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Galati L, Di Bonito P, Marinaro M, Chiantore MV, Gheit T. HPV16 Phylogenetic Variants in Anogenital and Head and Neck Cancers: State of the Art and Perspectives. Viruses 2024; 16:904. [PMID: 38932197 PMCID: PMC11209046 DOI: 10.3390/v16060904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
HPV16 is responsible for approximately 60% and 90% of global HPV-induced cervical and oropharyngeal cancers, respectively. HPV16 intratype variants have been identified by HPV genome sequencing and classified into four phylogenetic lineages (A-D). Our understanding of HPV16 variants mostly derives from epidemiological studies on cervical cancer (CC) in which HPV16 B, C, and D lineages (previously named "non-European" variants) were mainly associated with high-grade cervical lesions and cancer. Although a predominance of HPV16 lineage A (previously named "European variants") has been observed in head and neck squamous cell carcinoma (HNSCC), epidemiological and in vitro biological studies are still limited for this tumor site. Next Generation Sequencing (NGS) of the entire HPV genome has deepened our knowledge of the prevalence and distribution of HPV variants in CC and HNSCC. Research on cervical cancer has shown that certain HPV16 sublineages, such as D2, D3, A3, and A4, are associated with an increased risk of cervical cancer, and sublineages A4, D2, and D3 are linked to a higher risk of developing adenocarcinomas. Additionally, lineage C and sublineages D2 or D3 of HPV16 show an elevated risk of developing premalignant cervical lesions. However, it is still crucial to conduct large-scale studies on HPV16 variants in different HPV-related tumor sites to deeply evaluate their association with disease development and outcomes. This review discusses the current knowledge and updates on HPV16 phylogenetic variants distribution in HPV-driven anogenital and head and neck cancers.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer, 69007 Lyon, France
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Maria Vincenza Chiantore
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Tarik Gheit
- International Agency for Research on Cancer, 69007 Lyon, France
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Gameiro SF, Salnikov MY, Zeng PYF, Barrett JW, Nichols AC, Mymryk JS. HPV16 Intratypic Variants in Head and Neck Cancers: A North American Perspective. Viruses 2023; 15:2411. [PMID: 38140652 PMCID: PMC10747106 DOI: 10.3390/v15122411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Human papillomavirus (HPV) is the major causative agent for cervical and many head and neck cancers (HNCs). HPVs randomly acquire single nucleotide polymorphisms (SNPs) that may become established via positive selection. Within an HPV type, viral isolates differing by <2% in the L1 region are termed "variants" and classified based on combinations of SNPs. Studies in cervical cancer demonstrate clear differences between HPV16 intratypic variants in terms of persistence of infection, tumor histology, cancer risk, and death. Much less is known about the frequency of HPV16 variants in HNC, and their effects on clinical outcomes. We combined HPV16 positive (HPV16+) HNC samples from a local Southwestern Ontario, Canada cohort with those from the Cancer Genome Atlas to create a larger North American cohort of 149 cases with clinical data and determined the distribution of intratypic variants and their impact on clinical outcomes. Most isolates were lineage A, sublineage A1, or A2, with roughly half exhibiting the T350G polymorphism in E6. Univariable analysis identified significant differences between 350T and 350G intratypic variants in clinical T, N, and O staging, as well as disease-free survival. Multivariable analysis failed to identify any clinical factor as a statistically significant covariate for disease-free survival differences between 350T and 350G. Significant differences in several measures of B-cell mediated immune response were also observed between 350T and 350G intratypic variants. We suggest that HPV genetic variation may be associated with HNC clinical characteristics and may have prognostic value.
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Affiliation(s)
- Steven F. Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
| | - Mikhail Y. Salnikov
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
| | - Peter Y. F. Zeng
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
| | - John W. Barrett
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Anthony C. Nichols
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Oncology, The University of Western Ontario, London, ON N6A 5W9, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Oncology, The University of Western Ontario, London, ON N6A 5W9, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
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Ilahi NE, Siddique N, Rashid MI, Noreen M, Murad S. Decoding the Genetic and Structural Features of HPV16 E5 Oncogene in Cervical Cancer Isolates from Pakistan: A Pilot Study. IRANIAN BIOMEDICAL JOURNAL 2023; 27:388-96. [PMID: 38158635 PMCID: PMC10826910 DOI: 10.61186/ibj.3884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/12/2023] [Indexed: 01/03/2024]
Abstract
Background Many anogenital cancers are caused by high-risk HPV. The most common subtype is HPV16, which is prevalent in the world, including Pakistan. Various amino acid residues in HPV16 E5 are associated with high cell cycle progression and proliferation. Lack of studies on HPV16E5 in Pakistan prompted the current study. This is the first report on the occurrence of pathogenic E5 variant of HPV16 in tissue sections obtained from invasive cervical cancerous patients in Pakistan. Methods A subset of 11 samples from HPV-positive biopsies were subjected to E5 gene amplification using PCR and analyzed using bioinformatics programs. The bioinformatics analysis detected mutations causing structural variations, which potentially contribute to the oncogenic properties of proteins. Results The two-point mutations, C3979A and G4042A, observed in isolate 11 caused the substitution of isoleucine for leucine and valine at positions 44 and 65 in E5 protein. The rest of the isolates had Leu44Val65 amino acids. Intratypic variations and phylogenetic analysis revealed that the majority of the isolates were closely clustered with European-Asian lineage. Moreover, C3979A and G4042A contributed to higher degree of interactions with host receptors, i.e. EGFR. Conclusion This is the first study reporting HPV16 variants in a Pakistani population based on variations in the E5 region. Our findings indicate that isolate 11 has a strong interaction with the intracellular domain of EGFR, which may enhance the generation of downstream signals. Since this was a pilot study to explore E5 gene mutation, future studies with large samples are absolutely needed.
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Affiliation(s)
- Naureen Ehsan Ilahi
- Atta-Ur-Rehman School of Applied Biosciences, National University of Science and Technology, H-12 Campus, Hucknall Road, Islamabad, Pakistan
- Department of Biotechnology, Virtual University of Pakistan, Rawalpindi, Pakistan
| | - Nayyer Siddique
- Department of Molecular Biology and Genetics, Khyber Medical University, Peshawar, Pakistan
| | | | - Mamoona Noreen
- Department of Zoology, The Women University Multan, Multan, Pakistan
| | - Sheeba Murad
- Atta-Ur-Rehman School of Applied Biosciences, National University of Science and Technology, H-12 Campus, Hucknall Road, Islamabad, Pakistan
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Cochicho D, Nunes A, Sobral D, Gomes JP, Esteves S, Mendonça J, Vieira L, Martins L, Cunha M, Montalvão P, Magalhães M, Gil da Costa RM, Félix A. Distribution and Clinical Significance of HPV16 Variants in Head and Neck Squamous Cell Carcinomas: Data from a Portuguese Cohort and Systematic Review. Pathobiology 2023; 90:333-343. [PMID: 37040716 DOI: 10.1159/000529723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 04/13/2023] Open
Abstract
INTRODUCTION Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aimed to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical pathological characteristics and patient survival. METHODS We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing was used to obtain whole-genome sequences, and variants were established based on phylogenetic classification. RESULTS 74% of samples clustered in lineage A, 5.7% in lineage B, 2.9% in lineage C, and 17.1% in lineage D. Comparative genome analysis revealed 243 single nucleotide variations. Of these, one hundred were previously reported, according to our systematic review. No significant associations with clinical pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V, and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. CONCLUSION These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.
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Affiliation(s)
- Daniela Cochicho
- Research Department, NOVA Medical School University, Lisbon, Portugal,
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal,
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Daniel Sobral
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Susana Esteves
- Clinical Research Unit, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Joana Mendonça
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luis Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Martins
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Mario Cunha
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Pedro Montalvão
- Otorhinolaryngology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Miguel Magalhães
- Otorhinolaryngology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Rui M Gil da Costa
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- Post-graduate Programme in Adult Health (PPGSAD), University Hospital (HUUFMA) and Morphology Department, Federal University of Maranhão, São Luís, Brazil
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Ana Félix
- Research Department, NOVA Medical School University, Lisbon, Portugal
- Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
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Pre-Vaccination Human Papillomavirus Genotypes and HPV16 Variants among Women Aged 25 Years or Less with Cervical Cancer. Pathogens 2023; 12:pathogens12030451. [PMID: 36986373 PMCID: PMC10051959 DOI: 10.3390/pathogens12030451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Background: In 2007, Australia introduced a national human papillomavirus (HPV) vaccination program. In 2017, the onset of cervical screening changed from 18 to 25 years of age, utilising human papillomavirus (HPV) nucleic acid testing. The objective of the study is to describe the HPV genotypes and HPV16 variants in biopsies from women ≤ 25 years of age with cervical carcinoma (CC) (cases), compared with those aged >25 years (controls), in a pre-vaccination cohort. Methods: HPV genotyping of archival paraffin blocks (n = 96) was performed using the INNO-LiPA HPV Genotyping assay. HPV16-positive samples were analysed for variants by type-specific PCR spanning L1, E2 and E6 regions. Results: HPV16 was the commonest genotype in cases (54.5%, 12/22) and controls (66.7%, 46/69) (p = 0.30), followed by HPV18 (36.3%, 8/22 vs. 17.3% 12/69, respectively) (p = 0.08). Furthermore, 90% (20/22) of cases and 84.1% (58/69) of controls were positive for HPV16 or 18 (p = 0.42); 100% (22/22) of cases and 95.7% (66/69) of controls had at least one genotype targeted by the nonavalent vaccine (p = 0.3). The majority of HPV16 variants (87.3%, 48/55) were of European lineage. The proportion of unique nucleotide substitutions was significantly higher in cases (83.3%, 10/12) compared with controls (34.1%, 15/44), (p < 0.003, χ2, OR 9.7, 95%CI 1.7–97.7). Conclusions: Virological factors may account for the differences in CCs observed in younger compared with older women. All CCs in young women in this study had preventable 9vHPV types, which is important messaging for health provider adherence to new cervical screening guidelines.
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Tsakogiannis D, Nikolaidis M, Zagouri F, Zografos E, Kottaridi C, Kyriakopoulou Z, Tzioga L, Markoulatos P, Amoutzias GD, Bletsa G. Mutation Profile of HPV16 L1 and L2 Genes in Different Geographic Areas. Viruses 2022; 15:141. [PMID: 36680181 PMCID: PMC9867070 DOI: 10.3390/v15010141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 01/03/2023] Open
Abstract
The causal relationship between HPV and cervical cancer in association with the high prevalence of high risk HPV genotypes led to the design of HPV vaccines based on the major capsid L1 protein. In recent years, capsid protein L2 has also become a focal point in the field of vaccine research. The present review focuses on the variability of HPV16 L1 and L2 genes, emphasizing the distribution of specific amino acid changes in the epitopes of capsid proteins. Moreover, a substantial bioinformatics analysis was conducted to describe the worldwide distribution of amino acid substitutions throughout HPV16 L1, L2 proteins. Five amino acid changes (T176N, N181T; EF loop), (T266A; FG loop), (T353P, T389S; HI loop) are frequently observed in the L1 hypervariable surface loops, while two amino acid substitutions (D43E, S122P) are adjacent to L2 specific epitopes. These changes have a high prevalence in certain geographic regions. The present review suggests that the extensive analysis of the amino acid substitutions in the HPV16 L1 immunodominant loops may provide insights concerning the ability of the virus in evading host immune response in certain populations. The genetic variability of the HPV16 L1 and L2 epitopes should be extensively analyzed in a given population.
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Affiliation(s)
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, 11528 Athens, Greece
| | - Eleni Zografos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, 11528 Athens, Greece
| | - Christine Kottaridi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Zaharoula Kyriakopoulou
- Department of Environment, School of Technology, University of Thessaly, Gaiopolis, 41500 Larissa, Greece
| | - Lamprini Tzioga
- Research Center, Hellenic Anticancer Institute, 10680 Athens, Greece
| | | | - Grigoris D. Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece
| | - Garyfalia Bletsa
- Research Center, Hellenic Anticancer Institute, 10680 Athens, Greece
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Chandra S, Goswami A, Mandal P. Molecular Heterogeneity of Cervical Cancer Among Different Ethnic/Racial Populations. J Racial Ethn Health Disparities 2022; 9:2441-2450. [PMID: 34741276 DOI: 10.1007/s40615-021-01180-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 12/29/2022]
Abstract
The study aimed to find differential gene mutation profile and gene expression status among different ethnic/racial human populations relevant for cervical cancer pathogenesis. The study was based on freely available datasets of The Cancer Genome Atlas (TCGA) of cervical cancer samples in Genomic Data Commons (GDC) data portal. We identified that choline metabolism in cancer and Ras signaling pathways were significantly associated with the Hispanic and Latino group of cervical cancer patients. In these pathways, mutations in the PIK3CA gene, especially E545K, were significantly associated with the Hispanic and LATINO group. We found that AFF3 gene mutation was associated with downregulation of its expression only among the White racial category of cervical cancer cases. Additionally, hypomethylation of the CpG position in the S shore region of the PM20D1 gene was associated with overexpression among the Asian category of cervical cancer cases. Heterogeneity of the molecular profile of AFF3 and PM20D1 gene among racial groups reflects the potential of differential targeted therapy of cervical cancer.
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Affiliation(s)
- Sanchita Chandra
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, 713104, West Bengal, India
| | - Anindita Goswami
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, 713104, West Bengal, India
| | - Paramita Mandal
- Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Burdwan, 713104, West Bengal, India.
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Characterization of the Human Papillomavirus 16 Oncogenes in K14HPV16 Mice: Sublineage A1 Drives Multi-Organ Carcinogenesis. Int J Mol Sci 2022; 23:ijms232012371. [PMID: 36293226 PMCID: PMC9604181 DOI: 10.3390/ijms232012371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
The study of human papillomavirus (HPV)-induced carcinogenesis uses multiple in vivo mouse models, one of which relies on the cytokeratin 14 gene promoter to drive the expression of all HPV early oncogenes. This study aimed to determine the HPV16 variant and sublineage present in the K14HPV16 mouse model. This information can be considered of great importance to further enhance this K14HPV16 model as an essential research tool and optimize its use for basic and translational studies. Our study evaluated HPV DNA from 17 samples isolated from 4 animals, both wild-type (n = 2) and HPV16-transgenic mice (n = 2). Total DNA was extracted from tissues and the detection of HPV16 was performed using a qPCR multiplex. HPV16-positive samples were subsequently whole-genome sequenced by next-generation sequencing techniques. The phylogenetic positioning clearly shows K14HPV16 samples clustering together in the sub-lineage A1 (NC001526.4). A comparative genome analysis of K14HPV16 samples revealed three mutations to the human papillomaviruses type 16 sublineage A1 representative strain. Knowledge of the HPV 16 variant is fundamental, and these findings will allow the rational use of this animal model to explore the role of the A1 sublineage in HPV-driven cancer.
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Wang J, Guo Y, Wang H, Li Y, Zhang L, Wang Z, Song L, Liu H. Genetic diversity of E6, E7 and the long control region in human papillomavirus type 16 variants in Beijing, China. Biochem Biophys Rep 2022; 31:101286. [PMID: 35655951 PMCID: PMC9151740 DOI: 10.1016/j.bbrep.2022.101286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Background High-risk human papillomavirus type 16 (HPV16) is a risk factor for cervical cancer. The progression from initial infection to cervical cancer has been linked to properties of the viral sequences. However, the distribution of HPV16 variants among Chinese women has not been extensively addressed and the role of HPV16 variants in the risk of cervical carcinogenesis remains poorly understood. Methods HPV16 positive cervical exfoliated cell samples were collected from 249 women living in Beijing, China. PCR products from two fragments of E6-E7 and LCR of HPV16 in these samples were sequenced and analyzed. Results Lineage A was found in the subjects, including A1, A2, A3 and A4 sublineages. Based on the HPV16 reference sequences, 26 nucleotide mutations of A4 sublineage and 39 nucleotide mutations of A1-3 sublineages were found in the E6, E7 and LCR of HPV16 isolates. Point mutations T843C, A7287C and A7872G of A4 sublineage were significantly associated with high-grade cervical lesions. The high-frequency sites in HPV16 LCR located at regions that can bind to multiple transcription factors. Conclusions This study contributes to the identification of unique variants in the E6, E7 and LCR of HPV16 isolates infected in Chinese women. Mutations of T843C, A7287C and A7872G in A4 sublineages were significantly associated with high-grade cervical lesions, suggesting that mutations in the E7 and LCR region have potential effects on viral replication and progression of cervical cancer. Lineage A is the predominant HPV16 variant in Chinese women. Based on the HPV16 prototype, 25 nucleotide mutations in E6 and E7 were found and 41 nucleotide mutations in LCR were found. The mutations of C843T, A7287C and A7872G were significantly correlated with the cervical lesions.
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Affiliation(s)
- Jiao Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Yifan Guo
- Department of Obstetrics and Gynaecology, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, Hainan Province, China
| | - Hui Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Ying Li
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Li Zhang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Zhan Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Lei Song
- Department of Obstetrics and Gynaecology, Chinese PLA General Hospital, Beijing, 100048, China
| | - Hongtu Liu
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, Wuhan, 430071, Hubei Province, China
- Chinese Center for Disease Control and Prevention-Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Wuhan, 430071, Hubei Province, China
- Corresponding author. Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China.
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Recombination in Papillomavirus: Controversy and Possibility. Virus Res 2022; 314:198756. [DOI: 10.1016/j.virusres.2022.198756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
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Genetic Diversity of HPV 16 and HPV 18 Based on Partial Long Control Region in Iranian Women. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:4759871. [PMID: 35126798 PMCID: PMC8808245 DOI: 10.1155/2022/4759871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/28/2021] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Background Human papillomavirus (HPV) 16 and HPV 18 account for 75% of all cervical cancers. The L1 gene, encoding the major surface protein (MSP), is used to classify HPV types (lineages and sublineages), genotypes, and intratypic variants. Therefore, this study aimed to investigate the lineages, sublineages, genetic variabilities, and mutation effects on transcription factor binding sites by using partial sequences of the HPV 16 and HPV 18 long control regions (LCRs) in these samples. Materials and Methods After DNA isolation from 56 positive samples, the LCR of HPV 16 and HPV 18 were amplified using specific primers, and phylogenetic trees were drawn through MEGA X. Compared to the reference sequences, single nucleotide polymorphisms (SNPs) were identified. The transcription binding sites were also evaluated using the online PROMO database. Results The LCRs of 52 samples were successfully sequenced. Overall, 81.58% of all HPV 16 variants belonged to the D1 sublineage, followed by A4 (13.16%), A1 (2.63%), and C1 (2.63%) sublineages. All HPV 18 isolates belonged to A sublineage, 92.85% to A3 sublineage, and 7.15% to A4 sublineage. Out of 27 SNPs in the HPV 16 LCR, A7382T, T7384G, C7387T, C7393G, A7431G, T7448C, and C7783A were HPV 16-specific. Also, among 14 SNPs in the HPV 18 LCR, C7577A and A7943T were not previously reported. An insertion (C) between 7432 and 7433 positions was identified in all studied HPV 16 variants. Besides, most of the HPV 16 mutations were embedded in the YY1, TFIID, Oct-2, and NF-1 binding sites, while c-Fos and MBF1, as the most common binding sites, were affected by HPV 18 LCR mutations. Conclusion The present results showed that D1 and A3 were the dominant sublineages of HPV 16 and HPV 18, respectively. Therefore, women infected with these variants need to be examined in further longitudinal studies to obtain more information about the oncogenic potential of these dominant variants in Iran. Besides, YY1, TFIID, Oct-2, NF-1, c-Fos, and MBF1 were the most frequent binding sites, which were influenced by the mutations.
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Genetic variability of the HPV16 early genes and LCR. Present and future perspectives. Expert Rev Mol Med 2021; 23:e19. [PMID: 34847982 DOI: 10.1017/erm.2021.18] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Human papillomavirus 16 (HPV16) infection is the aetiologic factor for the development of cervical dysplasia and is regarded as highly carcinogen, because it is implicated in more than 50% of cervical cancer cases, worldwide. The tumourigenic potential of HPV16 has triggered the extensive sequence analysis of viral genome in order to identify nucleotide variations and amino acid substitutions that influence viral oncogenicity and subsequently the initiation and progression of cervical cancer. Nowadays, specific mutations of HPV16 DNA have been associated with an increased risk of high-grade squamous intraepithelial lesions and invasive cervical cancer (ICC) development, including E6: Q14H, H78Y, L83V, Ε7: N29S, S63F, E2: H35Q, P219S, T310K, E5: I65V, whereas highly conserved regions of viral DNA have been extensively characterised. In addition, numerous novel HPV16 mutations are observed among the studied populations from various geographic regions, hence advocating that different HPV16 strains seem to emerge with different tumourigenic capacities. The present review focuses on the variability of the early genes and the long control region, emphasising on the association of specific mutations with the development of severe dysplasia. Finally, it evaluates whether specific regions of HPV16 DNA are able to serve as valuable biomarkers for cervical cancer risk.
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Cochicho D, Gil da Costa R, Felix A. Exploring the roles of HPV16 variants in head and neck squamous cell carcinoma: current challenges and opportunities. Virol J 2021; 18:217. [PMID: 34749746 PMCID: PMC8573856 DOI: 10.1186/s12985-021-01688-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
The incidence of squamous cell carcinomas of the head and neck (HNSCC) is consistently increasing, in association with human papillomavirus (HPV) infection, especially HPV16. HPV variants show heterogeneity in the pathogenicity of cervical cancer, but little has been established about their relevance on HNSCC. This review addresses the distribution of HPV16 variants in HNSCC and their potential contribution to clinical practice. A search was performed in PubMed using the keywords HNSCC HPV16 variants. Sixty articles were identified between 2000 and 2020 and 9 articles were selected for a systematic analysis. Clinical cohorts comprised 4 to 253 patients aged between 17 and 91 years with confirmed HPV16-positive HNSCC. Samples were collected from fresh biopsies of the tumour, oral rinse or formol fixed/paraffin embedded tissue, from the oral cavity, oropharynx, hypopharynx, larynx and Waldeyer's tonsillar ring. HPV16 variants were identified using Sanger sequencing techniques. Seven studies addressed the HPV16 E6 gene, one studied E6 and E7, another studied L1 and one focused on the long control region. European variants represent 25-95%, Asian-American 5-57% and African 2-4% of the total isolates, suggesting a marked predominance of European strains. No correlations could be drawn with patient prognosis, partly because many studies relied on small patient cohorts. Additional studies are needed, particularly those employing next generation sequencing techniques (NGS), which will allow faster and accurate analysis of large numbers of samples.
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Affiliation(s)
- Daniela Cochicho
- NOVA Medical School, NOVA University of Lisbon, CEDOC, Campo Mártires da Pátria 130, 1169-056, Lisbon, Portugal
- Virology Laboratory IPOLFG, Rua Professor Lima Bastos, 1099-023, Lisbon, Portugal
| | - Rui Gil da Costa
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
- Post-graduate Programme in Adult Health (PPGSAD), University Hospital (HUUFMA) and Morphology Department, Federal University of Maranhão, Av. dos Portugueses 1966 - Vila Bacanga, São Luís, MA, 65080-805, Brazil
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Ana Felix
- NOVA Medical School, NOVA University of Lisbon, CEDOC, Campo Mártires da Pátria 130, 1169-056, Lisbon, Portugal.
- Pathology Department IPOLFG, Rua Professor Lima Bastos, 1099-023, Lisbon, Portugal.
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Mandal P, Bhattacharjee B, Sen S, Bhattacharya A, Saha SS, Chowdhury RR, Mondal NR, Chakrabarty B, Chatterjee T, Roy S, Sengupta S. Predominance of genomically defined A lineage of HPV16 over D lineage in Indian patients from eastern India with squamous cell carcinoma of the cervix in association with distinct oncogenic phenotypes. Transl Oncol 2021; 15:101256. [PMID: 34717279 PMCID: PMC8564679 DOI: 10.1016/j.tranon.2021.101256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/28/2021] [Accepted: 10/22/2021] [Indexed: 11/25/2022] Open
Abstract
The HPV16 lineage A viruses are predominantly associated with cervical squamous cell carcinoma (SCC) in the eastern region of India. Among lineage A viruses, the E5(Y44L, I65V), E6(L83V) and LCR: C7577T variants are associated with SCC. The risk alleles are distributed among 10 clades comprising of 64 HPV16 genomes. Low integration, high episomal copy numbers and high E7 mRNA expression in SCC contrasts lineage A viruses from lineage D.
Human papillomavirus type-16 (HPV16) is classified into lineages, A, B, C and D and 10 sub-lineages portraying variable infectivity, persistence, and cytological outcomes, however, with geographical variations. Our objective was to delineate the distinctive features of lineages among cervical squamous cell carcinoma (SCC) in the eastern region of India. A total of 145 SCC cases and 24 non-malignant specimens, harboring episomal HPV16, were included. The presence of higher proportion of lineage A over D was observed among SCC cases (86.89% A1, 8.97% D1 and 4.14% D2), while only A1 sub-lineage viruses were found among control specimens. Among the A1 viruses, an association of variants in the E5 (Y44L, I65V), E6 (L83V) genes and LCR: C7577T with SCC, with combined Odd's ratio (95% CI) of 20.5(4.61–91.25) was observed. Network analyses revealed the presence of 10 clades of lineage A viruses comprising of 64 HPV16 genomes harboring the risk alleles. High episomal HPV16 DNA copy numbers (adjusted p-value= 0.0271) and E7 mRNA expression (p-value=0.000017) predominated in SCC with lineage A, over D. Our study highlights the distinctive modalities of oncogenicity among different HPV16 lineages.
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Affiliation(s)
- Paramita Mandal
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Biomedical Genetics Laboratory, Department of Zoology, The University of Burdwan, Purba Burdwan, West Bengal 713104, India
| | - Bornali Bhattacharjee
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Amity Institute of Biotechnology, Amity University Kolkata, Kolkata, India.
| | - Shrinka Sen
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Department of Medical Genetics, University of British Columbia, 4500 Oak Street, Vancouver, British Columbia V6H 3N1, Canada
| | - Amrapali Bhattacharya
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; DBT-NIDAN Kendra on Rare Genetic Diseases, N. R. S. Medical College and Hospital, 138, A. J. C. Bose Road, Kolkata 700014, India
| | - Sweta Sharma Saha
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India; Translational and Clinical Research Institute, Faculty of Medical Sciences, Centre for Cancer, Newcastle University, NE2 4HH, UK
| | | | | | | | | | | | - Sharmila Sengupta
- National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West Bengal 741251, India.
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15
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Pakdel F, Farhadi A, Pakdel T, Andishe-Tadbir A, Alavi P, Behzad-Behbahani A, Ashraf MJ. The frequency of high-risk human papillomavirus types, HPV16 lineages, and their relationship with p16 INK4a and NF-κB expression in head and neck squamous cell carcinomas in Southwestern Iran. Braz J Microbiol 2020; 52:195-206. [PMID: 33169334 DOI: 10.1007/s42770-020-00391-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/17/2020] [Indexed: 12/14/2022] Open
Abstract
High-risk human papillomaviruses (hr-HPVs) are the key risk factors implicated in the development of a significant proportion of head and neck squamous cell carcinomas (HNSCCs). We aimed to investigate the distribution of hr-HPV types and HPV16 lineages in a sample of patients with HNSCC and the possible association between HPV status and the expression of P16INK4A and NF-κB in Iranian HNSCC patients. We examined 108 formalin-fixed, paraffin-embedded (FFPE) histologically confirmed primary SCC tissue specimens of different head and neck anatomical sites. HPV types and HPV16 lineages were determined by nested PCR and overlapping nested PCR assays, respectively, followed by gene sequencing and phylogenetic analysis. The expression of p16INK4a and NF-κB was evaluated by immunohistochemistry. Twenty-five (23.1%) HNSCC tissue specimens were tested positive for HPV infection. The most prevalent HPV type was HPV-16, followed by HPV18 and HPV11. HPV16 variants belonged to the lineage A and lineage D which were further sorted into sublineages A1, A2, and D2. A significant association between HPV status and p16INK4a immunoreactivity was observed in more than 76% of the HPV-related HNSCCs (P < 0.0001). The overexpression of p16INK4a and cytoplasmic NF-κB was more common in low-grade HNSCC tumors. Our data highlights that HPV16, in particular the A2 sublineage, followed by A1 and D2 sublineages are the major agents associated with HNSCCs in Iran. Based on HPV16 predominance and its lineage distribution pattern, it seems that the prophylactic vaccines developed for cervical cancer prevention could also be applicable for the prevention of HPV-related HNSCCs in our population.
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Affiliation(s)
- Fatemeh Pakdel
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Oral and Maxillofacial Pathology, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Farhadi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Tahereh Pakdel
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azadeh Andishe-Tadbir
- Oral and Dental Disease Research Center, School of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Parnian Alavi
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad J Ashraf
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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16
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High prevalence of human papillomavirus and European variants of HPV 16 infecting concomitantly to cervix and oral cavity in HIV positive women. PLoS One 2020; 15:e0227900. [PMID: 32320400 PMCID: PMC7176371 DOI: 10.1371/journal.pone.0227900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Identify the prevalence of HPV infections in the uterine cervix and oral cavity and HPV16 variants in HIV+ women. METHODS A total of 174 HIV+ women attended an HIV+ specialized clinic in Mexico City. Cells were obtained from the oral cavity and cervix to extract DNA. Polymerase chain reaction (PCR) was used to amplify the HPV sequence with generic primers. We detected specific HPV types using the INNO-LiPA HPV Genotyping Extra II Kit (INNOGENETICS). The identification of variants was studied by sequencing the E6 gene with a Big Dye Terminator Kit and an Applied Biosystems 3500/3500xL genetic analyzer. RESULTS HPV infection was very high in the uterine cervix (168/174, 96.6%) and oral cavity (161/174, 92.5%). The prevalence of HPV concurrent infections in the cervix and oral cavity was 155/174 (89.1%). We found hrHPVs to be more prevalent than low-risk HPVs (lrHPVs) in the oral cavity (90.2% versus 45.4%) and that infections simultaneously affected the cervix (94.3% versus 36.2%) and oral cavity (85.1% versus 20.1%). Surprisingly, only European variants of HPV type 16 were found in the uterine cervix of women and the oral cavity of all tested samples (52 oral cavity samples and 52 uterine cervix samples). CONCLUSIONS The high prevalence of HPV, multiple infections and presence of the EP350G intravariant in both anatomical regions are strongly related to the persistence of the virus, which is fundamental for the development of cancer. Therefore, it is very important to control and monitor this high-risk population as well as implement programs for the early detection of HPV and vaccination.
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Álvarez-Paredes L, Santibañez M, Galiana A, Rodríguez Díaz JC, Parás-Bravo P, Andrada-Becerra ME, Ruiz García MM, Rodríguez-Ingelmo JM, Portilla-Sogorb J, Paz-Zulueta M. Association of Human Papillomavirus Genotype 16 Viral Variant and Viral Load with Cervical High-grade Intraepithelial Lesions. Cancer Prev Res (Phila) 2019; 12:547-556. [PMID: 31208965 DOI: 10.1158/1940-6207.capr-18-0397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/15/2019] [Accepted: 06/11/2019] [Indexed: 11/16/2022]
Abstract
Human papillomavirus genotype 16 (HPV16) is by far the genotype most strongly associated with cervical cancer; viral variant and/or viral load of HPV16 could modulate this association. The objective was to determine the association between the viral variant and viral load of HPV16 and the presence of cervical high-grade lesions. This cross-sectional study included all women in whom HPV infection was found by cervical smear during routine gynecologic health checks. Women with single or multiple HPV16 infections (n = 176) were selected for viral variant and viral load analysis. Smear results were classified using the Bethesda system. HPV types were classified according to the International Agency for Research on Cancer. Odds ratios (OR) with their 95% confidence intervals (CI) were estimated by logistic regression, adjusted for age, immigrant status, and coinfection with other high-risk genotypes. No statistically significant associations were found regarding the detected viral variants. A viral load above the median (>1,367.79 copies/cell) was associated with a significant risk of high-grade epithelial lesion or carcinoma, after adjusting for age, immigrant status, coinfections, and viral variant: (adjusted OR 7.89; 95% CI: 2.75-22.68). This relationship showed a statistically significant dose-response pattern after categorizing by viral load tertiles: adjusted OR for a viral load greater than the third tertile was 17.23 (95% CI: 4.20-70.65), with adjusted linear P trend = 0.001. In patients infected with HPV16, viral load is associated with high-grade intraepithelial lesions or cervical carcinoma. This could be useful as prognostic biomarker of neoplastic progression and as screening for cervical cancer.
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Affiliation(s)
| | - Miguel Santibañez
- Department of Nursing, Nursing Research Group-IDIVAL, University of Cantabria, Cantabria, Spain
| | - Antonio Galiana
- Department of Microbiology, University General Hospital of Elche, Alicante, Spain
| | | | - Paula Parás-Bravo
- Department of Nursing, Nursing Research Group-IDIVAL, University of Cantabria, Cantabria, Spain
| | | | | | | | | | - María Paz-Zulueta
- Department of Nursing, University of Cantabria, Cantabria, Spain. IDIVAL, GI Derecho Sanitario y Bioetica, GRIDES, Cantabria, Spain.
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18
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Camacho-Ureta EA, Mendez-Martínez RS, Vázquez-Vega S, Martínez UO, Arenas RS, Castillo-Ureta H, Ramírez IO, Torres Montoya EH, López Moreno HS, García-Carranca A, Rendón-Maldonado JG. High frequency of HPV16 European variant E350G among Mexican women from Sinaloa. Indian J Med Res 2018; 148:323-328. [PMID: 30425223 PMCID: PMC6251263 DOI: 10.4103/ijmr.ijmr_61_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background & objectives: Human papillomavirus (HPV) infections play a crucial role in the aetiology of cervical cancer (CC), and HPV16 is the primary viral genotype associated with CC. A number of variants of the HPV16 E6 gene are involved in the progression of CC, differing in their prevalence and biological and biochemical properties. This study was designed to determine the frequency of HPV types 16/18 and to identify the presence of HPV16 E6-variants in asymptomatic Mexican women. Methods: A total of 189 cervical Pap smears were collected from women attending public health services in three different cities in Sinaloa, Mexico. Viral DNA was identified by amplification of E6 viral gene fragments using polymerase chain reaction (PCR). Identification of variants was done by sequencing a DNA fragment (321bp) of the HPV16 E6 gene. Results: More than half of the women tested were HPV-positive (52.38%), with HPV16 being the most frequent genotype (21.16%), followed by HPV18 (8.99%). Sequence analysis of the E6-HPV16 PCR products showed that in all cases, the viruses corresponded to European variants. It was further observed that the E350G intra-variant was the most common (>76%). Interpretation & conclusions: This study showed a predominance of European lineage variants of HPV16 among asymptomatic women from Sinaloa, Mexico, predominantly with of the E350G variant. This variant has been shown to be associated with an increased risk of early development of CC. The use of molecular identification of carcinogenic HPV and Pap test screening may be a good strategy for monitoring women to prevent CC.
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Affiliation(s)
| | - Rocío Susana Mendez-Martínez
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan; Laboratory of Virus & Cancer, Instituto Nacional de Cancerología, SS, Mexico City, Mexico
| | - Salvador Vázquez-Vega
- Unit of Epidemiological Research and Health Services SXXI, Centro Médico Nacional, Mexico City, Mexico
| | - Ulises Osuna Martínez
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan, Mexico
| | - Rosalinda Sánchez Arenas
- Unit of Epidemiological Research and Health Services SXXI, Centro Médico Nacional, Mexico City, Mexico
| | | | - Ignacio Osuna Ramírez
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan, Mexico
| | | | | | - Alejandro García-Carranca
- Laboratory of Virus & Cancer, Instituto Nacional de Cancerología, SS; Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018; 14:e1007352. [PMID: 30383862 PMCID: PMC6211759 DOI: 10.1371/journal.ppat.1007352] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/22/2018] [Indexed: 02/07/2023] Open
Abstract
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.
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Affiliation(s)
- Zigui Chen
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY, United States of America
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, United States of America
| | - Rolando Herrero
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Charles E. Wood
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, United States of America
| | - Julio C. Ruiz
- Department of Veterinary Sciences, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Gary M. Clifford
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul K. S. Chan
- Departments of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology; Epidemiology and Population Health; Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY, United States of America
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20
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Combes JD, Franceschi S. Human papillomavirus genome variants and head and neck cancers: a perspective. Infect Agent Cancer 2018; 13:13. [PMID: 29643933 PMCID: PMC5891965 DOI: 10.1186/s13027-018-0185-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022] Open
Abstract
Human papillomaviruses (HPV) cause infections that are responsible for diverse clinical manifestations from benign conditions to invasive cancer. As different HPV types are associated with variable pathogenic potential, minor genetic variations within a given high-risk HPV type might also be associated with distinct oncogenic capacities, through variable ability of persistence or risk of progression to precancer/cancer. Most recent HPV variant studies in the cervix using latest sequencing technology confirmed that minor changes in the HPV genome can have a major influence on carcinogenesis and have revealed key data that help better understand the carcinogenicity of HPV at a molecular level. Here we review the limited number of studies on HPV genome variants in head and neck cancers (HNC) and discuss their implications for cancer research in the light of accumulated knowledge for the cervix. Challenges in transposing HPV variant studies from the lower anogenital to the upper aerodigestive tract are also discussed, highlighting the main gaps of knowledge in the field of HPV-induced HNC. Specifically in the head and neck region, the lack of characterisation of precancerous lesions and the difficulty in sampling normal tissue will challenge the development of accurate studies. Although there is so far no indication that HPV variant research in HNC could directly translate into clinical application, such research is expected to be useful to disentangle unanswered questions in the pathogenesis of HNC. Yet, history of HPV variant research suggests that, to be successful, studies will require large international collaborative efforts.
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Affiliation(s)
- Jean-Damien Combes
- International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Cedex 08 Lyon, France
| | - Silvia Franceschi
- Cancer Epidemiology Unit, CRO Aviano National Cancer Institute IRCCS, Via Franco Gallini 2, 33081 Aviano, PN Italy
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21
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Zhang J, Zhang S, Wang M, Ding X, Wen Q, Chen Z, Cao M, Jing Y, Zhang S. Genetic variability in E5, E6, E7 and L1 genes of human papillomavirus type 31. Mol Med Rep 2018; 17:5498-5507. [PMID: 29393441 DOI: 10.3892/mmr.2018.8500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 12/13/2016] [Indexed: 11/05/2022] Open
Abstract
Human papillomavirus (HPV) type 31 is an important pathogenic subtype associated with cervical cancer. The aims of the present study were to analyze E5, E6, E7 and L1 gene mutations of HPV‑31 among females, and to elucidate the evolutionary associations between them. In total, 87 positive samples were collected. The E5, E6, E7 and L1 genes were amplified by polymerase chain reaction and sequenced. Subsequently, two phylogenetic trees were constructed from the nucleotide sequences of the E5, E6 and E7 and the L1 variants of HPV‑31. In total, 31 mutation sites of E5, E6 and E7 genes were identified, of which 16 were non‑synonymous. T4053A (F80I), C285T (H60Y), C520T (A138V) and A743G (K62E) were the most common non‑synonymous mutations. A total of 30 mutation sites of L1 genes were identified, of which four were non‑synonymous. The most common non‑synonymous mutations of L1 genes were A6350G (T29A) and C6372A (T36N). By phylogenetic analysis, A and C variants were most frequently detected, while B variants were less frequently detected in this population. The sequence variation data obtained in the present study provides a foundation for future research regarding HPV‑induced oncogenesis, and may prove valuable for developing diagnostic probes and in the design of HPV vaccines for targeted populations.
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Affiliation(s)
- Jianhui Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Shaohong Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Mengting Wang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Xianping Ding
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Qiang Wen
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Zuyi Chen
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Man Cao
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Yaling Jing
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Shun Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
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Vaezi T, Shoja Z, Hamkar R, Shahmahmoodi S, Nozarian Z, Marashi SM, Jalilvand S. Human papillomavirus type 16 lineage analysis based on E6 region in cervical samples of Iranian women. INFECTION GENETICS AND EVOLUTION 2017; 55:26-30. [PMID: 28847737 DOI: 10.1016/j.meegid.2017.08.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/18/2022]
Abstract
It is suggested that distinct HPV 16 variants differ in oncogenic potential and geographic distribution. As such, understanding the regional variants of HPV 16 would be of great importance for evolutionary, epidemiological and biological analysis. In this regard, the sequence variations of E6 gene were investigated to characterize more common variants of HPV 16 in normal cells, premalignant and malignant lesions of the cervix. In total, 106 isolates of HPV 16 were analyzed by PCR and sequencing. Overall, two different lineages (A and D) were identified. Lineage D comprised 70.7% of samples and the remaining 29.3% belonged to lineage A. Regarding to cytology/histology, lineage D was dominant in both normal+CIN I-II and CIN III+ICC groups as it was detected in 80% and 66.2% of cases, respectively. The comparison of the lineages between different groups (35 normal+CIN I-II samples and 71 CIN III+ICC samples) revealed that lineage A is more prevalent in cervical cancer cases (7 (20%) vs. 24 (33.8%)) although the difference observed did not reach statistical significance (p=0.07). In conclusion, our findings confirm that HPV lineages A and D are more prevalent in Iran, with the lineage D as the most dominant in all studied groups.
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Affiliation(s)
- Tayebeh Vaezi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Rasool Hamkar
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Shohreh Shahmahmoodi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zohreh Nozarian
- Department of Pathology, Farabi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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23
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Zhao PY, Jiang HC, Li Y, Wang JB, Zhang TT, Liu CH, Song LW, Cheng JJ. Comparison of the cervista HPV HR test and luminex XMAP technology for the diagnosis of cervical intraepithelial neoplasia. Eur J Obstet Gynecol Reprod Biol 2017; 214:150-155. [DOI: 10.1016/j.ejogrb.2017.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/08/2017] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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24
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Volpini LPB, Boldrini NAT, de Freitas LB, Miranda AE, Spano LC. The high prevalence of HPV and HPV16 European variants in cervical and anal samples of HIV-seropositive women with normal Pap test results. PLoS One 2017; 12:e0176422. [PMID: 28426837 PMCID: PMC5398673 DOI: 10.1371/journal.pone.0176422] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/10/2017] [Indexed: 02/02/2023] Open
Abstract
Human Immunodeficiency Virus (HIV)-seropositive women are more likely to have anogenital cancer, and high risk-HPV (HR-HPV) infection is the main associated factor. Between August 2013 and December 2015, we conducted a descriptive study to determine the HPV genotypes and HPV16 variants in cervical and anal samples of HIV-seropositive women with a normal Pap test. The viral DNA was amplified by PCR using the PGMY09/11 set of primers. Reverse line blot (RLB), restriction fragment length polymorphism (RFLP) and sequencing assays were used to determine the HPV genotypes. HPV16 variants were identified by gene sequencing. We found a high frequency of HR-HPV (60.3%; 76/126) at the anogenital site among HIV-seropositive women and without association with anal intercourse. HPV16 and European variant predominated among the HR-HPV. Mixed infections with at least three different HPV types were common, particularly at the anal site. CD4+ T-cell counts below 500 cells/mm3, a HIV viral load above 50 copies/mL and an age of 18 to 35 years old were all related to HPV anal infection. Our study showed a high frequency of HR-HPV in both cervical and anal sites of women with negative cytology belonging to a risk group for the development of anogenital cancer.
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Affiliation(s)
- Lays Paula Bondi Volpini
- Post-Graduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
- * E-mail:
| | | | - Luciana Bueno de Freitas
- Post-Graduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
| | - Angelica Espinosa Miranda
- Post-Graduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
- Department of Social Medicine, Center of Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
| | - Liliana Cruz Spano
- Post-Graduate Program in Infectious Diseases, Federal University of Espírito Santo, Vitória, Brazil
- Department of Pathology, Center of Health Sciences, Federal University of Espírito Santo, Vitória, Brazil
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25
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Variation of HPV Subtypes with Focus on HPV-Infection and Cancer in the Head and Neck Region. Recent Results Cancer Res 2017; 206:113-122. [PMID: 27699533 DOI: 10.1007/978-3-319-43580-0_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human papillomavirus (HPV) comprises a heterogeneous group of double-strand DNA viruses with variable potential to infect human epithelial cells and trigger neoplastic transformation. Its 8 kb genome encodes proteins required for virus replication and self-organized formation of infectious particles but also for early proteins E6 and E7 able to trigger neoplastic transformation. E6 and E7 of high-risk (HR) HPV subtypes can bind to p53 or release E2F and abrogate replication control. Due to variable amino acid sequence (AAS) in the binding sites of E6 and E7 particular HR-HPV variants within subtypes are essentially heterogeneous in efficacy triggering neoplastic transformation and cancer development. This could explain differences in the clinical course of HPV-driven head and neck cancer.
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26
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Mahato DR, Fischer WB. Weak Selectivity Predicted for Modeled Bundles of Viral Channel-Forming Protein E5 of Human Papillomavirus-16. J Phys Chem B 2016; 120:13076-13085. [PMID: 27976908 DOI: 10.1021/acs.jpcb.6b10050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein E5 is a polytopic 83 amino acid membrane protein with three transmembrane domains (TMDs), encoded by high-risk human papillomavirus-16 (HPV-16). HPV-16 is found to be the causative agent for cervical cancer. Protein E5, among other proteins (e.g., E6, E7), is expressed at an "early" (E) stage when the cell turns malignant. It has been experimentally found that E5 forms hexameric assemblies, which show the characteristics of the class of so-called channel-forming proteins by rendering lipid membranes permeable to ions and small molecules. Protein E5 is used to achieve structural models of the protein in assembled bundles using a force field-based docking approach. Extended molecular dynamics simulations of selected bundles in fully hydrated lipid bilayers suggest the second TMD to be pore-lining, allowing for water columns to exist within the lumen of the pore. Full correlation analysis indicates asymmetric dynamics within the monomers of the bundle. Potential of mean force calculations of a snapshot structure of the putative open pore of the protein bundle propose low selectivity.
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Affiliation(s)
- Dhani Ram Mahato
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University , Taipei 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University , Taipei 112, Taiwan
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27
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Chen Z, Jing Y, Wen Q, Ding X, Zhang S, Wang T, Zhang Y, Zhang J. L1 and L2 gene polymorphisms in HPV-58 and HPV-33: implications for vaccine design and diagnosis. Virol J 2016; 13:167. [PMID: 27717385 PMCID: PMC5055703 DOI: 10.1186/s12985-016-0629-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022] Open
Abstract
Background Cervical cancer is associated with infection by certain subtypes of human papillomavirus (HPV). The L1 protein comprising HPV vaccine formulations elicits high-titre neutralizing antibodies and confers protection against specific HPV subtypes. HPV L2 protein is an attractive candidate for cross-protective vaccines. HPV-33 and HPV-58 are very prevalent among Chinese women. Methods To study the gene intratypic variations and polymorphisms of HPV-33 and HPV-58 L1/L2 in Sichuan China, HPV-33 and HPV-58 L1 and L2 genes were sequenced and compared with other genes submitted to GenBank. Phylogenetic trees were constructed by maximum-likelihood and the Kimura 2-parameters methods (MEGA 6). The secondary structure was analyzed by PSIPred software, and HPV-33 and HPV-58 L1 homology models were created by SWISS-MODEL software. The selection pressures acting on the L1/L2 genes were estimated by PAML 4.8. Results Among 124 HPV-33 L1 sequences 20 single nucleotide mutations were observed included 8/20 non-synonymous and 12/20 synonymous mutations. The 101 HPV-33 L2 sequences included 12 single nucleotide mutations comprising 7/12 non-synonymous and 5/12 synonymous mutations. The 223 HPV-58 L1 sequences included 32 single nucleotide mutations comprising 9/32 non-synonymous and 23/32 synonymous mutations. The 201 HPV-58 L2 sequences comprised 26 single nucleotide mutations including 9/26 non-synonymous and 17/26 synonymous mutations. Selective pressure analysis showed that most of the common non-synonymous mutations showed a positive selection. HPV-33 and HPV-58 L2 were more stable than HPV-33 and HPV-58 L1. Conclusions HPV-33 and HPV-58 L2 were better candidates as clinical diagnostic targets compared with HPV-33 and HPV-58 L1. Clinical diagnostic probes and second-generation polyvalent vaccines should be designed on the basis of the unique sequence of HPV-33 and 58 L1/L2 variations in Sichuan, to improve the accuracy of clinical detection and the protective efficiency of vaccines. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0629-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zuyi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Yaling Jing
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Qiang Wen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China. .,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China.
| | - Shun Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Yiwen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
| | - Jianhui Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu, China.,Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan and Chongqing, China
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28
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Nicolás-Párraga S, Gandini C, Pimenoff VN, Alemany L, de Sanjosé S, Xavier Bosch F, Bravo IG. HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus. Cancer Med 2016; 5:2909-2919. [PMID: 27654117 PMCID: PMC5083745 DOI: 10.1002/cam4.870] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/13/2016] [Accepted: 07/27/2016] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus (HPV)16 is the most oncogenic human papillomavirus, responsible for most papillomavirus‐induced anogenital cancers. We have explored by sequencing and phylogenetic analysis the viral variant lineages present in 692 HPV16‐monoinfected invasive anogenital cancers from Europe, Asia, and Central/South America. We have assessed the contribution of geography and anatomy to the differential prevalence of HPV16 variants and to the nonsynonymous E6 T350G polymorphism. Most (68%) of the variance in the distribution of HPV16 variants was accounted for by the differential abundance of the different viral lineages. The most prevalent variant (above 70% prevalence) in all regions and in all locations was HPV16_A1‐3, except in Asia, where HPV16_A4 predominated in anal cancers. The differential prevalence of variants as a function of geographical origin explained 9% of the variance, and the differential prevalence of variants as a function of anatomical location accounted for less than 3% of the variance. Despite containing similar repertoires of HPV16 variants, we confirm the worldwide trend of cervical cancers being diagnosed significantly earlier than other anogenital cancers (early fifties vs. early sixties). Frequencies for alleles in the HPV16 E6 T350G polymorphism were similar across anogenital cancers from the same geographical origin. Interestingly, anogenital cancers from Central/South America displayed higher 350G allele frequencies also within HPV16_A1‐3 lineage compared with Europe. Our results demonstrate ample variation in HPV16 variants prevalence in anogenital cancers, which is partly explained by the geographical origin of the sample and only marginally explained by the anatomical location of the lesion, suggesting that tissue specialization is not essential evolutionary forces shaping HPV16 diversity in anogenital cancers.
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Affiliation(s)
- Sara Nicolás-Párraga
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Carolina Gandini
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Ville N Pimenoff
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Silvia de Sanjosé
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain
| | - F Xavier Bosch
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Ignacio G Bravo
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Barcelona, Spain. .,MIVEGEC, National Center for Scientific Research (CNRS), Montpellier, France.
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29
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Moussavou PB, Koumakpayi IH, Nkili-Meyong AA, Labouba I, Bisvigou U, Chansi JK, Engohan-Aloghe C, Dissanami F, Ambounda N, Delannoy-Vieillard AS, Diancourt L, Nkoghe D, Leroy EM, Belembaogo E, Berthet N. Molecular analysis of human Papillomavirus detected among women positive for cervical lesions by visual inspection with acetic acid/Lugol's iodine (VIA/VILI) in Libreville, Gabon. Infect Agent Cancer 2016; 11:50. [PMID: 27610192 PMCID: PMC5015258 DOI: 10.1186/s13027-016-0098-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/23/2016] [Indexed: 11/16/2022] Open
Abstract
Background The human papillomavirus (HPV) is the causative agent of cervical cancer, which is the leading cancer-related cause of death for women in Sub-Saharan Africa. In 2013, the Gabonese Ministry of Health and the Sylvia Bongo Ondimba Foundation implemented cervical cancer screening programs based on the detection of cancerous lesions by visual inspection with acetic acid and/or Lugol’s iodine (VIA/VILI). This pilot study was set up to determine the HPV profile and analyze the nucleotide sequence variation of HPV16 circulating in patients with cervical abnormalities detected by VIA/VILI testing. Methods The cervical abnormalities observed upon VIA/VILI were confirmed by liquid-based cytology for all tested women. Nested PCR using the MY09/11 and GP5+/6+ primer sets was used to detect HPVs present in the extracted DNA. HPV genotypes were determined after sequencing of amplicons based on a high-throughput sequencing approach. For isolates of the HPV16 genotype, the E6 gene and the long control region (LCR) were directly sequenced using Sanger method. Results The study included 87 women who showed a positive VIA/VILI result. Cervical abnormalities were found in 40.23 % of women and 40 % were classified as high-grade lesions. The HPV detection rate was 82.9 % among women with abnormal cytology. Among all the identified high-risk HPV genotypes, HPV16, 18 and 33 were the most frequent. Multiple HPV infections were observed in 42.31 % of HPV-infected women. Analysis of the HPV16 sequence variation in the E6 gene and in the LCR showed that 85.3 and 14.7 % belonged to the African and European lineages, respectively. Among the African branch variants, Af2 was the most frequently identified in this study. Conclusion This study offers the first report of the HPV detection rate and molecular epidemiology among Gabonese women with a positive result in a VIA/VILI screening test. Moreover, data on the HPV16 sequence variation confirm the predominance of African variants in high-grade lesions. Electronic supplementary material The online version of this article (doi:10.1186/s13027-016-0098-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pamela Boundzanga Moussavou
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon
| | | | - Andriniaina Andy Nkili-Meyong
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon
| | - Ingrid Labouba
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon
| | - Ulrich Bisvigou
- Institut de Cancérologie de Libreville (ICL), Libreville, Gabon
| | - Junie K Chansi
- Institut de Cancérologie de Libreville (ICL), Libreville, Gabon
| | | | - Frederic Dissanami
- Centre Hospitalier Universitaire de Libreville (CHUL), Service de gynécologie obstétrique, Libreville, Gabon
| | - Nathalie Ambounda
- Centre Hospitalier Universitaire de Libreville (CHUL), Service de gynécologie obstétrique, Libreville, Gabon
| | | | - Laure Diancourt
- Institut Pasteur, Unité Environnement et risques infectieux, Cellule d'Intervention Biologique d'Urgence, Paris, France
| | - Dieudonne Nkoghe
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon ; Ministère de la Santé, Direction général de la Santé, Libreville, Gabon
| | - Eric M Leroy
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon ; Institut de Recherches et de Développement (IRD), Maladies Infectieuses et vecteurs: Ecologie, génétique, Evolution et Contrôle (IRD 224 - CNRS 5290 6 UM1- UM2), Montpellier, France
| | | | - Nicolas Berthet
- Department of Zoonosis and Emerging Diseases, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, BP 769 Gabon ; Centre National de la Recherche Scientifique, UMR3569, Paris, France
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30
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Park JS, Shin S, Kim EC, Kim JE, Kim YB, Oh S, Roh EY, Yoon JH. Association of human papillomavirus type 16 and its genetic variants with cervical lesion in Korea. APMIS 2016; 124:950-957. [PMID: 27546189 DOI: 10.1111/apm.12592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/10/2016] [Indexed: 12/21/2022]
Abstract
Persistent human papillomavirus type 16 (HPV16) is the major risk factor for cervical cancer. HPV16 intratypic variants differ in their geographical distribution and oncogenic potential. This study aimed to analyze the distribution of HPV16 variants and their association with cervical lesion histopathology in Korean women. In total, 133 HPV16-positive cervical samples from women admitted to Seoul National University Boramae Hospital were analyzed by sequencing E6, E7, and L1 genes and the long control region (LCR), and the variant distribution according to cervical lesion grade was determined. Isolates were grouped into a phylogenetic lineage, and A1-3, A4, C, and D sublineages were detected in 54.1, 37.8, 0.7, and 7.4% of samples, respectively. The most commonly observed LCR variations were 7521G>A (91.5%), 7730A>C (59.6%), and 7842G>A (59.6%). Furthermore, A4 or D sublineage-positive women had a higher risk for cervical cancer than women who were positive for A1-3. Among HPV phylogenetic clusters, A1-3 was the predominant sublineage, and within A1-3, the 350G polymorphism was highly frequent. These results differed from those of previous studies in Korea and other Asian countries. The findings suggest that cervical neoplasia incidence in HPV16-infected patients could be affected by the distribution of HPV16 variants in the population.
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Affiliation(s)
- Jeong Su Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Gyeonggi-do, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea. .,Department of Laboratory Medicine, Seoul National University Boramae Hospital, Seoul, Korea.
| | - Eui-Chong Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Eun Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Beom Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Korea
| | - Sohee Oh
- Department of Biostatistics, Seoul National University Boramae Hospital, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Boramae Hospital, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Boramae Hospital, Seoul, Korea
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31
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Variants of human papillomaviruses 16 (HPV16) in Uigur women in Xinjiang, China. Infect Agent Cancer 2016; 11:44. [PMID: 27540411 PMCID: PMC4989296 DOI: 10.1186/s13027-016-0089-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Persistent infection of high-risk human papillomaviruses 16 (HPV16) has been considered as the leading cause of cervical cancer. In this study we assessed HPV16 sequence variation and genetic diversity of HPV16 variants in cervical cancer in Uigur women in Xinjiang, China. We analyzed the nucleotide sequences of the open reading frames of E6 and E7, and part of the open reading frames of L1 of HPV16 in Uigur women. METHODS Biopsies of histologically confirmed HPV16 infections with cervical cancer were obtained from 43 Uigur women in Xinjiang, China. E6, E7 and L1 genes of HPV16 of all samples were amplified and sequenced; the sequences were used in phylogenetic analysis of HPV16 variants. RESULTS Our analysis revealed nine nucleotide changes in E6 (five changes), E7 (one change) and L1 (three changes) gene. The most frequently observed variations were T350G (79.1 %). One variation T295G (D64E) at E6 were detected in 6 cases (KT959536, KT959542, KT959546, KT959550, KT959553, KT959558). Deletion (464Asp) along with insertion (448Ser) were observed in L1 (100 %). Most variants were European lineage (97.7 %); only one belongs to Asia variants with common T178G (D25E) in E6 and A647G (N29S) in E7. CONCLUSION The most prevalent HPV16 variants in the Uigur women we studied were of the European lineage. Our results indicate that HPV16 European lineage may serve as a harmful factor associated with the development and progression of cervical cancer.
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Cao M, Chenzhang Y, Ding X, Zhang Y, Jing Y, Chen Z. Genetic variability and lineage phylogeny of human papillomavirus type-16 and -53 based on the E6, E7, and L1 genes in Southwest China. Gene 2016; 592:49-59. [PMID: 27450917 DOI: 10.1016/j.gene.2016.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
Human papillomaviruses (HPVs) are circular double-stranded DNA viruses that are highly prevalent in the general population, and account for the cervical cancer burden in women worldwide. In this study, we analyzed HPV-16, the most prevalent type worldwide, and HPV-53, a possible high-risk type from infected women in Southwest China. To characterize mutations, intratypic variants, and genetic variability in the E6, E7, and L1 genes of HPV-16 (n=97) and HPV-53 (n=15), these genes were sequenced and submitted to GenBank. Phylogenetic trees were constructed using Bayesian trees, followed by secondary structure analysis and B-cell epitope prediction. Moreover, the selection pressures of the E6, E7, and L1 genes were estimated. In total, 27 novel variants of HPV-16 and 11 novel variants of HPV-53 were identified. In the HPV-16 E6-E7-L1 sequences, 73 nucleotide changes were observed with 40/73 being non-synonymous mutations (two in the alpha helix and five in the beta sheet) and 33/73 being synonymous. In the HPV-53 E6-E7-L1 sequences, 64 nucleotide changes were observed with 26/64 being non-synonymous mutations (three in the alpha helix and one in the beta sheet) and 38/64 being synonymous. Selective pressure analysis showed that most of these mutations did not reflect positive selection. The maximal divergence between any two variants within each gene of these two HPV types ranging from 0.94%(HPV-16 L1 gene)to 2.80%(HPV-53 E6 gene). Identifying new variants of HPV-16 and -53 from women in Southwest China may be helpful to design vaccines specifically for women in Southwest China and testing methods specifically for this region. The results of our study may contribute to future researches in diagnostic probes, vaccines improvement, or screening methods for a particular population.
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Affiliation(s)
- Man Cao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China
| | - Yuwei Chenzhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China.
| | - Yiwen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China
| | - Yaling Jing
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China
| | - Zuyi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, and Chongqing, China
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Complete Genome Sequences of Eight Human Papillomavirus Type 16 Asian American and European Variant Isolates from Cervical Biopsies and Lesions in Indian Women. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00243-16. [PMID: 27198009 PMCID: PMC4878291 DOI: 10.1128/genomea.00243-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Human papillomavirus type 16 (HPV16), a member of the Papillomaviridae family, is the primary etiological agent of cervical cancer. Here, we report the complete genome sequences of four HPV16 Asian American variants and four European variants, isolated from cervical biopsies and scrapings in India.
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Siqueira JD, Alves BM, Prellwitz IM, Furtado C, Meyrelles ÂR, Machado ES, Seuánez HN, Soares MA, Soares EA. Identification of novel human papillomavirus lineages and sublineages in HIV/HPV-coinfected pregnant women by next-generation sequencing. Virology 2016; 493:202-8. [PMID: 27060563 DOI: 10.1016/j.virol.2016.03.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/04/2023]
Abstract
Infection by human papillomavirus (HPV) is a necessary condition for development of cervical cancer, and has also been associated with malignancies of other body anatomical sites. Specific HPV types have been associated with premalignant lesions and invasive carcinoma, but mounting evidence suggests that within-type lineages and sublineages also display distinct biological characteristics associated with persistent infections and evolution to cervical cancer. In the present study, we have assessed HPV multiple infection and variation from a cohort of highly susceptible, HIV(+) pregnant women using next-generation sequencing and an in-house pipeline for HPV full-length genome assembly. Seventy-two consensus sequences representing complete or near-complete (>97%) HPV genomes were assembled, spanning 28 different types. Genetic distance and phylogenetic analyses allowed us to propose the classification of novel HPV lineages and sublineages across nine HPV types, including two high-risk types. HPV diversity may be a hallmark of immunosuppressed patients upon HIV infection and AIDS progression.
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Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Brunna M Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Isabel M Prellwitz
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ângela R Meyrelles
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil.
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Hochmann J, Sobrinho JS, Villa LL, Sichero L. The Asian-American variant of human papillomavirus type 16 exhibits higher activation of MAPK and PI3K/AKT signaling pathways, transformation, migration and invasion of primary human keratinocytes. Virology 2016; 492:145-54. [PMID: 26945151 DOI: 10.1016/j.virol.2016.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 12/20/2022]
Abstract
Asian-American (AA) HPV-16 variants are associated with higher risk of cancer. Abnormal activation of intracellular signaling play a critical role in cancer development and progression. Our aim was to elucidate mechanisms underlying the higher oncogenic potential attributed to AA variant. We evaluated activation of MAPK and PI3K/AKT pathways in primary human keratinocytes (PHKs) transduced with E6/E7 of three HPV-16 variants: E-P, AA, E-350G. Phenotypes examined included migration, anchorage independent growth and invasion. AA PHKs presented the highest levels of active proteins involved in all cascades analyzed: MAPK-ERK, MAPK-p38 and PI3K-AKT. AA PHKs were more efficient in promoting anchorage independent growth, and in stimulating cell migration and invasion. MEK1 inhibition decreased migration. The mesenchymal phenotype marker vimentin was increased in AA PHKs. Our results suggest that MEK1, ERK2, AKT2 hyperactivation influence cellular behavior by means of GSK-3b inactivation and EMT induction prompting AA immortalized PHKs to more efficiently surpass carcinogenesis steps.
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Affiliation(s)
- Jimena Hochmann
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil.
| | - João S Sobrinho
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil.
| | - Luisa L Villa
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil; Department of Radiology and Oncology, School of Medicine, University of São Paulo, Brazil.
| | - Laura Sichero
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil.
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Zhang Y, Cao M, Wang M, Ding X, Jing Y, Chen Z, Ma T, Chen H. Genetic variability in E6, E7, and L1 genes of human papillomavirus genotype 52 from Southwest China. Gene 2016; 585:110-118. [PMID: 26968892 DOI: 10.1016/j.gene.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 03/01/2016] [Indexed: 12/19/2022]
Abstract
Human papillomavirus (HPV) is the major causative agent of cervical cancer, which accounts for the second highest cancer burden in women worldwide. HPV-52, the prevalent subtype in Asia, especially in southwest China, was analyzed in this study. To analyze polymorphisms, intratypic variants, and genetic variability in the E6-E7 (n=26) and L1 (n=53) genes of HPV-52, these genes were sequenced and the sequences were submitted to GenBank. Phylogenetic trees were constructed using the neighbor-joining and Kimura 2-parameters methods, followed by analysis of the diversity of secondary structure. Finally, we estimated the selection pressures acting on the E6-E7 and L1 genes. Fifty-one novel variants of HPV-52 L1, and two novel variants of HPV-52 E6-E7 were identified in this study. Thirty single nucleotide changes were observed in HPV-52 E6-E7 sequences with 19/30 non-synonymous mutations and 11/30 synonymous mutations (five in the alpha helix and five in the beta sheet). Fifty-five single nucleotide changes were observed in HPV-52 L1 sequences with 17/55 non-synonymous mutations (seven in the alpha helix and fourteen in the beta sheet) and 38/55 synonymous mutations. Selective pressure analysis predicted that most of these mutations reflect positive selection. Identifying new variants in HPV-52 may inform the rational design of new vaccines specifically for women in southwest China. Knowledge of genetic variation in HPV may be useful as an epidemiologic correlate of cervical cancer risk, or may even provide critical information for developing diagnostic probes.
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Affiliation(s)
- Yiwen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Man Cao
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Mengting Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Xianping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Yaling Jing
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Zuyi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Tengjiao Ma
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
| | - Honghan Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education; Institute of Medical Genetics, College of Life Science, Sichuan University, China; Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Sichuan, Chongqing, China.
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HPV Population Profiling in Healthy Men by Next-Generation Deep Sequencing Coupled with HPV-QUEST. Viruses 2016; 8:v8020028. [PMID: 26821041 PMCID: PMC4776183 DOI: 10.3390/v8020028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/11/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
Multiple-type human papillomaviruses (HPV) infection presents a greater risk for persistence in asymptomatic individuals and may accelerate cancer development. To extend the scope of HPV types defined by probe-based assays, multiplexing deep sequencing of HPV L1, coupled with an HPV-QUEST genotyping server and a bioinformatic pipeline, was established and applied to survey the diversity of HPV genotypes among a subset of healthy men from the HPV in Men (HIM) Multinational Study. Twenty-one HPV genotypes (12 high-risk and 9 low-risk) were detected in the genital area from 18 asymptomatic individuals. A single HPV type, either HPV16, HPV6b or HPV83, was detected in 7 individuals, while coinfection by 2 to 5 high-risk and/or low-risk genotypes was identified in the other 11 participants. In two individuals studied for over one year, HPV16 persisted, while fluctuations of coinfecting genotypes occurred. HPV L1 regions were generally identical between query and reference sequences, although nonsynonymous and synonymous nucleotide polymorphisms of HPV16, 18, 31, 35h, 59, 70, 73, cand85, 6b, 62, 81, 83, cand89 or JEB2 L1 genotypes, mostly unidentified by linear array, were evident. Deep sequencing coupled with HPV-QUEST provides efficient and unambiguous classification of HPV genotypes in multiple-type HPV infection in host ecosystems.
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Siddiqa A, Bhatti MF. Genetic variation of high-risk HPV-16 from a cervical cancer biopsy collected in Pakistan. Future Virol 2016. [DOI: 10.2217/fvl.15.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: HPV-16 is one of the causative agents of cervical cancer. The HPV-16 genome is characterized widely to assist mutagenesis studies, phylogenetic analysis and protein annotations. This is the first report of HPV-16 sequence analysis from Pakistan. Materials & methods: The gene and long control region specific primers were used to generate the targeted amplicons that were then cloned and sequenced. Results: The complete genome analysis revealed nine changes both at amino acid and nucleotide level including seven novel and two previously reported mutations. The evolutionary relationship of HPV from Pakistan and reported sequences shows that strain reported in this study segregates with European taxa. Conclusion: This report lays foundation to conduct HPV genome mutation analysis in Pakistan.
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Affiliation(s)
- Abida Siddiqa
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Kashmir Highway, Islamabad 44000, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Kashmir Highway, Islamabad 44000, Pakistan
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Wulandari D, Rachmadi L, Sudiro TM. Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia. MEDICAL JOURNAL OF INDONESIA 2015. [DOI: 10.13181/mji.v24i4.1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of Indonesian isolates, which were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.
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Tsakogiannis D, Gortsilas P, Kyriakopoulou Z, Ruether IGA, Dimitriou TG, Orfanoudakis G, Markoulatos P. Sites of disruption within E1 and E2 genes of HPV16 and association with cervical dysplasia. J Med Virol 2015; 87:1973-80. [PMID: 25959607 DOI: 10.1002/jmv.24256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 04/28/2015] [Indexed: 12/25/2022]
Abstract
Integration of HPV16 DNA into the host chromosome usually disrupts the E1 and/or E2 genes. The present study investigated the disruption of E1, E2 genes in a total of eighty four HPV16-positive precancerous and cervical cancer specimens derived from Greek women (seventeen paraffin-embedded cervical biopsies and sixty seven Thin Prep samples). Complete E2 and E1 genes were amplified using three and nine overlapping primer sets respectively, in order to define the sites of disruption. Extensive mapping analysis revealed that disruption/deletion events within E2 gene occurred in high grade and cervical cancer samples (x(2) test, P < 0.01), while no evidence of E2 gene disruption was documented among low grade cervical intraepithelial neoplasias. In addition, disruptions within the E1 gene occur both in high and low grade cervical intraepithelial neoplasia. This leads to the assumption that in low grade cervical intraepithelial neoplasias only E1 gene disruption was involved (Fisher's exact test, P < 0.05), while in high grade malignancies and cervical cancer cases deletions in both E1 and E2 genes occurred. Furthermore, the most prevalent site of disruption of E1 gene was located between nucleotides 1059 and 1323, while the most prevalent deleted region of the E2 gene was located between nucleotides 3172 and 3649 (E2 hinge region). Therefore, it is proposed that each population has its own profile of frequencies and sites of disruptions and extensive mapping analysis of E1 and E2 genes is mandatory in order to determine suitable markers for HPV16 DNA integration analysis in distinct populations.
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Affiliation(s)
- D Tsakogiannis
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - P Gortsilas
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Z Kyriakopoulou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - I G A Ruether
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - T G Dimitriou
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - G Orfanoudakis
- University of Strasbourg, Ecole Superieure de Biotechnologie de Strasbourg, CNRS FRE 3211-Oncoprotein Group, Illkirch, France
| | - P Markoulatos
- Department of Biochemistry and Biotechnology, Microbiology-Virology Laboratory, School of Health Sciences, University of Thessaly, Larissa, Greece
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Boumba LMA, Assoumou SZ, Hilali L, Mambou JV, Moukassa D, Ennaji MM. Genetic variability in E6 and E7 oncogenes of human papillomavirus Type 16 from Congolese cervical cancer isolates. Infect Agent Cancer 2015; 10:15. [PMID: 25991921 PMCID: PMC4437748 DOI: 10.1186/s13027-015-0010-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 04/21/2015] [Indexed: 11/18/2022] Open
Abstract
Background The molecular epidemiological studies showed that some variants of HPV-16, distributed geographically, would present a higher risk of causing cervical cancer. This study aimed to analyze nucleotide changes of HPV-16 E6 and E7 genomic regions from infected Southwestern Congolese women. Methods DNA of twenty HPV-16 isolates was analyzed by amplifying the E6 and E7 genes using type-specific primers PCR and direct sequencing. The sequences obtained were aligned with the HPV-16 GenBank reference sequences. Results Thirteen (65.0%) out of 20 DNA-samples were successfully amplified. Genetic analysis revealed 18 and 4 nucleotide changes in E6 and E7 genomic regions respectively. The most frequently observed nucleotide variations were the missense C143G, G145T and C335T in E6 (100%), leading to the non-synonymous amino acid variation Q14D and H78Y. E7 genomic region was found to be highly conserved with two most common T789C and T795G (100%) silent variations. All HPV-16 variants identified belonged to the African lineage: 7 (53.8%) belonged to Af-1 lineage and 6 (46.1%) to Af-2 lineage. The missense mutation G622A (D21N) in the E7 region seems to be described for the first time in this study. Conclusion This study reported for the first time the distribution of HPV-16 E6 and E7 genetic variants in infected women from southwest Congo. The findings confirmed almost ascendancy of the African lineage in our study population.
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Affiliation(s)
- Luc Magloire Anicet Boumba
- Laboratoire de Virologie, Microbiologie et Qualité/ETB, Faculté des Sciences et Techniques de Mohammedia, Université Hassan II Casablanca, B.P. 146, 20650 Mohammedia, Maroc ; Laboratoire d'Agroalimentaire et Santé, Département de Biologie Appliquée, Faculté des Sciences et Techniques, Université Hassan 1er Settat B.P. 577 Settat, Mohammedia, Maroc ; Laboratoire d'Analyses Médicales et Morphologiques, Hôpital Général de Loandjili, B.P. 8122, Pointe-Noire, Congo
| | - Samira Zoa Assoumou
- Laboratoire de Virologie, Microbiologie et Qualité/ETB, Faculté des Sciences et Techniques de Mohammedia, Université Hassan II Casablanca, B.P. 146, 20650 Mohammedia, Maroc ; Laboratoire d'Agroalimentaire et Santé, Département de Biologie Appliquée, Faculté des Sciences et Techniques, Université Hassan 1er Settat B.P. 577 Settat, Mohammedia, Maroc
| | - Lahoucine Hilali
- Laboratoire d'Agroalimentaire et Santé, Département de Biologie Appliquée, Faculté des Sciences et Techniques, Université Hassan 1er Settat B.P. 577 Settat, Mohammedia, Maroc
| | - Jean Victor Mambou
- Centre Médico-social de la Mairie Centrale de Pointe-Noire, B.P. 383, Place de la Liberté, 97116 Pointe-Noire, Congo
| | - Donatien Moukassa
- Laboratoire d'Analyses Médicales et Morphologiques, Hôpital Général de Loandjili, B.P. 8122, Pointe-Noire, Congo
| | - Mustapha Moulay Ennaji
- Laboratoire de Virologie, Microbiologie et Qualité/ETB, Faculté des Sciences et Techniques de Mohammedia, Université Hassan II Casablanca, B.P. 146, 20650 Mohammedia, Maroc
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Yang L, Yang H, Wu K, Shi X, Ma S, Sun Q. Prevalence of HPV and variation of HPV 16/HPV 18 E6/E7 genes in cervical cancer in women in South West China. J Med Virol 2014; 86:1926-36. [PMID: 25111286 DOI: 10.1002/jmv.24043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Lijuan Yang
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
| | - Hongying Yang
- The Third Affiliated Hospital of Kunming Medical University (Yunnan Provincial Tumor Hospital); Kunming China
| | - Kun Wu
- The First Affiliated Hospital of Kunming Medical University; Kunming China
| | - Xinan Shi
- Southwest Guizhou Vocational and Technical College for Nationalities; Xingyi China
| | - Shaohui Ma
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
| | - Qiangming Sun
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
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Jackson R, Togtema M, Lambert PF, Zehbe I. Tumourigenesis driven by the human papillomavirus type 16 Asian-American e6 variant in a three-dimensional keratinocyte model. PLoS One 2014; 9:e101540. [PMID: 24983759 PMCID: PMC4077794 DOI: 10.1371/journal.pone.0101540] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/30/2014] [Indexed: 12/22/2022] Open
Abstract
Infection with a transforming human papillomavirus (HPV) such as type 16 (of species Alphapapillomavirus 9) causes ano-genital and oral tumours via viral persistence in human squamous cell epithelia. Epidemiological studies showed that the naturally occurring HPV16 Asian-American (AA) variant (sublineage D2/D3) is found more often than the European Prototype (EP) (sublineage A1) in high-grade cervical neoplasia and tumours compared to non-cancer controls. Just three amino acid changes within the early gene, E6, of HPV16 AA have been linked to this augmented tumourigenicity. The AAE6 variant's greater immortalizing and transforming potential over EPE6 has recently been confirmed in retrovirally-transduced keratinocytes expressing the E6 gene only. However, the tumourigenic role of the full-length viral genome of HPV16 has not yet been addressed with regard to these E6 variants. To investigate this process in the context of these two HPV16 E6 genotypes, an organotypic tissue culture model was used to simulate the HPV infectious life cycle. The AAE6 variant demonstrated an enhanced ability over EPE6 to drive the viral life cycle toward tumourigenesis, as evidenced phenotypically—by a more severe grade of epithelial dysplasia with higher proliferation and deregulated differentiation, and molecularly—by high viral oncogene E6 and E7 expression, but lack of productive viral life cycle markers. In contrast, EPE6 had low E6 and E7 but high E1∧E4 expression, indicative of a productive life cycle. We suggest increased viral integration into the host genome for AAE6 as one possible mechanism for these observed differences from EPE6. Additionally, we found downstream effects on immortalization and host innate immune evasion. This study highlights how minor genomic variations in transforming viruses can have a significant affect on their tumourigenic ability.
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Affiliation(s)
- Robert Jackson
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Melissa Togtema
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ingeborg Zehbe
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
- * E-mail:
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Liu M, He Z, Xi L, Li J, Liu F, Liu Y, Pan Y, Ning T, Guo C, Xu R, Zhang L, Cai H, Ke Y. The distribution and common amino acid polymorphisms of human papillomavirus (HPV)-31 variants in 2700 women from Northern China. PLoS One 2014; 9:e99141. [PMID: 24901850 PMCID: PMC4047102 DOI: 10.1371/journal.pone.0099141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/10/2014] [Indexed: 11/18/2022] Open
Abstract
To investigate the distribution of Human papillomavirus (HPV)-31 A, B and C variants as well as the common amino acid polymorphisms in Chinese women, all 14 HPV-31 positive cervical exfoliated cell specimens identified from a descriptive study including ∼2700 women from Northern China were analyzed. HPV-31 positive specimens were identified by Mass Spectrometry and the fragments of partial Long Control Region, E6 and E7 were amplified and directly sequenced or cloned into vector and then sequenced to confirm the variant information. HPV-31 prevalence in Northern Chinese female population was 0.52%. Six different sequences represented all 14 isolates, and these isolates were subsequently classified into variant lineage A (9), B (0) and C (5) by phylogenetic analysis. Five common amino acid polymorphism sites (2 in E6 and 3 in E7) and a novel non-synonymous mutation were detected in the current study. Our investigation suggested that HPV-31 was much less detected in Chinese women population than that in western countries. A and C variants were commonly detected while B variants were rarely detected in this population.
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Affiliation(s)
- Mengfei Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Zhonghu He
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Longfu Xi
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jingjing Li
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Fangfang Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Ying Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Yaqi Pan
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Tao Ning
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Chuanhai Guo
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Ruiping Xu
- Anyang Cancer Hospital, Anyang, Henan, P. R. China
| | - Lixin Zhang
- Anyang Cancer Hospital, Anyang, Henan, P. R. China
| | - Hong Cai
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
- * E-mail: (HC); (YK)
| | - Yang Ke
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
- * E-mail: (HC); (YK)
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HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants. J Med Virol 2014; 86:968-74. [DOI: 10.1002/jmv.23924] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2014] [Indexed: 11/07/2022]
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Tsakogiannis D, Kyriakopoulou Z, Darmis F, Ruether I, Dimitriou T, Orfanoudakis G, Panotopoulou E, Markoulatos P. Prevalence of HPV16 E1-1374^63nt variants in Greek women. J Med Virol 2014; 86:778-84. [DOI: 10.1002/jmv.23896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/14/2014] [Indexed: 11/07/2022]
Affiliation(s)
- D. Tsakogiannis
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
| | - Z. Kyriakopoulou
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
| | - F. Darmis
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
| | - I.G.A. Ruether
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
| | - T.G. Dimitriou
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
| | - G. Orfanoudakis
- Oncoprotein Group; University of Strasbourg; CNRS FRE 3211, The Biotechnology School of Strasbourg, ESBS, University of Strasbourg; Illkirch France
| | - E. Panotopoulou
- Papanicolaou Research Centre of Oncology and Experimental Surgery; Anticancer Oncology Hospital of Athens “St Savvas”; Athens Greece
| | - P. Markoulatos
- Department of Biochemistry & Biotechnology, Microbiology-Virology Laboratory; School of Health Sciences; University of Thessaly; Larissa Greece
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Yang L, Yang H, Chen J, Huang X, Pan Y, Li D, Ding X, Wu K, Shi X, Fu J, Shi H, Ma S, Sun Q. Genetic variability of HPV-58 E6 and E7 genes in Southwest China. INFECTION GENETICS AND EVOLUTION 2013; 21:395-400. [PMID: 24368255 DOI: 10.1016/j.meegid.2013.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/04/2013] [Accepted: 12/17/2013] [Indexed: 01/18/2023]
Abstract
HPV accounts for most of incidence of cervical cancer. Genetic variations of E6 and E7 may be associated with the development of cervical cancer in specific geographic regions. HPV-58 has been found to be a relatively prevalent high-risk HPV among southwest Chinese women. To explore gene intratypic variations and polymorphisms of HPV-58 E6 and E7 genes originating in Southwest China, a total of 2000 scraped cell samples were collected for DNA extraction and HPV typing. Then, the E6 and E7 genes of HPV-58 (n=22) were sequenced and compared to others submitted to GenBank, followed by an analysis of the diversity of secondary structure by DNASTAR software. Phylogenetic trees were then constructed by Neighbor-Joining and the Kimura 2-parameters methods, followed by an analysis of selection pressures acting on the E6/E7 genes by PAML software. 22 were HPV-58 positive among 215 high-risk types' samples. The nucleotide variation rate of E6 was 86.36% (19/22) among the 22 HPV-58 E6 sequences studied. 4 single nucleotide changes were identified among the E6 sequences with 3/4 synonymous mutations (C187T, A260C, C307T) and 1/4 non-synonymous mutations (A388C, from Lys to Asn, in alpha helix). The most common mutations of E6 genes are the C307T and A388C. 8 single nucleotide changes were identified among the HPV-58 E7 sequences with 2/8 synonymous mutations (T726C, T744G) and 6/8 non-synonymous mutations (G599A, C632T, G694A, G760A, G761A, T803C). The nucleotide variation rate of E7 was 72.73% (17/22). The most common mutations of E7 genes are C632T, G694A, T744G, G760A (from Gly to Ser, in turn), G761A and T803C. The phylogenetic analyses demonstrate that all HPV-58 E6/E7 variants identified belonged to the Southeast Asia lineage. There was no evidence of positive selection in the sequence alignment of HPV-58 E6 and E7 genes.
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Affiliation(s)
- Lijuan Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Hongying Yang
- The Third Affiliated Hospital of Kunming Medical University, Yunnan Provincial Tumor Hospital, Kunming 650118, PR China
| | - Junying Chen
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xinwei Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Yue Pan
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Duo Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Xiaojie Ding
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Kun Wu
- The First Affiliated Hospital of Kunming Medical University, Kunming 650032, PR China
| | - Xinan Shi
- Southwest Guizhou Vocational and Technical College for Nationalities, Xingyi 562400, PR China
| | - Juanjuan Fu
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Haijing Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Shaohui Ma
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China
| | - Qiangming Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College, Kunming 650118, PR China; Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, PR China.
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Geraets DT, van Doorn LJ, Kleter B, Colau B, Harper DM, Quint WGV. Long-term follow-up of HPV16-positive women: persistence of the same genetic variant and low prevalence of variant co-infections. PLoS One 2013; 8:e80382. [PMID: 24244682 PMCID: PMC3823622 DOI: 10.1371/journal.pone.0080382] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/11/2013] [Indexed: 02/06/2023] Open
Abstract
HPV16 variants correlate with geographic origin and ethnicity. The association between infection with a specific variant and the cervical disease risk remains unclear. We studied the prevalence, persistence and association with cervical intraepithelial neoplasia (CIN) of different HPV16 variants, using cervical swabs and whole tissue sections (WTS) of biopsies from 548 women in the placebo group of a HPV16/18 vaccine trial. In HPV16-positive samples, HPV16 variants were identified by a reverse hybridization assay (RHA). Laser-capture micro-dissection (LCM) was performed for localized detection of HPV. HPV16 variants were determined in 47 women. Frequency of mixed HPV16 variant infections was lower (8.5%) than for multiple HPV genotypes (39.1%). Among 35 women having consecutive HPV16 variant-positive swabs, 32 (91.4%) had the same variant while in three (8.6%) women a change in variant(s) was observed. HPV16-positive WTS were obtained from 12 women having consecutive HPV16 variant-positive swabs. The same variant was present in WTS of 10 women, while two were negative. WTS of five women were histologically normal. A single HPV16 variant was detected in four women having CIN1-3, while additional HPV genotypes were found in three other women having CIN2 and CIN3. In the WTS of one woman with mixed genotypes, the HPV16 variant was assigned to a CIN2 lesion by LCM. HPV16 variant infections can be effectively studied in cervical swabs and tissue specimens by the HPV16 variant RHA. Multiple HPV16 variants in one woman are rare. The HPV16 genotype consistently detected in follow-up samples usually involves a persistent infection with the same variant.
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49
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Molecular and evolutionary analysis of HPV16 E6 and E7 genes in Greek women. J Med Microbiol 2013; 62:1688-1696. [DOI: 10.1099/jmm.0.055491-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) non-European variants have been associated with persistent infection and cervical cancer development, while the L83V variant of the E6 gene has been correlated with the progression of cervical malignancy. The present study investigated the presence of the HPV16 L83V variant in Greek women. Molecular evolutionary analysis of the HPV16 E6 and E7 oncogenes was conducted in order to estimate the evolution of the HPV16 genome in the Greek population. The E6 L83V variant was found in 78.2 % of high- and 64.28 % of low-grade specimens. Moreover, the prototype and E6 L83V variants were both prevalent in high- and low-grade malignancies in Greek women. Selective pressure analysis of the individual amino acid residues of HPV16 sequences from the Greek population indicates that codon 83 of the E6 protein, as well as codon 85 of the E7 protein, are undergoing positive selection. Novel sequence variations were recorded within the E6 and E7 genes in cervical samples, characterized as (T350G) European variants. However, no signal of intratypic recombination event was identified within the E6–E7 region. Molecular and evolutionary analyses of HPV16 genomes from distinct geographical locations might provide valuable information about viral evolution and oncogenecity.
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50
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Svahn MF, Faber MT, Christensen J, Norrild B, Kjaer SK. Prevalence of human papillomavirus in epithelial ovarian cancer tissue. A meta-analysis of observational studies. Acta Obstet Gynecol Scand 2013; 93:6-19. [PMID: 24033121 DOI: 10.1111/aogs.12254] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/25/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVE The role of human papillomavirus (HPV) in the pathogenesis of ovarian cancer is controversial, and conflicting results have been published. We conducted a systematic review and meta-analysis to estimate the prevalence of HPV in epithelial ovarian cancer tissue. MATERIAL AND METHODS Observational studies published until 4 March 2013 were identified in PubMed and Embase. We adhered to MOOSE guidelines and included 22 studies (case-control, cross-sectional studies). A pooled estimate of the HPV prevalence with corresponding 95% confidence interval (CI) was calculated based on a random effect model. In a meta-regression analysis we examined the contribution of different factors to heterogeneity. Furthermore, publication bias was evaluated. RESULTS The pooled HPV prevalence in ovarian cancer tissue was 15.5%, but wide variation was found (0-66.7%). After stratification by geographical region, publication year, tissue type and method of HPV detection, we found that the prevalence of HPV varied most markedly by geographical area, the prevalence being 45.6% (95% CI, 31.0-60.3) in Asia, 18.5% (95% CI, 8.5-28.6) in Eastern Europe, 1.1% (95% CI, -1.6 to 3.8) in Western Europe and zero in North America. A meta-regression analysis revealed that the difference between geographical regions could not be explained by HPV detection method or type of tissue. CONCLUSIONS Great geographical variation exists in HPV prevalence in ovarian cancer tissue, which is not explained by different HPV detection methods. The results suggest that HPV is unlikely to play an important role in Western European and American women, but cannot reject a role of HPV in other populations.
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Affiliation(s)
- Malene F Svahn
- Danish Cancer Society Research Center, Copenhagen, Denmark
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