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Shing JZ, Porras C, Pinheiro M, Herrero R, Hildesheim A, Liu D, Gail MH, Romero B, Schiller JT, Zúñiga M, Mishra S, Burdette L, Jones K, Schussler J, Ocampo R, Fang J, Liu Z, Lowy DR, Tsang SH, Rodríguez AC, Schiffman M, Haas CB, Carvajal LJ, Brown JR, Kreimer AR, Mirabello L. Differential long-term bivalent HPV vaccine cross-protection by variants in the Costa Rica HPV vaccine trial. NPJ Vaccines 2024; 9:101. [PMID: 38851816 PMCID: PMC11162434 DOI: 10.1038/s41541-024-00896-y] [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: 01/23/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
The AS04-adjuvanted human papillomavirus (HPV)16/18 vaccine, an L1-based vaccine, provides strong vaccine efficacy (VE) against vaccine-targeted type infections, and partial cross-protection to phylogenetically-related types, which may be affected by variant-level heterogeneity. We compared VE against incident HPV31, 33, 35, and 45 detections between lineages and SNPs in the L1 region among 2846 HPV-vaccinated and 5465 HPV-unvaccinated women through 11-years of follow-up in the Costa Rica HPV Vaccine Trial. VE was lower against HPV31-lineage-B (VE=60.7%;95%CI = 23.4%,82.8%) compared to HPV31-lineage-A (VE=94.3%;95%CI = 83.7%,100.0%) (VE-ratio = 0.64;95%CI = 0.25,0.90). Differential VE was observed at several lineage-associated HPV31-L1-SNPs, including a nonsynonymous substitution at position 6372 on the FG-loop, an important neutralization domain. For HPV35, the only SNP-level difference was at position 5939 on the DE-loop, with significant VE against nucleotide-G (VE=65.0%;95%CI = 28.0,87.8) but not for more the common nucleotide-A (VE=7.4%;95%CI = -34.1,36.7). Because of the known heterogeneity in precancer/cancer risk across cross-protected HPV genotype variants by race and region, our results of differential variant-level AS04-adjuvanted HPV16/18 vaccine efficacy has global health implications.
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Affiliation(s)
- Jaimie Z Shing
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Maísa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Danping Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mitchell H Gail
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Byron Romero
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - John T Schiller
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Michael Zúñiga
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Sambit Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Laurie Burdette
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - John Schussler
- Information Management Services Inc, Silver Spring, MD, USA
| | - Rebeca Ocampo
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Jianwen Fang
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Douglas R Lowy
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Sabrina H Tsang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Cameron B Haas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Loretto J Carvajal
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Agencia Costarricense de Investigaciones Biomédicas (ACIB), formerly Proyecto Epidemiológico Guanacaste, Fundación INCIENSA, San José, Costa Rica
| | - Jalen R Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Aimée R Kreimer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [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: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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3
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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Debernardi A, Valot B, Almarcha J, Guenat D, Hocquet D, Algros MP, Riethmuller D, Ramanah R, Mougin C, Prétet JL, Lepiller Q. Longitudinal follow-up of HPV16 sequence after cervical infection: Low intrahost variation and no correlation with clinical evolution. J Med Virol 2022; 94:5512-5518. [PMID: 35799409 DOI: 10.1002/jmv.27978] [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: 04/07/2022] [Revised: 06/12/2022] [Accepted: 07/05/2022] [Indexed: 12/15/2022]
Abstract
Human papillomavirus (HPV) 16 exhibits different variants that may differ in their carcinogenic risk. To identify some high-risk variants, we sequenced and compared HPV16 whole genomes obtained from a longitudinal cohort of 34 HPV16-infected women who had either spontaneously cleared their infection (clearance group or "C"), or developed cervical high-grade lesions following a viral persistence (group persistence or "P"). Phylogenetic analysis of paired samples obtained at the beginning (C0 or P0) and at the end (C2 or P2) of the follow-up (median intervals between C0-C2 and between P0-P2 were 16 and 36.5 months, respectively) revealed a low genetic variability within the host compared to the genetic interhost diversity. By comparing our HPV16 sequences to a reference sequence, we observed 301 different substitutions, more often transitions (60.9%) than transversions (39.1%), that occurred throughout the viral genome, but with a low frequency in E6 and E7 oncogenes (10 and 9 substitutions), suggesting a high conservation of these genes. Deletions and insertions were mostly observed in intergenic regions of the virus. The only significant substitution found between the subgroups C2 and P2 was observed in the L2 gene (L330F), with an unclear biological relevance. Our results suggest a low longitudinal intrahost evolution of HPV16 sequences and no correlation between genetic variations and clinical evolution.
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Affiliation(s)
- Alice Debernardi
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Benoit Valot
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Julien Almarcha
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
| | - David Guenat
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Didier Hocquet
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France.,UMR CNRS 6249 Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | | | - Didier Riethmuller
- Department of Gynecology and Obstetrics, Hôpital Couple-Enfant, University Hospital Grenoble Alpes, La Tronche, France
| | - Rajeev Ramanah
- Gynecology Department, CHU de Besançon, Besançon, France
| | - Christiane Mougin
- Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,UMR U1098 RIGHT, Université de Bourgogne Franche-Comté, Besançon, France
| | - Jean-Luc Prétet
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,Laboratoire De Biologie Cellulaire, CHU de Besançon, Besançon, France
| | - Quentin Lepiller
- EA3181, LabEx LipSTIC ANR-11-LABX-0021, Université de Bourgogne-Franche-Comté, Besançon, France.,Centre National de Référence Papillomavirus, CHU de Besançon, Besançon, France.,Laboratoire De Virologie, CHU de Besançon, Besançon, France
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Wang X, Han S, Li X, Wang X, Wang S, Ma L. Prevalence and distribution of human papillomavirus (HPV) in Luoyang city of Henan province during 2015-2021 and the genetic variability of HPV16 and 52. Virol J 2022; 19:37. [PMID: 35246180 PMCID: PMC8896270 DOI: 10.1186/s12985-022-01759-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/05/2022] [Indexed: 12/09/2022] Open
Abstract
Background Persistent high-risk Human papillomavirus (HPV) subtypes infection has been implicated as a causative of cervical cancer. Distribution and genotypes of HPV infection among females and their variations would assist in the formulation of preventive strategy for cervical cancer. The purpose of the present study is to investigate the prevalence of HPV among females in central China. Methods The distribution and genotypes of HPV among 9943 females attending the gynecological examinations in central of China during 2015–2021 were investigated. HPV genotypes were detected using a commercial kit. Nucleotides sequences of L1, E6 and E7 genes in HPV16 or HPV52 positive samples collected in 2021 were amplified by polymerase chain reaction (PCR). Variations of L1, E6 and E7 in HPV16 and HPV52 were gained by sequencing and compared with the reference sequence. Sublineages of HPV16 and HPV52 were determined by the construction of phylogenetic tree based on L1 gene. Results The overall prevalence of HPV infection was 22.81%, with the infection rate of high-risk human papillomavirus (HR-HPV) was 19.02% and low-risk human papillomavirus (LR-HPV) was 6.40%. The most top five genotypes of HPV infection were HPV16 (7.49%), HPV52 (3.04%), HPV58 (2.36%), HPV18 (1.65%) and HPV51 (1.61%). Plots of the age-infection rate showed that the single HPV, multiple HPV, HR-HPV, LR-HPV infection revealed the same tendency with two peaks of HPV infection were observed among females aged ≤ 20 year-old and 60–65 year-old. The predominant sublineage of HPV16 was A1 and B2 for HPV52. For HPV16, The most prevalent mutations were T266A (27/27) and N181T (7/27) for L1, D32E for E6 and S63F for E7 in HPV16. For HPV52, all of the nucleotide changes were synonymous mutation in L1 (except L5S) and E7 genes. The K93R mutation was observed in most HPV52 E6 protein. Conclusions The present study provides basic information about the distribution, genotypes and variations of HPV among females population in Henan province, which would assist in the formulation of preventive strategies and improvements of diagnostic probe and vaccine for HPV in this region.
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Affiliation(s)
- Xiuli Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Shuizhong Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingwei Li
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Xiaochuan Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Shan Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Li Ma
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China.
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Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK. HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Res 2021; 12:200221. [PMID: 34175494 PMCID: PMC8287217 DOI: 10.1016/j.tvr.2021.200221] [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: 11/19/2020] [Revised: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration. We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5). Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet, Oslo Metropolitan University, Oslo, Norway
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway.
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway.
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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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Dai MZ, Qiu Y, Di XH, Shi WW, Xu HH. Association of cervical carcinogenesis risk with HPV16 E6 and E7 variants in the Taizhou area, China. BMC Cancer 2021; 21:769. [PMID: 34217247 PMCID: PMC8254333 DOI: 10.1186/s12885-021-08531-y] [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: 08/03/2020] [Accepted: 06/23/2021] [Indexed: 01/17/2023] Open
Abstract
Background Human papillomavirus (HPV) type 16 accounts for a larger share of cervical cancer and has been a major health problem worldwide for decades. The progression of initial infection to cervical cancer has been linked to viral sequence properties; however, the role of HPV16 variants in the risk of cervical carcinogenesis, especially with longitudinal follow-up, is not fully understood in China. Methods We aimed to investigate the genetic variability of HPV16 E6 and E7 oncogenes in isolates from cervical exfoliated cells. Between December 2012 and December 2014, a total of 310 single HPV16-positive samples were selected from women living in the Taizhou area, China. Sequences of all E6 and E7 oncogenes were analysed by PCR-sequencing assay. Detailed sequence comparison, genetic heterogeneity analyses and maximum-likelihood phylogenetic tree construction were performed with BioEdit Sequence Alignment Editor and MEGA X software. Data for cytology tests and histological diagnoses were obtained from our Taizhou Area Study with longitudinal follow-up for at least 5 years. The relationship between HPV16 variants and cervical carcinogenesis risk was analysed by the chi-square test or Fisher’s exact test. Results In this study, we obtained 64 distinct variation patterns with the accession GenBank numbers MT681266-MT681329. Phylogenetic analysis revealed that 98.3% of HPV16 variants belong to lineage A, in which the A4 (Asian) sublineage was dominant (64.8%), followed by A2 (12.1%), A1 (11.4%), and A3 (10.0%). The A4 (Asian) sublineage had a higher risk of CIN2+ than the A1–3 (European) sublineages (OR = 2.69, 95% CI = 1.04–6.97, P < 0.05). Furthermore, nucleotide variation in HPV16 E6 T178G is associated with the development of cervical cancer. Conclusion These data could provide novel insights into the role of HPV16 variants in cervical carcinogenesis risk in China. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08531-y.
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Affiliation(s)
- Mei-Zhen Dai
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Yi Qiu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Xing-Hong Di
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Wei-Wu Shi
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, China
| | - Hui-Hui Xu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, Zhejiang, 317000, China.
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Hirose Y, Yamaguchi-Naka M, Onuki M, Tenjimbayashi Y, Tasaka N, Satoh T, Tanaka K, Iwata T, Sekizawa A, Matsumoto K, Kukimoto I. High Levels of Within-Host Variations of Human Papillomavirus 16 E1/E2 Genes in Invasive Cervical Cancer. Front Microbiol 2020; 11:596334. [PMID: 33324377 PMCID: PMC7721666 DOI: 10.3389/fmicb.2020.596334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/22/2020] [Indexed: 12/01/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) is the most common HPV genotype found in invasive cervical cancer (ICC). Recent comprehensive genomics studies of HPV16 have revealed that a large number of minor nucleotide variations in the viral genome are present in each infected woman; however, it remains unclear whether such within-host variations of HPV16 are linked to cervical carcinogenesis. Here, by employing next-generation sequencing approaches, we explored the mutational profiles of the HPV16 genome within individual clinical specimens from ICC (n = 31) and normal cervix (n = 21) in greater detail. A total of 367 minor nucleotide variations (167 from ICC and 200 from the normal cervix) were detected throughout the viral genome in both groups, while nucleotide variations at high frequencies (>10% abundance in relative read counts in a single sample) were more prevalent in ICC (10 in ICC versus 1 in normal). Among the high-level variations found in ICC, six were located in the E1/E2 genes, and all of them were non-synonymous substitutions (Q142K, M207I, and L262V for E1; D153Y, R302T, and T357A for E2). In vitro functional analyses of these E1/E2 variants revealed that E1/M207I, E2/D153Y, and E2/R302T had reduced abilities to support viral replication, and that E2/D153Y and E2/R302T failed to suppress the viral early promoter. These results imply that some within-host variations of E1/E2 present at high levels in ICC may be positively selected for and contribute to cervical cancer development through dysfunction or de-stabilization of viral replication/transcription proteins.
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Affiliation(s)
- Yusuke Hirose
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mayuko Yamaguchi-Naka
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Yuri Tenjimbayashi
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Nobutaka Tasaka
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Toyomi Satoh
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kohsei Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Akihiko Sekizawa
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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10
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Rijsbergen M, Rijneveld R, Todd M, Feiss GL, Kouwenhoven STP, Quint KD, van Alewijk DCJG, de Koning MNC, Klaassen ES, Burggraaf J, Rissmann R, van Poelgeest MIE. Results of phase 2 trials exploring the safety and efficacy of omiganan in patients with human papillomavirus-induced genital lesions. Br J Clin Pharmacol 2020; 86:2133-2143. [PMID: 31755993 DOI: 10.1111/bcp.14181] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/14/2019] [Accepted: 10/21/2019] [Indexed: 12/22/2022] Open
Abstract
AIMS To assess safety and tolerability and explore pharmacodynamics and efficacy of omiganan in external anogenital warts (AGW) and vulvar high-grade squamous intraepithelial lesions (HSIL). METHODS Two randomized controlled trials in patients with external AGW and vulvar HSIL were conducted. Patients received topical omiganan 2.5% or placebo gel once daily for 12 weeks with a follow-up of 12 weeks. Safety and tolerability were monitored and pharmacodynamics and clinical efficacy of omiganan were assessed by analysing lesion count, size and viral load. Self-reported pain, itch and quality of life were assessed by an electronic diary and questionnaire. RESULTS Twenty-four AGW and 12 vulvar HSIL patients were enrolled. All patients had a high treatment adherence (99%). No serious adverse events occurred and all adverse events (n = 27) were mild, transient and self-limiting. The treatment groups were not different in terms of safety and tolerability, lesion count and size, and patient-reported outcomes pain, itch and quality of life. Human papillomavirus load significantly reduced after 12 weeks of treatment with omiganan compared to placebo (-96.6%; 95% confidence interval -99.9 to -7.4%; P = .045) in AGW patients only. CONCLUSION Topical omiganan appears to be safe in patients with AGW and vulvar HSIL and reduced human papillomavirus load after 12 weeks of treatment in AGW patients.
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Affiliation(s)
| | | | - Marina Todd
- Centre for Human Drug Research, Leiden, the Netherlands
| | | | - Stijn T P Kouwenhoven
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Koen D Quint
- Department of Dermatology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | | | | | - Jacobus Burggraaf
- Centre for Human Drug Research, Leiden, the Netherlands.,Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Robert Rissmann
- Centre for Human Drug Research, Leiden, the Netherlands.,Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mariëtte I E van Poelgeest
- Centre for Human Drug Research, Leiden, the Netherlands.,Department of Gynecology, Leiden University Medical Centre, Leiden, the Netherlands
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11
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Zhu B, Xiao Y, Yeager M, Clifford G, Wentzensen N, Cullen M, Boland JF, Bass S, Steinberg MK, Raine-Bennett T, Lee D, Burk RD, Pinheiro M, Song L, Dean M, Nelson CW, Burdett L, Yu K, Roberson D, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Schiffman M, Mirabello L. Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance. Nat Commun 2020; 11:886. [PMID: 32060290 PMCID: PMC7021686 DOI: 10.1038/s41467-020-14730-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
HPV16 causes half of cervical cancers worldwide; for unknown reasons, most infections resolve within two years. Here, we analyze the viral genomes of 5,328 HPV16-positive case-control samples to investigate mutational signatures and the role of human APOBEC3-induced mutations in viral clearance and cervical carcinogenesis. We identify four de novo mutational signatures, one of which matches the COSMIC APOBEC-associated signature 2. The viral genomes of the precancer/cancer cases are less likely to contain within-host somatic HPV16 APOBEC3-induced mutations (Fisher's exact test, P = 6.2 x 10-14), and have a 30% lower nonsynonymous APOBEC3 mutation burden compared to controls. We replicate the low prevalence of HPV16 APOBEC3-induced mutations in 1,749 additional cases. APOBEC3 mutations also historically contribute to the evolution of HPV16 lineages. We demonstrate that cervical infections with a greater burden of somatic HPV16 APOBEC3-induced mutations are more likely to be benign or subsequently clear, suggesting they may reduce persistence, and thus progression, within the host.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gary Clifford
- Infections and Cancer Epidemiology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372, Lyon, Cedex 08, France
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mia K Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tina Raine-Bennett
- Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - DongHyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA, USA
| | | | - Philip E Castle
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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12
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New Diagnostic Approaches to Viral Sexually Transmitted Infections. Sex Transm Infect 2020. [DOI: 10.1007/978-3-030-02200-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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13
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Molet L, Girlich D, Bonnin RA, Proust A, Bouligand J, Bachelerie F, Hantz S, Deback C. Identification by high-throughput sequencing of HPV variants and quasispecies that are untypeable by linear reverse blotting assay in cervical specimens. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2019; 8:100169. [PMID: 31283993 PMCID: PMC6620621 DOI: 10.1016/j.pvr.2019.100169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/11/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
The linear reverse blotting assays are valid methods for accurate human papillomavirus (HPV) typing required to manage women at risk of developing cervical cancer. However, some samples showed a positive signal in HPV lines but failed to display a positive signal in subsequent typing lines (designated as HPV-X), which indicate that certain types were not available on the respective typing blots. The aim of this study is to elucidate the types or variants of HPV through the high-throughput sequencing (HTS) of 54 ASCUS cervical samples in which the viruses remained untypeable with INNO LiPA HPV® assays. Low-risk (LR)-HPV types (HPV6, 30, 42, 62, 67, 72, 74, 81, 83, 84, 87, 89, 90 and 114), high-risk (HR)-HPV35 and possibly (p)HR-HPV73 were detected among HPV-X. Individual multiple infections (two to seven types) were detected in 40.7% of samples. Twenty-two specimens contained variants characterised by 2-10 changes. HPV30 reached the maximal number of 17 variants with relative abundance inferior or equal to 2.7%. The presence of L1 quasispecies explains why linear reverse blotting assays fail when variants compete or do not match the specific probes. Further studies are needed to measure the LR-HPV quasispecies dynamics and its role during persistent infection.
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Affiliation(s)
- Lucie Molet
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Sud, Hôpital Paul Brousse, Villejuif, France; INSERM UMR-996 « Inflammation, Chimiokines et Immunopathologies », Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculté de Médecine, Clamart, France
| | - Delphine Girlich
- EA7361 « Structure, Dynamics, Function and Expression of Broad-spectrum β-lactamases », Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculté de Médecine, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- EA7361 « Structure, Dynamics, Function and Expression of Broad-spectrum β-lactamases », Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculté de Médecine, Le Kremlin-Bicêtre, France
| | - Alexis Proust
- Laboratoire de génétique moléculaire, pharmacogénétique et hormonologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Jérôme Bouligand
- Laboratoire de génétique moléculaire, pharmacogénétique et hormonologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France; INSERM UMR-1185 « Signalisation Hormonale, Physiopathologie Endocrinienne et Métabolique », Université Paris Sud, Université Paris Saclay, Faculté de Médecine, Le Kremlin Bicêtre, France
| | - Françoise Bachelerie
- INSERM UMR-996 « Inflammation, Chimiokines et Immunopathologies », Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculté de Médecine, Clamart, France
| | - Sébastien Hantz
- Univ. Limoges, RESINFIT, U1092, F-87000, Limoges, France; CHU Limoges, Laboratoire de Bactériologie-Virologie-Hygiène, F-87000, Limoges, France
| | - Claire Deback
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris Sud, Hôpital Paul Brousse, Villejuif, France; INSERM UMR-996 « Inflammation, Chimiokines et Immunopathologies », Université Paris Sud, Université Paris Saclay, LabEx Lermit, Faculté de Médecine, Clamart, France.
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14
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Zhao J, Zhu J, Guo J, Zhu T, Zhong J, Liu M, Ruan Y, Liao S, Li F. Genetic variability and functional implication of HPV16 from cervical intraepithelial neoplasia in Shanghai women. J Med Virol 2019; 92:372-381. [PMID: 31670402 DOI: 10.1002/jmv.25618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022]
Abstract
Human papillomavirus (HPV)16 gene mutation is usually associated with persistent HPV infection and cervical intraepithelial neoplasia (CIN). However, the functional implications of HPV16 mutations remain poorly understood.145 LCR/E6/E7 of the HPV16 isolates were amplified and sequenced, and HPV16 integration status was detected. In total, 89 SNPs (68 in the LCR, 13 in E6, 8 in E7) were discovered, 11 of which were nonsynonymous mutations (8 in E6, 3 in E7). The H85Y and E120D variants in E6 were significantly reduced in the high-grade squamous intraepithelial lesion (HSIL) group compared to the <HSIL group (P = .046 and .005), conversely the N29S in E7(P = .01). Amino acid substitutions (D32N/E, E36Q, H85Y, and E120D in E6 and N29H/S and R77C in E7) were predicted to have an effect on conserved structural and functional residues, and five amino acid substitutions (H85Y, E36Q, I34L, and D32E in E6; R77C in E7) would potentially change the secondary structure. "6329G>T," a potential binding site for TATA-binding protein, is the most common in LCR variants. A4 (Asian) was associated with an increased risk of HSIL compared to A1-3(P = .009). The H85/E120 in E6 and N29 in HPV16 E7 might play a critical role in carcinogenesis by disrupting p53 and Rb degradation due to affecting their interaction, respectively. In a word, the findings in this study provide preventative and therapeutic interventions of HPV16 -related cervical lesions/cancer.
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Affiliation(s)
- Junwei Zhao
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiacheng Zhu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Maternal and Child Health Research Institute, BGI-Shenzhen, Shenzhen, China
| | - Junhan Guo
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tailin Zhu
- School of Physics HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Jixing Zhong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Min Liu
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shujie Liao
- Shujie Liao Cancer Biology Research Center, Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Li
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
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15
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Lagström S, van der Weele P, Rounge TB, Christiansen IK, King AJ, Ambur OH. HPV16 whole genome minority variants in persistent infections from young Dutch women. J Clin Virol 2019; 119:24-30. [PMID: 31446251 DOI: 10.1016/j.jcv.2019.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND Chronic infections by one of the oncogenic human papillomaviruses (HPVs) are responsible for near 5% of the global cancer burden and HPV16 is the type most often found in cancers. HPV genomes display unexpected levels of variation when deep-sequenced. Minor nucleotide variations (MNVs) may reveal HPV genomic instability and HPV-related carcinogenic transformation of host cells. OBJECTIVES The objective of this study was to investigate HPV16 genome variation at the minor variant level on persisting HPV16 cervical infections from a population of young Dutch women. STUDY DESIGN 15 HPV16 infections were sequenced using a whole-HPV genome deep sequencing protocol (TaME-seq). One infection was followed over a three-year period, eight were followed over a two-year period, three were followed over a one-year period and three infections had a single sampling point. RESULTS AND CONCLUSIONS Using a 1% variant frequency cutoff, we find on average 48 MNVs per HPV16 genome and 1717 MNVs in total when sequencing coverage was >100 × . We find the transition mutation T > C to be the most common, in contrast to other studies detecting APOBEC-related C > T mutation profiles in pre-cancerous and cancer samples. Our results suggest that the relative mutagenic footprint of HPV16 genomes may differ between the infections in this study and transforming lesions. In addition, we identify a number of MNVs that have previously been associated with higher incidence of high-grade lesions (CIN3+) in a population study. These findings may provide a starting point for future studies exploring causality between emerging HPV minor genomic variants and cancer development.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pascal van der Weele
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Research, Diagnostics and Screening, Bilthoven, the Netherlands; Vrije Universiteit-University Medical Center (VUmc), Department of Pathology, Amsterdam, the Netherlands
| | | | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Audrey J King
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Research, Diagnostics and Screening, Bilthoven, the Netherlands.
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway.
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16
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Shen-Gunther J, Cai H, Zhang H, Wang Y. Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. Front Genet 2019; 10:489. [PMID: 31231420 PMCID: PMC6558378 DOI: 10.3389/fgene.2019.00489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The aim of this study was to explore the Human Papillomavirus (HPV) genotype composition and intra-genotype variants within individual samples of low- and high-grade cervical cytology by deep sequencing. Clinical, cytological, sequencing, and functional/structural data were forged into an integrated variant profiling pipeline for the detection of potentially vaccine-resistant genotypes or variants. Methods: Low- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples with +HPV were subjected to amplicon (L1 gene fragment) sequencing by dideoxy (Sanger) and deep methods. Taxonomic, abundance, diversity, and phylogenetic analyses were conducted to determine HPV genotypes/sub-lineages, relative abundance, species diversity and phylogenetic distances within and between samples. Variant detection and functional analysis of translated L1 amino acid sequences determined structural variations of interest. Results: Pure and mixed HPV infections were common among LSIL (n = 6) and HSIL (n = 6) samples. Taxonomic profiling revealed loss of species richness and gain of dominance by carcinogenic genotypes in HSIL samples. Phylogenetic analysis showed excellent correlation between HPV-type specific genetic distances and carcinogenic potential. For combined LSIL/HSIL samples (n = 12), 11 HPV genotypes and 417 mutations were detected: 375 single-nucleotide variants (SNV), 29 insertion/deletion (indel), 12 multi-nucleotide variants (MNV), and 1 replacement variant. The proportion of nonsynonymous mutations was lower for HSIL (0.38) than for LSIL samples (0.51) (p < 0.05). HPV variant analysis pinpointed nucleotide-level mutations and amino acid-level structural modifications. Conclusion: HPV L1 intra-host and intra-genotype variants are abundant in LSIL and HSIL samples with potential functional/structural consequences. An integrated multi-omics approach to variant analysis may provide a sensitive and practical means of detecting changes in HPV evolution and dynamics within individuals or populations.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology and Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX, United States
| | - Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States
| | - Hao Zhang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States
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17
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Whole-Genome Analysis of Human Papillomavirus Type 16 Prevalent in Japanese Women with or without Cervical Lesions. Viruses 2019; 11:v11040350. [PMID: 30995759 PMCID: PMC6520816 DOI: 10.3390/v11040350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/12/2019] [Accepted: 04/13/2019] [Indexed: 12/23/2022] Open
Abstract
Recent large-scale genomics studies of human papillomaviruses (HPVs) have shown a high level of genomic variability of HPV16, the most prevalent genotype in HPV-associated malignancies, and provided new insights into the biological and clinical relevance of its genetic variations in cervical cancer development. Here, we performed deep sequencing analyses of the viral genome to explore genetic variations of HPV16 that are prevalent in Japan. A total of 100 complete genome sequences of HPV16 were determined from cervical specimens collected from Japanese women with cervical intraepithelial neoplasia and invasive cervical cancer, or without cervical malignancies. Phylogenetic analyses revealed the variant distribution in the Japanese HPV16 isolates; overall, lineage A was the most prevalent (94.0%), in which sublineage A4 was dominant (52.0%), followed by sublineage A1 (21.0%). The relative risk of sublineage A4 for cervical cancer development was significantly higher compared to sublineages A1/A2/A3 (odds ratio = 6.72, 95% confidence interval = 1.78–28.9). Interestingly, a novel cluster of variants that branched from A1/A2/A3 was observed for the Japanese HPV16 isolates, indicating that unique HPV16 variants are prevalent among Japanese women.
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18
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van der Weele P, King AJ, Meijer CJLM, Steenbergen RDM. HPV16 variant analysis in primary and recurrent CIN2/3 lesions demonstrates presence of the same consensus variant. PAPILLOMAVIRUS RESEARCH 2019; 7:168-172. [PMID: 30991124 PMCID: PMC6477513 DOI: 10.1016/j.pvr.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/01/2019] [Accepted: 04/07/2019] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Recurrent cervical intraepithelial lesions (rCIN2/3) after treatment of CIN2/3 occur in 5-15% of cases. rCIN2/3 can result from incomplete resection of CIN2/3, where the same HPV type and variant remains present. rCIN2/3 could also occur following a new infection with a different HPV variant of the same HPV type as the initial lesion. This study investigates HPV16 consensus variants in paired HPV16 positive scrapes from baseline CIN2/3 and rCIN2/3 lesions. METHODS Paired HPV16 positive cervical scrapes of women with CIN2/3 at baseline and rCIN2/3 6 or 12 months after treatment were selected for whole-genome amplification and Illumina sequencing. Sequences were compared and nucleotide changes over time were characterized. RESULTS From 14 paired samples, 10 had identical consensus variants in baseline CIN2/3 and rCIN2/3. Four paired samples showed one to three nucleotide variations at recurrent disease compared to baseline. CONCLUSION Identical or nearly identical HPV16 consensus variants were found in scrapes of paired HPV16 positive baseline CIN2/3 and rCIN2/3 lesions after treatment, suggesting no need for HPV variant analysis when the same HPV type is found in both lesions. These results argue for either incomplete excision of baseline CIN2/3 or inability of clearance of the original HPV infection.
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Affiliation(s)
- Pascal van der Weele
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Antonie van Leeuwenhoeklaan 9, Bilthoven, the Netherlands; Amsterdam UMC, Vrije Universiteit, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Audrey J King
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Antonie van Leeuwenhoeklaan 9, Bilthoven, the Netherlands
| | - Chris J L M Meijer
- Amsterdam UMC, Vrije Universiteit, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
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Disease Manifestation and Viral Sequences in a Bonobo More Than 30 Years after Papillomavirus Infection. Pathogens 2019; 8:pathogens8010013. [PMID: 30691118 PMCID: PMC6470980 DOI: 10.3390/pathogens8010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/27/2018] [Accepted: 01/15/2019] [Indexed: 12/02/2022] Open
Abstract
Pan paniscus Papillomavirus 1 (PpPV1) causes focal epithelial hyperplasia (FEH) in infected animals. Here, we analyzed the present disease manifestation and PpPV1 genomic sequence of an animal that was afflicted by an FEH epizootic outbreak in 1987 for which the sequence of the responsible PpPV1 was determined. The animal displayed FEH more than 30 years after the initial diagnosis, indicating persistence or recurrence of the disease, and evidence for active PpPV1 infection was obtained. Moreover, the sequences of the viral genomes present in the late 1980s and in 2018 differed at 23 nucleotide positions, resulting in 11 amino acid exchanges within coding regions. These findings suggest that PpPV1-induced FEH might not undergo complete and/or permanent remission in a subset of afflicted animals.
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Galati L, Equestre M, Bruni R, Accardi L, Torti C, Fiorillo MT, Surace G, Barreca GS, Liberto MC, Focà A, Ciccaglione AR, Di Bonito P. Identification of human papillomavirus type 16 variants circulating in the Calabria region by sequencing and phylogenetic analysis of HPV16 from cervical smears. INFECTION GENETICS AND EVOLUTION 2018; 68:185-193. [PMID: 30578936 DOI: 10.1016/j.meegid.2018.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/04/2023]
Abstract
Sequence analysis of HPV16 isolates reveals the presence of genome variants with characteristic mutations. The HPV16 variants have different geographical distribution and diverge into four phylogenetic lineages (A, B, C and D) and 16 sub-lineages: A1, A2, A3 (previously known as European variants), A4 (Asian variant), B1, B2, B3, B4, C1, C2, C3, and C4 (African variants), D1 (North-American variant), D2, D3 (Asian-American variants) and D4. Population studies showed that infections with viruses belonging to specific HPV16 sublineages confer different risks of viral persistence and cancer. In this study, 39 HPV16-positive cervical smears from European women living in Calabria (Italy) were analyzed for the presence of HPV16 variants. Cervical DNA extracts were processed by PCR to amplify L1, the Long Control Region (LCR), E6 and E7, which were sequenced. The sequences were concatenated and the 3169 nucleotides long fragments were characterized by BLAST and phylogenetic analysis. A total of 96 Single Nucleotide Polymorphism (SNPs) were detected, 29 of which mapping in the L1, 45 in the LCR, 15 in the E6 and 7 in the E7. The most common SNP was the T350G (29/39 samples, 74.4%), causing the L83 V amino acid change in the E6. Most of the HPV16 isolates (89.7%) had 99% of nucleotide (nt) identity to members of the A1 and A2 sublineages, while 4 isolates had 99% nt identity to members of the B2, B4, C1 and D4 sublineages. In conclusion, viruses belonging to the A1, A2, B2, B4, C1 and D4 HPV16 sublineages were found to circulate in the Calabria region.
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Affiliation(s)
- Luisa Galati
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy; Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Michele Equestre
- Department Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Bruni
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Luisa Accardi
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of "Magna Graecia", Catanzaro, Italy
| | - Maria Teresa Fiorillo
- Unit of Microbiology and Virology, Polo Sanitario Nord ASP 5, Reggio Calabria, Italy
| | - Giovanni Surace
- Unit of Microbiology and Virology, Polo Sanitario Nord ASP 5, Reggio Calabria, Italy
| | - Giorgio Settimo Barreca
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Maria Carla Liberto
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Alfredo Focà
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Anna Rita Ciccaglione
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Di Bonito
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy.
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Cossellu G, Fedele L, Badaoui B, Angiero F, Farronato G, Monti E, Liverani CA, Gorni C, Botti S. Prevalence and concordance of oral and genital HPV in women positive for cervical HPV infection and in their sexual stable partners: An Italian screening study. PLoS One 2018; 13:e0205574. [PMID: 30335788 PMCID: PMC6193646 DOI: 10.1371/journal.pone.0205574] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/27/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES This cross-sectional study aimed to evaluate the prevalence and type of oral HPV-infection in women with a cervical HPV-lesion and in the oral and genital mucosa of their male partners. METHODS The study group comprised 44 sexually-active women, 20-45 years with abnormal PAP smear, not more than 6 months prior to referral together with the male partners cohabiting in stable partnerships. A detailed questionnaire was administered concerning the HPV-related risk factors. Oral swabs, oral rinses, cervical swabs and urine samples were collected. HPV DNA was detected using two different polymerase chain reactions (PCRs): MY09-11 and FAP59-64. Positive samples were genotyped by Sanger sequencing and the INNO-LiPA HPV Genotyping Extra II probe assay. The association with risk factors was assessed by fitting a generalized model, using the General Linear Model function in the R-software; correlations were calculated between all data. RESULTS HPV was detected in 84% of Cervical Samples, in 24.3% of oral samples and in one urine sample. Only 27% of the HPV-positive results were identical with both PCR DNA assays. 8 male had oral HPV-positive samples different from women cervical samples. In one couple the urine-male sample had the same HPV present in the female-cervical sample. A significant association resulted between women/oral sex practices and men/n. of partners. CONCLUSIONS This study reports that women (20.4%) with a diagnosis of cervical-HPV and their male partners (30,7%) are at high risk for subclinical oral HPV infection.
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Affiliation(s)
- Gianguido Cossellu
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
- * E-mail:
| | - Luigi Fedele
- Dipartimento Donna - Bambino - Neonato, Centro di riferimento per la prevenzione, la diagnosi e la cura della patologia genitale HPV correlate, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology and Genome; Mohamed V University, Rabat, Maroc
| | - Francesca Angiero
- Department of Medical Sciences and Diagnostic Integrated, S. Martino Hospital, University of Genoa, Italy
| | - Giampietro Farronato
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Ermelinda Monti
- Dipartimento Donna - Bambino - Neonato, Centro di riferimento per la prevenzione, la diagnosi e la cura della patologia genitale HPV correlate, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Carlo Antonio Liverani
- Dipartimento Donna - Bambino - Neonato, Centro di riferimento per la prevenzione, la diagnosi e la cura della patologia genitale HPV correlate, Fondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Gorni
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
| | - Sara Botti
- Parco Tecnologico Padano - CERSA, Integrative Biology Group, Lodi, Italy
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Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome. J Virol 2018; 92:JVI.00017-18. [PMID: 29593040 DOI: 10.1128/jvi.00017-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/08/2018] [Indexed: 01/05/2023] Open
Abstract
Persistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied by the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here, we explored within-host genetic diversity of HPV by performing deep-sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52, and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC) and were deep sequenced. After constructing a reference viral genome sequence for each specimen, nucleotide positions showing changes with >0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1, n = 56; CIN2/3, n = 68; ICC, n = 27), with various numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the trinucleotide context encompassing substituted bases revealed that TpCpN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions.IMPORTANCE HPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep-sequencing analyses, we show for the first time a comprehensive snapshot of the within-host genetic diversity of high-risk HPVs during cervical carcinogenesis. Quasispecies harboring minor nucleotide variations in viral whole-genome sequences were extensively observed across different grades of CIN and cervical cancer. Among the within-host variations, C-to-T transitions, a characteristic change mediated by cellular APOBEC cytosine deaminases, were predominantly detected throughout the whole viral genome, most strikingly in low-grade CIN lesions. The results strongly suggest that within-host variations of the HPV genome are primarily generated through the interaction with host cell DNA-editing enzymes and that such within-host variability is an evolutionary source of the genetic diversity of HPVs.
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23
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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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24
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van der Weele P, Meijer CJLM, King AJ. High Whole-Genome Sequence Diversity of Human Papillomavirus Type 18 Isolates. Viruses 2018; 10:v10020068. [PMID: 29414918 PMCID: PMC5850375 DOI: 10.3390/v10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
Background: The most commonly found human papillomavirus (HPV) types in cervical cancer are HPV16 and HPV18. Genome variants of these types have been associated with differential carcinogenic potential. To date, only a handful of studies have described HPV18 whole genome sequencing results. Here we describe HPV18 variant diversity and conservation of persistent infections in a longitudinal retrospective cohort study. Methods: Cervical self-samples were obtained annually over four years and genotyped on the SPF10-DEIA-LiPA25 platform. Clearing and persistent HPV18 positive infections were selected, amplified in two overlapping fragments, and sequenced using 32 sequence primers. Results: Complete viral genomes were obtained from 25 participants with persistent and 26 participants with clearing HPV18 infections, resulting in 52 unique HPV18 genomes. Sublineage A3 was predominant in this population. The consensus viral genome was completely conserved over time in persistent infections, with one exception, where different HPV18 variants were identified in follow-up samples. Conclusions: This study identified a diverse set of HPV18 variants. In persistent infections, the consensus viral genome is conserved. The identification of only one HPV18 infection with different major variants in follow-up implies that this is a potentially rare event. This dataset adds 52 HPV18 genome variants to Genbank, more than doubling the currently available HPV18 information resource, and all but one variant are unique additions.
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Affiliation(s)
- Pascal van der Weele
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, 3721 MA Bilthoven, The Netherlands.
- Department of Pathology, Vrije Universiteit-University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands.
| | - Chris J L M Meijer
- Department of Pathology, Vrije Universiteit-University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands.
| | - Audrey J King
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, 3721 MA Bilthoven, The Netherlands.
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25
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de Sanjosé S, Brotons M, Pavón MA. The natural history of human papillomavirus infection. Best Pract Res Clin Obstet Gynaecol 2018; 47:2-13. [DOI: 10.1016/j.bpobgyn.2017.08.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 01/14/2023]
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26
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Alizon S, Murall CL, Bravo IG. Why Human Papillomavirus Acute Infections Matter. Viruses 2017; 9:v9100293. [PMID: 28994707 PMCID: PMC5691644 DOI: 10.3390/v9100293] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/25/2017] [Accepted: 10/02/2017] [Indexed: 02/06/2023] Open
Abstract
Most infections by human papillomaviruses (HPVs) are `acute', that is non-persistent. Yet, for HPVs, as for many other oncoviruses, there is a striking gap between our detailed understanding of chronic infections and our limited data on the early stages of infection. Here we argue that studying HPV acute infections is necessary and timely. Focusing on early interactions will help explain why certain infections are cleared while others become chronic or latent. From a molecular perspective, descriptions of immune effectors and pro-inflammatory pathways during the initial stages of infections have the potential to lead to novel treatments or to improved handling algorithms. From a dynamical perspective, adopting concepts from spatial ecology, such as meta-populations or meta-communities, can help explain why HPV acute infections sometimes last for years. Furthermore, cervical cancer screening and vaccines impose novel iatrogenic pressures on HPVs, implying that anticipating any viral evolutionary response remains essential. Finally, hints at the associations between HPV acute infections and fertility deserve further investigation given their high, worldwide prevalence. Overall, understanding asymptomatic and benign infections may be instrumental in reducing HPV virulence.
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Affiliation(s)
- Samuel Alizon
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
| | - Carmen Lía Murall
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
| | - Ignacio G Bravo
- MIVEGEC (UMR CNRS 5290, UR IRD 224, UM), 911 avenue Agropolis, 34394 Montpellier CEDEX 5, France.
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