhancer, and promoter of the HPV16 genome covering 19 CpG sites were evaluated by bisulfite sequencing. Statistically significant methylation biomarkers distinguishing between cervical precursor lesions from normal cervix were primarily C13ORF18 and secondly CCNA1, and those distinguishing cervical cancer from normal or cervical precursor lesions were CCNA1, C13ORF18, hTERT1, hTERT2 and TWIST1. In addition, the methylation analysis of individual CpG sites of the HPV16 genome in different sample groups, notably the 7455 and 7694 sites, proved to be more important than the overall methylation frequency. The majority of HPV18 positive samples contained both methylated and unmethylated L1 gene, and samples with L1-gene methylated forms alone had better prognosis when correlated with the host cell gene promoters’ methylation profiles. In conclusion, both cellular and viral methylation biomarkers should be used for monitoring cervical lesion progression to prevent invasive cervical cancer.
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Affiliation(s)
| | - Ivan Sabol
- Rudjer Boskovic Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - Pavao Planinić
- Department of Gynecologic Oncology, Clinic for Gynecology and Obstetrics, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Goran Grubišić
- Obstetrics and Gynaecology Clinic, Clinical Hospital “Sestre milosrdnice,” Zagreb, Croatia
| | | | - Ante Ćorušić
- Department of Gynecologic Oncology, Clinic for Gynecology and Obstetrics, Clinical Hospital Center Zagreb, Zagreb, Croatia
| | - Magdalena Grce
- Rudjer Boskovic Institute, Division of Molecular Medicine, Zagreb, Croatia
- * E-mail:
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89
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Frimer M, Sun C, McAndrew T, Smith B, Harari A, Chen Z, Mirabello L, Wentzensen N, Goldberg GL, Rodriguez AC, Schiffman M, Burk RD. HPV16 CpG methyl-haplotypes are associated with cervix precancer and cancer in the Guanacaste natural history study. Gynecol Oncol 2015; 138:94-100. [PMID: 26001326 DOI: 10.1016/j.ygyno.2015.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/02/2015] [Indexed: 01/14/2023]
Abstract
OBJECTIVE To evaluate HPV16 CpG methylation and methyl-haplotypes and their association with cervix precancer and cancer utilizing massively parallel single molecule next-generation sequencing (NGS). METHODS A nested case-control study of HPV16 positive women was performed in a prospective cohort from Guanacaste, Costa Rica designed to study the natural history of HPV and cervical neoplasia. Controls encompassed 31 women with transient infections; there were 44 cases, including 31 women with CIN3 and 13 with cervical cancer. DNA samples from exfoliated cervical cells were treated with bisulfite and four regions (E6, E2, L2 and L1) were amplified with barcoded primers and tested by NGS. CpG methylation was quantified using a bioinformatics pipeline. RESULTS Median methylation levels were significantly different between the CIN3+ cases versus controls in the E2, L2, and L1 regions. Methyl-haplotypes, specifically in 5 CpG sites included in the targeted L2 region, with the pattern "--+-+" had the highest Area Under the Curve value (AUC=88.40%) observed for CIN3 vs. CONTROLS The most significant CpG site, L2 4277, determined by bisulfite NGS had an AUC=78.62%. CONCLUSIONS This study demonstrates that NGS of bisulfite treated HPV DNA is a useful and efficient technique to survey methylation patterns in HPV16. This procedure provides quantitative information on both individual CpG sites and methyl-haplotypes that identify women with elevated present or subsequent risk for HPV16 CIN3 and cancer.
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Affiliation(s)
- Marina Frimer
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine/Montefiore Medical Center, United States.
| | - Chang Sun
- Department of Pediatrics, Albert Einstein College of Medicine, United States
| | - Thomas McAndrew
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, United States
| | - Benjamin Smith
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, United States
| | - Ariana Harari
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, United States
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, United States
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, United States
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, United States
| | - Gary L Goldberg
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine/Montefiore Medical Center, United States
| | - Ana C Rodriguez
- Proyecto Epidemiologico Guanacaste, Fundacion INCIENSA, San Jose, Costa Rica
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, United States
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, United States; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, United States; Department of Microbiology and Immunology, Albert Einstein College of Medicine, United States
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90
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Qiu C, Zhi Y, Shen Y, Gong J, Li Y, Li X. High-resolution melting analysis of HPV-16L1 gene methylation: A promising method for prognosing cervical cancer. Clin Biochem 2015; 48:855-9. [PMID: 25982893 DOI: 10.1016/j.clinbiochem.2015.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Methylation-sensitive high-resolution melting (MS-HRM) is a new technique for DNA methylation analysis, but it is rarely used for the detection of viral DNA methylation. In this study, we investigated the HPV-16L1 gene methylation that is detected by MS-HRM as a potential biomarker for prognosing cervical dysplasia and cancer. DESIGN AND METHODS A total of 114 HPV-16 infected patients (normal (17), CIN1 (25), CIN2 (29), CIN3 (32), SCC (11)) who underwent liquid-based cytology test and biopsy were included in this study. 17 cases with HPV-16 infection and negative cytologic and histologic results served as the control group. The HPV-16L1 gene methylation statuses of these samples were investigated using a methylation-sensitive high-resolution melting (MS-HRM) assay after bisulfite modification. RESULTS The HPV-16L1 gene methylation statuses of all the 114 specimens were successfully detected by MS-HRM, and we observed increasing methylation levels in severe lesions, as determined using histologic assays. In addition, the methylation levels of CIN2+ (CIN2, CIN3 and SCC) were significantly higher than that of CIN2- (normal and CIN1, P<0.001). When taking CIN2+ as the reference, our HPV-16L1 DNA methylation assay achieved 91.7% sensitivity and 59.5% specificity, respectively. CONCLUSIONS The results of the present work demonstrated that HPV-16L1 gene methylation was closely associated with cervical precancerosis and cancer. Moreover, using MS-HRM to detect HPV-16L1 gene methylation may be a powerful assay for the triage of HPV-16-positive females, which could identify patients with high risk of invasive cancer.
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Affiliation(s)
- Cui Qiu
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yanfang Zhi
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Yong Shen
- The Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Street, Jinshui District, Zhengzhou 450008, China
| | - Jiaomei Gong
- The Second Affiliated Hospital of Zhengzhou University, No. 2 Jingba Street, Guancheng Hui District, Zhengzhou 450014, China
| | - Ya Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China
| | - Xiaofu Li
- Department of Cytopathology, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou 450052, China.
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91
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RNA Binding Proteins that Control Human Papillomavirus Gene Expression. Biomolecules 2015; 5:758-74. [PMID: 25950509 PMCID: PMC4496695 DOI: 10.3390/biom5020758] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/15/2015] [Accepted: 04/21/2015] [Indexed: 12/23/2022] Open
Abstract
The human papillomavirus (HPV) life cycle is strictly linked to the differentiation program of the infected mucosal epithelial cell. In the basal and lower levels of the epithelium, early genes coding for pro-mitotic proteins and viral replication factors are expressed, while terminal cell differentiation is required for activation of late gene expression and production of viral particles at the very top of the epithelium. Such productive infections are normally cleared within 18–24 months. In rare cases, the HPV infection is stuck in the early stage of the infection. Such infections may give rise to cervical lesions that can progress to cancer, primarily cancer of the uterine cervix. Since cancer progression is strictly linked to HPV gene expression, it is of interest to understand how HPV gene expression is regulated. Cis-acting HPV RNA elements and cellular RNA-binding proteins control HPV mRNA splicing and polyadenylation. These interactions are believed to play a particularly important role in the switch from early to late gene expression, thereby contributing to the pathogenesis of HPV. Indeed, it has been shown that the levels of various RNA binding proteins change in response to differentiation and in response to HPV induced cervical lesions and cancer. Here we have compiled published data on RNA binding proteins involved in the regulation of HPV gene expression.
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92
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Schiffman M, Wentzensen N. Transitioning to a new era in cervical cancer screening. Gynecol Oncol 2015; 136:175-7. [PMID: 25680631 DOI: 10.1016/j.ygyno.2015.01.538] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/04/2015] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
Affiliation(s)
- Mark Schiffman
- Room 6e544, 9609 Medical Center Drive, Rockville, MD 20850 (MS), United States.
| | - Nicolas Wentzensen
- Room 6e544, 9609 Medical Center Drive, Rockville, MD 20850 (MS), United States.
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Louvanto K, Franco EL, Ramanakumar AV, Vasiljević N, Scibior-Bentkowska D, Koushik A, Cuzick J, Coutlée F, Lorincz AT. Methylation of viral and host genes and severity of cervical lesions associated with human papillomavirus type 16. Int J Cancer 2015; 136:E638-45. [PMID: 25203794 DOI: 10.1002/ijc.29196] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 08/06/2014] [Accepted: 08/12/2014] [Indexed: 12/19/2022]
Abstract
Methylation of human papillomavirus (HPV) and host genes may predict cervical cancer risk. We examined the methylation status of selected sites in HPV16 and human genes in DNA extracted from exfoliated cervical cell samples of 244 women harboring HPV16-positive cancer or cervical intraepithelial neoplasia (CIN) or negative for intraepithelial lesions or malignancy (NILM). We quantified the methylation of CpG sites in the HPV16 L1 gene (CpG 6367 and 6389) and in the human genes EPB41L3 (CpG 438, 427, 425) and LMX1 (CpG 260, 262, 266, 274) following bisulfite treatment and pyrosequencing. Receiver operating characteristic (ROC) curves were used to analyze the diagnostic utility of methylation level for the different sites and for a joint predictor score. Methylation in all sites significantly increased with lesion severity (p < 0.0001). Area under the curve (AUC) was highest among the CIN2/3 vs. cancer ranging from 0.786 to 0.853 among the different sites. Site-specific methylation levels strongly discriminated CIN2/3 from NILM/CIN1 and cancer from CIN2/3 (range of odds ratios [OR]: 3.69-12.76, range of lower 95% confidence bounds: 1.03-4.01). When methylation levels were mutually adjusted for each other EPB41L3 was the only independent predictor of CIN2/3 vs. NILM/CIN1 contrasts (OR = 9.94, 95%CI: 2.46-40.27). High methylation levels of viral and host genes are common among precancerous and cancer lesions and can serve as independent risk biomarkers. Methylation of host genes LMX1 and EPB41L3 and of the viral HPV16 L1 sites has the potential to distinguish among precancerous lesions and to distinguish the latter from invasive disease.
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Affiliation(s)
- Karolina Louvanto
- Department of Oncology, Division of Cancer Epidemiology, McGill University, Montreal, QC, Canada
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94
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Koeneman MM, Kruitwagen RFPM, Nijman HW, Slangen BFM, Van Gorp T, Kruse AJ. Natural history of high-grade cervical intraepithelial neoplasia: a review of prognostic biomarkers. Expert Rev Mol Diagn 2015; 15:527-46. [PMID: 25703310 DOI: 10.1586/14737159.2015.1012068] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The natural history of high-grade cervical intraepithelial neoplasia (CIN) is largely unpredictable and current histopathological examination is unable to differentiate between lesions that will regress and those that will not. Therefore, most high-grade lesions are currently treated by surgical excision, leading to overtreatment and unnecessary complications. Prognostic biomarkers may differentiate between lesions that will regress and those that will not, making individualized treatment of high-grade CIN possible. This review identifies several promising prognostic biomarkers. These biomarkers include viral genotype and viral DNA methylation (viral factors), human leukocyte antigen-subtypes, markers of lymphoproliferative response, telomerase amplification and human papillomavirus-induced epigenetic effects (host factors) and Ki-67, p53 and pRb (cellular factors). All identified biomarkers were evaluated according to their role in the natural history of high-grade CIN and according to established criteria for evaluation of biomarkers (prospective-specimen-collection, retrospective-blinded-evaluation [PROBE] criteria). None of the biomarkers meets the PROBE criteria for clinical applicability and more research on prognostic biomarkers in high-grade CIN is necessary.
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Affiliation(s)
- Margot M Koeneman
- GROW, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
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95
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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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96
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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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97
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Wang HY, Yang GF, Huang YH, Huang QW, Gao J, Zhao XDA, Huang LM, Chen HL. Reduced expression of autophagy markers correlates with high-risk human papillomavirus infection in human cervical squamous cell carcinoma. Oncol Lett 2014; 8:1492-1498. [PMID: 25202355 PMCID: PMC4156245 DOI: 10.3892/ol.2014.2417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 07/08/2014] [Indexed: 02/05/2023] Open
Abstract
Infection by an oncogenic human papillomavirus (HPV), in particular HPV16 and 18, is a high risk factor for developing cervical cancer; however, viral infection alone is not sufficient for cancer progression. Autophagy is hypothesized to be an important process during carcinogenesis. The aim of the present study was to investigate the association between autophagy and high-risk HPV (hrHPV) infection in human cervical squamous cell carcinomas (SCCs), and to analyze the clinical significance of this association. Quantum dot (QD)-based immunofluorescence histochemistry was used to detect the expression of autophagy markers, Beclin-1 and microtubule-associated proteins 1A/1B light chain 3B (LC3B) proteins, in 104 cases of cervical cancer (including 80 SCCs and 24 adenocarcinomas) and 20 normal cervical tissues. hrHPV (HPV16/18) infection was detected by QDs based fluorescence in situ hybridization in cervical cancers. The results revealed that the expression levels of Beclin-1 and LC3B were significantly lower in cervical cancer cells when compared with those of normal cervical squamous epithelial cells, and were found to negatively correlate with hrHPV infection. The expression levels of Beclin-1 and LC3B were not associated with age, tumor grade, tumor stage, tumor node metastasis stage or lymph node metastasis. However, a positive correlation was identified between Beclin-1 and LC3B protein expression. In addition, the absence of autophagy in combination with hrHPV infection may accelerate the progression of cervical SCC. In conclusion, decreased expression of Beclin-1 and LC3B may be important in cervical carcinogenesis. The hrHPV-host cell interaction may inhibit autophagy, which may aid virus duplication and infection, as well as cervical cancer development.
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Affiliation(s)
- Hua-Yi Wang
- Department of Pathology, Jingzhou Second People's Hospital, Jingzhou, Hubei 434000, P.R. China
| | - Gui-Fang Yang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yan-Hua Huang
- Department of Molecular Pathology, Wuhan Nano Tumor Diagnosis Engineering Research Center, Wuhan, Hubei 430075, P.R. China
| | - Qi-Wen Huang
- Department of Pathology, Jingzhou Second People's Hospital, Jingzhou, Hubei 434000, P.R. China
| | - Jun Gao
- Department of Molecular Pathology, Wuhan Nano Tumor Diagnosis Engineering Research Center, Wuhan, Hubei 430075, P.R. China
| | - Xian-DA Zhao
- Department of Pathology, School of Basic Medical Science, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Li-Ming Huang
- Department of Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Hong-Lei Chen
- Department of Pathology, School of Basic Medical Science, Wuhan University, Wuhan, Hubei 430071, P.R. China
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98
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Anton L, Brown AG, Bartolomei MS, Elovitz MA. Differential methylation of genes associated with cell adhesion in preeclamptic placentas. PLoS One 2014; 9:e100148. [PMID: 24963923 PMCID: PMC4070941 DOI: 10.1371/journal.pone.0100148] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/22/2014] [Indexed: 12/16/2022] Open
Abstract
Preeclampsia (PE), a hypertensive disorder of pregnancy, is hypothesized to be associated with, if not mechanistically related to abnormal placental function. However, the exact mechanisms regulating the pathogenesis of PE remain unclear. While many studies have investigated changes in gene expression in the PE placenta, the role of epigenetics in PE associated placental dysfunction remains unclear. Using the genome-wide Illumina Infinium Methylation 450 BeadChip array, we analyzed gene-specific alterations in DNA methylation in placental biopsies collected from normal pregnant women delivering at term (n = 14), with term PE (≥37 weeks; n = 19) or with preterm PE (<37 weeks, n = 12). Of the 485,582 gene loci on the array, compared to controls, 229 loci were differentially methylated in PE placentas and 3411 loci were differentially methylated in preterm PE (step up p-value <0.05 and >5% methylation difference). Functional annotation of the differentially methylated genes in preterm PE placentas revealed a 32 gene cluster in the cadherin and cell adhesion functional groups (Benjamini p<0.00001). Hypermethylation of CDH11 (p = 0.0143), COL5A1 (p = 0.0127) and TNF (p = 0.0098) and hypomethylation of NCAM1 (p = 0.0158) was associated with altered mRNA expression in preterm PE placentas. Demethylation of first trimester extravillous trophoblast cells resulted in altered CDH11 (p = 0.0087), COL5A1 (p = 0.0043), NCAM1 (p = 0.0260) and TNF (p = 0.0022) mRNA expression. These studies demonstrate aberrant methylation, correlating with disease severity, in PE placentas. Furthermore, we provide evidence that disruption of gene-specific methylation in preterm PE placentas and first trimester trophoblasts is significantly associated with altered gene expression demonstrating that epigenetic modifications early in pregnancy can have effects on trophoblast function contributing to PE.
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Affiliation(s)
- Lauren Anton
- Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Amy G. Brown
- Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marisa S. Bartolomei
- Department of Cell & Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michal A. Elovitz
- Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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99
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Sun C, McAndrew T, Smith BC, Chen Z, Frimer M, Burk RD. Characterization of HPV DNA methylation of contiguous CpG sites by bisulfite treatment and massively parallel sequencing-the FRAGMENT approach. Front Genet 2014; 5:150. [PMID: 24917876 PMCID: PMC4042685 DOI: 10.3389/fgene.2014.00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/08/2014] [Indexed: 11/13/2022] Open
Abstract
Invasive cervix cancer (ICC) is the third most common malignant tumor in women and human papillomavirus 16 (HPV16) causes more than 50% of ICC. DNA methylation is a covalent modification predominantly occurring at CpG dinucleotides and increased methylation across the HPV16 genome is strongly associated with ICC development. Next generation (Next Gen) sequencing has been proposed as a novel approach to determine DNA methylation. However, utilization of this method to survey CpG methylation in the HPV16 genome is not well described. Moreover, it provides additional information on methylation “haplotypes.” In the current study, we chose 12 random samples, amplified multiple segments in the HPV16 bisulfite treated genome with specific barcodes, inspected the methylation ratio at 31 CpG sites for all samples using Illumina sequencing, and compared the results with quantitative pyrosequencing. Most of the CpG sites were highly consistent between the two approaches (overall correlation, r = 0.92), thus verifying that Next Gen sequencing is an accurate and convenient method to survey HPV16 methylation and thus can be used in clinical samples for risk assessment. Moreover, the CpG methylation patterns (methylation haplotypes) in single molecules identified an excess of complete-and non-methylated molecules and a substantial amount of partial-methylated ones, thus indicating a complex dynamic for the mechanisms of HPV16 CpG methylation. In summary, the advantages of Next Gen sequencing compared to pyrosequencing for HPV genome methylation analyses include higher throughput, increased resolution, and improved efficiency of time and resources.
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Affiliation(s)
- Chang Sun
- Department of Pediatrics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Thomas McAndrew
- Department of Pediatrics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Benjamin C Smith
- Department of Pediatrics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine Bronx, NY, USA
| | - Marina Frimer
- Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine Bronx, NY, USA
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine Bronx, NY, USA ; Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine Bronx, NY, USA ; Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY, USA ; Department of Epidemiology and Population Health, Albert Einstein College of Medicine Bronx, NY, USA
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100
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Steenbergen RDM, Snijders PJF, Heideman DAM, Meijer CJLM. Clinical implications of (epi)genetic changes in HPV-induced cervical precancerous lesions. Nat Rev Cancer 2014; 14:395-405. [PMID: 24854082 DOI: 10.1038/nrc3728] [Citation(s) in RCA: 255] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infection of cervical epithelium with high-risk human papilloma virus (hrHPV) might result in productive or transforming cervical intraepithelial neoplasia (CIN) lesions, the morphology of which can overlap. In transforming CIN lesions, aberrations in host cell genes accumulate over time, which is necessary for the ultimate progression to cancer. On the basis of (epi)genetic changes, early and advanced transforming CIN lesions can be distinguished. This paves the way for new molecular tools for cervical screening, diagnosis and management of cervical cancer precursor lesions.
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Affiliation(s)
- Renske D M Steenbergen
- Department of Pathology, VU University Medical Center, PO box 7057, 1007 Amsterdam, The Netherlands
| | - Peter J F Snijders
- Department of Pathology, VU University Medical Center, PO box 7057, 1007 Amsterdam, The Netherlands
| | - Daniëlle A M Heideman
- Department of Pathology, VU University Medical Center, PO box 7057, 1007 Amsterdam, The Netherlands
| | - Chris J L M Meijer
- Department of Pathology, VU University Medical Center, PO box 7057, 1007 Amsterdam, The Netherlands
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