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Nilyanimit P, Chansaenroj J, Poomipak W, Praianantathavorn K, Payungporn S, Poovorawan Y. Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR. Ann Lab Med 2018; 38:139-146. [PMID: 29214758 PMCID: PMC5736673 DOI: 10.3343/alm.2018.38.2.139] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/09/2017] [Accepted: 11/02/2017] [Indexed: 11/19/2022] Open
Abstract
Background Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Methods Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Results Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Conclusions Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations.
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Affiliation(s)
- Pornjarim Nilyanimit
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok
| | - Witthaya Poomipak
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok.
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2
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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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3
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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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4
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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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5
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da Fonseca AJ, Galvão RS, Miranda AE, Ferreira LCDL, Chen Z. Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing. J Med Virol 2015; 88:888-94. [PMID: 26496186 DOI: 10.1002/jmv.24413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2015] [Indexed: 11/10/2022]
Abstract
To compare the diagnostic performance for HPV infection using three laboratorial techniques. Ninty-five cervicovaginal samples were randomly selected; each was tested for HPV DNA and genotypes using 3 methods in parallel: Multiplex-PCR, the Nested PCR followed by Sanger sequencing, and the Next_Gen Sequencing (NGS) with two assays (NGS-A1, NGS-A2). The study was approved by the Brazilian National IRB (CONEP protocol 16,800). The prevalence of HPV by the NGS assays was higher than that using the Multiplex-PCR (64.2% vs. 45.2%, respectively; P = 0.001) and the Nested-PCR (64.2% vs. 49.5%, respectively; P = 0.003). NGS also showed better performance in detecting high-risk HPV (HR-HPV) and HPV16. There was a weak interobservers agreement between the results of Multiplex-PCR and Nested-PCR in relation to NGS for the diagnosis of HPV infection, and a moderate correlation for HR-HPV detection. Both NGS assays showed a strong correlation for detection of HPVs (k = 0.86), HR-HPVs (k = 0.91), HPV16 (k = 0.92) and HPV18 (k = 0.91). NGS is more sensitive than the traditional Sanger sequencing and the Multiplex PCR to genotype HPVs, with promising ability to detect multiple infections, and may have the potential to establish an alternative method for the diagnosis and genotyping of HPV.
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Affiliation(s)
- Allex Jardim da Fonseca
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, University of State of Amazonas, Manaus, Brazil.,Center of Infectious Diseases Research, Federal University of Espírito Santo, Vitória, Brazil
| | - Renata Silva Galvão
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, University of State of Amazonas, Manaus, Brazil
| | | | | | - Zigui Chen
- Department of Microbiology & Immunology, Epidemiology & Population Health, and Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine, New York.,Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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6
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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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7
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Galvan SC, García Carrancá A, Song J, Recillas-Targa F. Epigenetics and animal virus infections. Front Genet 2015; 6:48. [PMID: 25788901 PMCID: PMC4349154 DOI: 10.3389/fgene.2015.00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/02/2015] [Indexed: 01/13/2023] Open
Affiliation(s)
- Silvia C Galvan
- Lab Virus and Cancer, Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México Mexico City, Mexico
| | - Alejandro García Carrancá
- Lab Virus and Cancer, Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México Mexico City, Mexico ; Lab Virus and Cancer, Instituto Nacional de Cancerología, Investigación Básica Mexico City, Mexico
| | - Jiuzhou Song
- Animal and Avian Sciences, University of Maryland College Park, MD, USA
| | - Félix Recillas-Targa
- Genética Molecular, Lab Chromatin Structure and Transcription, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México Mexico City, Mexico
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