1
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Mlynarczyk-Bonikowska B, Rudnicka L. HPV Infections-Classification, Pathogenesis, and Potential New Therapies. Int J Mol Sci 2024; 25:7616. [PMID: 39062859 PMCID: PMC11277246 DOI: 10.3390/ijms25147616] [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: 05/10/2024] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
To date, more than 400 types of human papillomavirus (HPV) have been identified. Despite the creation of effective prophylactic vaccines against the most common genital HPVs, the viruses remain among the most prevalent pathogens found in humans. According to WHO data, they are the cause of 5% of all cancers. Even more frequent are persistent and recurrent benign lesions such as genital and common warts. HPVs are resistant to many disinfectants and relatively unsusceptible to external conditions. There is still no drug available to inhibit viral replication, and treatment is based on removing lesions or stimulating the host immune system. This paper presents the systematics of HPV and the differences in HPV structure between different genetic types, lineages, and sublineages, based on the literature and GenBank data. We also present the pathogenesis of diseases caused by HPV, with a special focus on the role played by E6, E7, and other viral proteins in the development of benign and cancerous lesions. We discuss further prospects for the treatment of HPV infections, including, among others, substances that block the entry of HPV into cells, inhibitors of viral early proteins, and some substances of plant origin that inhibit viral replication, as well as new possibilities for therapeutic vaccines.
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2
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Galati L, Chiantore MV, Marinaro M, Di Bonito P. Human Oncogenic Viruses: Characteristics and Prevention Strategies-Lessons Learned from Human Papillomaviruses. Viruses 2024; 16:416. [PMID: 38543781 PMCID: PMC10974567 DOI: 10.3390/v16030416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Approximately 12% of human cancers worldwide are associated with infectious agents, which are classified by the International Agency for Research on Cancer (IARC) as Group 1 within the agents that are carcinogenic to humans. Most of these agents are viruses. Group 1 oncogenic viruses include hepatitis C virus, hepatitis B virus (HBV), human T-cell lymphotropic virus type 1, Epstein-Barr virus, Kaposi sarcoma-associated herpesvirus, human immunodeficiency virus-1 and high-risk human papillomaviruses (HPVs). In addition, some human polyomaviruses are suspected of inducing cancer prevalently in hosts with impaired immune responses. Merkel cell polyomavirus has been associated with Merkel cell carcinoma and included by the IARC in Group 2A (i.e., probably carcinogenic to humans). Linking viruses to human cancers has allowed for the development of diagnostic, prophylactic and therapeutic measures. Vaccination significantly reduced tumours induced by two oncogenic viruses as follows: HBV and HPV. Herein, we focus on mucosal alpha HPVs, which are responsible for the highest number of cancer cases due to tumour viruses and against which effective prevention strategies have been developed to reduce the global burden of HPV-related cancers.
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Affiliation(s)
- Luisa Galati
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Maria Vincenza Chiantore
- Department of Infectious Diseases, Viral Hepatitis and Oncovirus and Retrovirus Diseases (EVOR) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Microorganisms and Host Response: Research and Technological Innovation (MICROS) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Paola Di Bonito
- Department of Infectious Diseases, Viral Hepatitis and Oncovirus and Retrovirus Diseases (EVOR) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
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3
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Gelbard MK, Munger K. Human papillomaviruses: Knowns, mysteries, and unchartered territories. J Med Virol 2023; 95:e29191. [PMID: 37861365 PMCID: PMC10608791 DOI: 10.1002/jmv.29191] [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: 08/25/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
There has been an explosion in the number of papillomaviruses that have been identified and fully sequenced. Yet only a minute fraction of these has been studied in any detail. Most of our molecular research efforts have focused on the E6 and E7 proteins of "high-risk," cancer-associated human papillomaviruses (HPVs). Interactions of the high-risk HPV E6 and E7 proteins with their respective cellular targets, the p53 and the retinoblastoma tumor suppressors, have been investigated in minute detail. Some have thus questioned if research on papillomaviruses remains an exciting and worthwhile area of investigation. However, fundamentally new insights on the biological activities and cellular targets of the high-risk HPV E6 and E7 proteins have been discovered and previously unstudied HPVs have been newly associated with human diseases. HPV infections continue to be an important cause of human morbidity and mortality and since there are no antivirals to combat HPV infections, research on HPVs should remain attractive to new investigators and biomedical funding agencies, alike.
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Affiliation(s)
- Maya K. Gelbard
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
| | - Karl Munger
- Genetics, Molecular and Cellular Biology Program, Graduate School of Biomedical Sciences
- Department of Developmental, Molecular and Cellular Biology, Tufts University School of Medicine, Boston, MA 02111
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Li Y, Zhang X, Zhao C, Lei X, Huang H, Shi Y, Li C, Bi J, Sun W, Lan T, Zheng M. Genetic characterization of Sus scrofa papillomavirus type 1 from domestic pigs in Guangxi Province, China. Braz J Microbiol 2023; 54:2437-2443. [PMID: 37578737 PMCID: PMC10484830 DOI: 10.1007/s42770-023-01092-1] [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: 06/07/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023] Open
Abstract
Sus scrofa papillomatosis (SsP) is a tumour caused by Sus scrofa papillomaviruses (SsPVs). To investigate the presence of SsPVs in China, 354 domestic pig skin samples collected from Guangxi Province were examined for SsPV DNA by PCR. Three SsPV1s (GX12, GX14, and GX18) were identified with a prevalence of 0.847% (3/354). Sequence analysis showed that L1 of SsPV1/GX12 and SsPV1/GX14 had 99.7% and 99.6% nucleotide identify with the reference SsPV1a, respectively. Phylogenetic and evolutionary analyses showed that SsPV1/GX12 and SsPV1/14 clustered into SsPV1a and that SsPV1/GX18 clustered into SsPV1b. Compared with other SsPV L1 and L2 proteins, we found that the SsPV1/GX18 and SsPV1b strains shared the same unique substitutions, and SsPV1/GX12, SsPV1/GX14, and SsPV1a shared almost identical amino acid sequences. This study reports the first detection of SsPV DNA in China based on whole genome information and provides a scientific basis for the development of SsPV pathogenic biology, epidemiology, and prevention, as well as control technology research.
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Affiliation(s)
- Yuying Li
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Xinyu Zhang
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Chenchen Zhao
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Xiaoxiao Lei
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Haixin Huang
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China
| | - Yaokai Shi
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Chengkai Li
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Jingshan Bi
- Guangxi Centre for Animal Disease Control and Prevention, Nanning, 530001, China
| | - Wenchao Sun
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China.
| | - Tian Lan
- Institute of Virology, Wenzhou University, Wenzhou, 325035, China.
| | - Min Zheng
- Guangxi Centre for Animal Disease Control and Prevention, Nanning, 530001, China.
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Chen Z, Utro F, Platt D, DeSalle R, Parida L, Chan PKS, Burk RD. K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses. Int J Mol Sci 2021; 22:9657. [PMID: 34502564 PMCID: PMC8432194 DOI: 10.3390/ijms22179657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022] Open
Abstract
Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differences in tissue tropism and carcinogenicity. The evolutionary features associated with the divergence of Papillomaviridae are not well understood. Using a combination of k-mer distributions, genetic metrics, and phylogenetic algorithms, we sought to evaluate the characteristics and differences of Alpha-, Beta- and Gamma-PVs constituting the majority of HPV genomes. A total of 640 PVs including 442 HPV types, 27 non-human primate PV types, and 171 non-primate animal PV types were evaluated. Our analyses revealed the highest genetic diversity amongst Gamma-PVs compared to the Alpha and Beta PVs, suggesting reduced selective pressures on Gamma-PVs. Using a sequence alignment-free trimer (k = 3) phylogeny algorithm, we reconstructed a phylogeny that grouped most HPV types into a monophyletic clade that was further split into three branches similar to alignment-based classifications. Interestingly, a subset of low-risk Alpha HPVs (the species Alpha-2, 3, 4, and 14) split from other HPVs and were clustered with non-human primate PVs. Surprisingly, the trimer-constructed phylogeny grouped the Gamma-6 species types originally isolated from the cervicovaginal region with the main Alpha-HPV clade. These data indicate that characterization of papillomavirus heterogeneity via orthogonal approaches reveals novel insights into the biological understanding of HPV genomes.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Filippo Utro
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Daniel Platt
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA;
| | - Laxmi Parida
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Hošnjak L, Kocjan BJ, Pirš B, Seme K, Poljak M. The genetic diversity of human papillomavirus types from the species Gammapapillomavirus 15: HPV135, HPV146, and HPV179. PLoS One 2021; 16:e0249829. [PMID: 33956809 PMCID: PMC8101917 DOI: 10.1371/journal.pone.0249829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES To determine the prevalence, viral load, tissue tropism, and genetic variability of novel human papillomavirus (HPV) type 179, which is etiologically associated with sporadic cases of common warts in immunocompromised patients, and phylogenetically related HPV types 135 and 146. METHODS The representative collection of 850 HPV-associated clinical samples (oral/nasopharyngeal/anal, archival specimens of oral/oropharyngeal/conjunctival/cervical/skin cancer, benign lesions of the larynx/conjunctiva/skin, and eyebrows), obtained from immunocompetent individuals, was tested for the presence of HPV179, HPV135, and HPV146 using type-specific real-time PCRs. To assess the genetic diversity of the HPVs investigated in the non-coding long control region (LCR), several highly sensitive nested PCR protocols were developed for each HPV type. The genetic diversity of HPV179 was additionally determined in 12 HPV179 isolates from different anatomical sites of an only immunocompromised patient included in the study. RESULTS HPV179, HPV135, and HPV146 were detected in 1.4, 2.0, and 1.5% of the samples tested, respectively, with no preference for cutaneous or mucosal epithelial cells. One (with five single nucleotide polymorphisms; SNPs), four (with one to six SNPs), and four (with one to eight SNPs) genetic variants of HPV179, HPV135, and HPV146, respectively, were identified among eligible samples. HPV179 isolates from the immunocompromised patient exhibited the identical LCR nucleotide sequence, suggesting that HPV179 can cause generalized HPV infections. CONCLUSIONS HPV179, HPV135, and HPV146 have a mucocutaneous tissue tropism and are associated with sporadic infections in immunocompromised and immunocompetent individuals. Because the majority of mutations were found outside the major functional domains of the respective LCRs, we assume that HPV179, HPV135, and HPV146 genetic variants pathogenically do not differ from their prototypes. In addition, no association was found between specific HPV179, HPV135, and HPV146 genetic variants and anatomical sites of infection and/or specific neoplasms.
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Affiliation(s)
- Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katja Seme
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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Characterization and Diversity of 243 Complete Human Papillomavirus Genomes in Cervical Swabs Using Next Generation Sequencing. Viruses 2020; 12:v12121437. [PMID: 33327447 PMCID: PMC7764970 DOI: 10.3390/v12121437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 12/21/2022] Open
Abstract
In recent years, next generation sequencing (NGS) technology has been widely used for the discovery of novel human papillomavirus (HPV) genotypes, variant characterization and genotyping. Here, we compared the analytical performance of NGS with a commercial PCR-based assay (Anyplex II HPV28) in cervical samples of 744 women. Overall, HPV positivity was 50.2% by the Anyplex and 45.5% by the NGS. With the NGS, we detected 25 genotypes covered by Anyplex and 41 additional genotypes. Agreement between the two methods for HPV positivity was 80.8% (kappa = 0.616) and 84.8% (kappa = 0.652) for 28 HPV genotypes and 14 high-risk genotypes, respectively. We recovered and characterized 243 complete HPV genomes from 153 samples spanning 40 different genotypes. According to phylogenetic analysis and pairwise distance, we identified novel lineages and sublineages of four high-risk and 16 low-risk genotypes. In total, 17 novel lineages and 14 novel sublineages were proposed, including novel lineages of HPV45, HPV52, HPV66 and a novel sublineage of HPV59. Our study provides important genomic insights on HPV types and lineages, where few complete genomes were publicly available.
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8
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Bolatti EM, Hošnjak L, Chouhy D, Casal PE, Re-Louhau MF, Bottai H, Komloš KF, Poljak M, Giri AA. Assessing Gammapapillomavirus infections of mucosal epithelia with two broad-spectrum PCR protocols. BMC Infect Dis 2020; 20:274. [PMID: 32264841 PMCID: PMC7140492 DOI: 10.1186/s12879-020-4893-3] [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: 02/20/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Background Human papillomaviruses (HPVs) have been divided into mucosal and cutaneous types according to their primary epithelial tissue tropism. However, recent studies showed the presence of several cutaneous types in mucosal lesions and healthy mucosa from different anatomical sites. Methods Here, the HPV prevalence and type-specific distribution were assessed in a variety of mucosal samples from 435 individuals using a combination of two established broad-spectrum primer systems: Gamma-PV PCR and CUT PCR. Results Overall HPV prevalence in anal canal swabs, cervical cancer biopsies, genital warts and oral swabs was 85, 47, 62 and 4%, respectively. In anal canal swabs, Alpha-PVs were most frequently found (59%), followed by Gamma- (37%) and Beta-PVs (4%). The prevalence and persistence of HPV infection in the anal canal of 226 individuals were further explored. Overall HPV, Gamma-PVs and multiple HPV infections were significantly higher in men vs. women (p = 0.034, p = 0.027 and p = 0.003, respectively); multiple HPV infections were more common in individuals ≤40 years (p = 0.05), and significantly higher prevalence of Gamma-PVs and multiple HPV infections was observed in HIV-1-positive vs. HIV-1-negative individuals (p = 0.003 and p = 0.04, respectively). Out of 21 patients with follow-up anal swabs, only one persistent infection with the same type (HPV58) was detected. Conclusions Our findings suggest that Gamma-PVs (except species Gamma-6) are ubiquitous viruses with dual muco-cutaneous tissue tropism. Anal canal Gamma-PV infections may be associated with sexual behavior and the host immune status. This study expands the knowledge on Gamma-PVs’ tissue tropism, providing valuable data on the characteristics of HPV infection in the anal canal.
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Affiliation(s)
- Elisa M Bolatti
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Diego Chouhy
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina.,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Pablo E Casal
- Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - María F Re-Louhau
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina
| | - Hebe Bottai
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Kristina Fujs Komloš
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška 4, 1000, Ljubljana, Slovenia.
| | - Adriana A Giri
- Grupo Virología Humana, Instituto de Biología Molecular y Celular de Rosario (CONICET), Suipacha 590, 2000, Rosario, Argentina. .,Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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Preti M, Rotondo JC, Holzinger D, Micheletti L, Gallio N, McKay-Chopin S, Carreira C, Privitera SS, Watanabe R, Ridder R, Pawlita M, Benedetto C, Tommasino M, Gheit T. Role of human papillomavirus infection in the etiology of vulvar cancer in Italian women. Infect Agent Cancer 2020; 15:20. [PMID: 32266002 PMCID: PMC7110671 DOI: 10.1186/s13027-020-00286-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
Background Vulvar squamous cell carcinoma (VSCC) is a rare malignancy of the female genital tract. We aimed to determine the mucosal high-risk human papillomavirus (HPV)-attributable fraction of VSCCs from Italian women using multiple markers of viral infections. Methods VSCCs and 8 metastatic lymph node samples from 107 Italian women were analyzed by a highly type-specific multiplex genotyping assay for the presence of DNA from 119 different HPVs. Tissues were further analyzed for HPV RNA and for upregulation of the cellular protein p16INK4a. Results The rate of mucosal HPV-related tumors defined by viral DNA and RNA positivity was low (7.8%). HPV16 was the most prevalent, followed by 53, 56, and 58. Only five (4.9%) p16INK4a-positive tumors were also positive for both viral DNA and RNA. One (14.3%) metastatic lymph node sample was positive for all three markers. DNA of cutaneous HPVs was detected in only two VSCCs, i.e. genus beta types 5 and 110. Conclusion A small proportion of Italian VSCCs is putatively HPV-related, i.e. positive for both viral DNA and RNA of the same type, thus reinforcing the importance of HPV vaccination. Moreover, this study suggests that a direct role of HPV from genus beta and gamma in vulvar carcinogenesis is unlikely.
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Affiliation(s)
- Mario Preti
- 1Department of Surgical Sciences, University of Turin, Turin, Italy
| | - John Charles Rotondo
- 2International Agency for Research on Cancer, Lyon, France.,3Department of Morphology, Surgery and Experimental Medicine; Section of Pathology, Oncology and Experimental Biology; Laboratories of Cell Biology and Molecular Genetics, University of Ferrara, Ferrara, Italy
| | - Dana Holzinger
- 4Infections and Cancer Epidemiology, Infections and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Niccolò Gallio
- 1Department of Surgical Sciences, University of Turin, Turin, Italy
| | | | | | | | - Reiko Watanabe
- 2International Agency for Research on Cancer, Lyon, France
| | - Ruediger Ridder
- Roche mtm laboratories, Mannheim, Germany.,7Ventana Medical Systems Inc., Tucson, AZ USA
| | - Michael Pawlita
- 4Infections and Cancer Epidemiology, Infections and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiara Benedetto
- 1Department of Surgical Sciences, University of Turin, Turin, Italy
| | | | - Tarik Gheit
- 2International Agency for Research on Cancer, Lyon, France
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10
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Ling Y, Wang J, Yin J, Xu J, Wu Y, Zhou R, Lu J, Yang S, Wang X, Shen Q, Zhang W. Genomic organization of a Gamma-6 papillomavirus metagenomic discovered from vaginal swab samples of Chinese pregnant women. Virol J 2020; 17:44. [PMID: 32234038 PMCID: PMC7110641 DOI: 10.1186/s12985-020-01319-9] [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: 10/19/2019] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
A complete genome sequence of human papillomaviruses (HPV) named as HPV-ujs-21015 was determined by viral metagenomic and PCR methods. The complete genome is 7354 bp in length with GC content of 41.7%, of which the genome was predicted to contain six ORFs (Open Reading Frame, ORF) coding for four early proteins (E7, E1, E4, and E2) and two late proteins (L1 and L2). Phylogenetic analysis based on the complete genome and the L1 protein showed that HPV-ujs-21015 belongs to a type 214 member within genus Gamma-6 papillomavirus. It is the first complete genome of Gamma-6 papillomavirus discovered from pregnant women in China.
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Affiliation(s)
- Yu Ling
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.,Department of Laboratory Medicine, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, 210004, People's Republic of China
| | - Jianqiang Wang
- Intensive Care Unit, Jintan District Hospital of Traditional Chinese Medicine, 1006 Huixian Road, Changzhou, Jiangsu, 213200, People's Republic of China
| | - Jun Yin
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Jianpu Xu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Yufan Wu
- Zhangjiagang Customs, 28 Renmin Road, Zhangjiagang, Jiangsu, 215699, People's Republic of China
| | - Rui Zhou
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Juan Lu
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Shixing Yang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Quan Shen
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, People's Republic of China.
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11
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Barbu MG, Condrat CE, Thompson DC, Bugnar OL, Cretoiu D, Toader OD, Suciu N, Voinea SC. MicroRNA Involvement in Signaling Pathways During Viral Infection. Front Cell Dev Biol 2020; 8:143. [PMID: 32211411 PMCID: PMC7075948 DOI: 10.3389/fcell.2020.00143] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/20/2020] [Indexed: 12/15/2022] Open
Abstract
The study of miRNAs started in 1993, when Lee et al. observed their involvement in the downregulation of a crucial protein known as LIN-14 in the nematode Caenorhabditis elegans. Since then, great progress has been made regarding research on microRNAs, which are now known to be involved in the regulation of various physiological and pathological processes in both animals and humans. One such example is represented by their interaction with various signaling pathways during viral infections. It has been observed that these pathogens can induce the up-/downregulation of various host miRNAs in order to elude the host's immune system. In contrast, some miRNAs studied could have an antiviral effect, enabling the defense mechanisms to fight the infection or, at the very least, they could induce the pathogen to enter a latent state. At the same time, some viruses encode their own miRNAs, which could further modulate the host's signaling pathways, thus favoring the survival and replication of the virus. The goal of this extensive literature review was to present how miRNAs are involved in the regulation of various signaling pathways in some of the most important and well-studied human viral infections. Further on, knowing which miRNAs are involved in various viral infections and what role they play could aid in the development of antiviral therapeutic agents for certain diseases that do not have a definitive cure in the present. The clinical applications of miRNAs are extremely important, as miRNAs targeted inhibition may have substantial therapeutic impact. Inhibition of miRNAs can be achieved through many different methods, but chemically modified antisense oligonucleotides have shown the most prominent effects. Though scientists are far from completely understanding all the molecular mechanisms behind the complex cross-talks between miRNA pathways and viral infections, the general knowledge is increasing on the different roles played by miRNAs during viral infections.
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Affiliation(s)
- Madalina Gabriela Barbu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
| | - Carmen Elena Condrat
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
| | - Dana Claudia Thompson
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
| | - Oana Larisa Bugnar
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
| | - Dragos Cretoiu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
- Department of Cell and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Oana Daniela Toader
- Division of Obstetrics, Gynecology and Neonatology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Department of Obstetrics and Gynecology, Alessandrescu-Rusescu National Institute for Mother and Child Health, Polizu Clinical Hospital, Bucharest, Romania
| | - Nicolae Suciu
- Alessandrescu-Rusescu National Institute for Mother and Child Health, Fetal Medicine Excellence Research Center, Bucharest, Romania
- Division of Obstetrics, Gynecology and Neonatology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
- Department of Obstetrics and Gynecology, Alessandrescu-Rusescu National Institute for Mother and Child Health, Polizu Clinical Hospital, Bucharest, Romania
| | - Silviu Cristian Voinea
- Department of Surgical Oncology, Institute of Oncology Prof. Dr. Alexandru Trestioreanu, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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Gheit T. Mucosal and Cutaneous Human Papillomavirus Infections and Cancer Biology. Front Oncol 2019; 9:355. [PMID: 31134154 PMCID: PMC6517478 DOI: 10.3389/fonc.2019.00355] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Papillomaviridae is a family of small non-enveloped icosahedral viruses with double-stranded circular DNA. More than 200 different human papillomaviruses (HPVs) have been listed so far. Based on epidemiological data, a subgroup of alphapapillomaviruses (alpha HPVs) was referred to as high-risk (HR) HPV types. HR HPVs are the etiological agents of anogenital cancer and a subset of head and neck cancers. The cutaneous HPV types, mainly from beta and gamma genera, are widely present on the surface of the skin in the general population. However, there is growing evidence of an etiological role of betapapillomaviruses (beta HPVs) in non-melanoma skin cancer (NMSC), together with ultraviolet (UV) radiation. Studies performed on mucosal HR HPV types, such as 16 and 18, showed that both oncoproteins E6 and E7 play a key role in cervical cancer by altering pathways involved in the host immune response to establish a persistent infection and by promoting cellular transformation. Continuous expression of E6 and E7 of mucosal HR HPV types is essential to initiate and to maintain the cellular transformation process, whereas expression of E6 and E7 of cutaneous HPV types is not required for the maintenance of the skin cancer phenotype. Beta HPV types appear to play a role in the initiation of skin carcinogenesis, by exacerbating the accumulation of UV radiation-induced DNA breaks and somatic mutations (the hit-and-run mechanism), and they would therefore act as facilitators rather than direct actors in NMSC. In this review, the natural history of HPV infection and the transforming properties of various HPV genera will be described, with a particular focus on describing the state of knowledge about the role of cutaneous HPV types in NMSC.
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Affiliation(s)
- Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer (IARC), Lyon, France
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13
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Human Papilloma Virus and Chlamydia trachomatis: Casual Acquaintances or Partners in Crime? CURRENT CLINICAL MICROBIOLOGY REPORTS 2019. [DOI: 10.1007/s40588-019-00117-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Murahwa AT, Meiring TL, Mbulawa ZZA, Williamson AL. Discovery, characterisation and genomic variation of six novel Gammapapillomavirus types from penile swabs in South Africa. PAPILLOMAVIRUS RESEARCH 2019; 7:102-111. [PMID: 30844514 PMCID: PMC6416656 DOI: 10.1016/j.pvr.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/14/2019] [Accepted: 02/25/2019] [Indexed: 12/21/2022]
Abstract
Six novel human papillomaviruses from penile swabs were characterised. Multiple full genome clones for each novel type were generated, and complete genome sizes were: HPV211 (7253bp), HPV212 (7208bp), HPV213 (7096bp), HPV214 (7357), HPV215 (7186bp) and HPV216 (7233bp). Phylogenetically the novel papillomaviruses all clustered with Gammapapillomaviruses: HPV211 is most closely related to HPV168 (72% identity in the L1 nucleotide sequence) of the Gamma-8 species, HPV212 is most closely related to HPV144 (82.9%) of the Gamma-17 species, HPV213 is most closely related to HPV153 (71.8%) of the Gamma-13 species, HPV214 is most closely related to HPV103 (75.3%) of the Gamma-6 species, HPV215 and HPV216 are most closely related to HPV129 (76.8% and 79.2% respectively) of the Gamma-9 species. The novel HPV types demonstrated the classical genomic organisation of Gammapapillomavirusess, with seven open reading frames (ORFs) encoding five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) proteins. Typical of Gammapapillomavirusess the novel types all lacked the E5 ORF and HPV214 also lacked the E6 ORF. HPV212 had nine unique variants, HPV213 had five and HPV215 had four variants. Conserved domains observed among the novel types are the Zinc finger Binding Domain and PDZ domains. A retinoblastoma binding domain (pRB) binding domain in E7 protein was additionally identified in HPV214. This study expands the knowledge of the rapidly growing Gammapapillomavirus genus.
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Affiliation(s)
- Alltalents T Murahwa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tracy L Meiring
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Zizipho Z A Mbulawa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Center for HIV and STIs, National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa; SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Adnan Ali SM, Mirza Y, Ahmad Z, Zahid N, Enam SA. Human Papillomavirus and Human Cytomegalovirus Infection and Association with Prognosis in Patients with Primary Glioblastoma in Pakistan. World Neurosurg 2019; 121:e931-e939. [DOI: 10.1016/j.wneu.2018.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 01/07/2023]
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Latsuzbaia A, Arbyn M, Dutta S, Fischer M, Gheit T, Tapp J, Tommasino M, Weyers S, Mossong J. Complete Genome Sequence of a Novel Human Gammapapillomavirus Isolated from a Cervical Swab in Luxembourg. GENOME ANNOUNCEMENTS 2018; 6:e00114-18. [PMID: 29545294 PMCID: PMC5854775 DOI: 10.1128/genomea.00114-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 11/26/2022]
Abstract
A novel human papillomavirus genotype was detected in a cervical swab specimen by next-generation sequencing after rolling circular amplification. It was fully cloned and characterized. The L1 open reading frame showed 77% nucleotide similarity with the closest genotype, HPV101, belonging to the gamma-6 species.
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Affiliation(s)
- Ardashel Latsuzbaia
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre Scientific Institute of Public Health, Brussels, Belgium
| | - Sankhadeep Dutta
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Marc Fischer
- Gynaecological Cytology, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Jessica Tapp
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Steven Weyers
- Department of Obstetrics and Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Joël Mossong
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
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17
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Structural Insights in Multifunctional Papillomavirus Oncoproteins. Viruses 2018; 10:v10010037. [PMID: 29342959 PMCID: PMC5795450 DOI: 10.3390/v10010037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 02/08/2023] Open
Abstract
Since their discovery in the mid-eighties, the main papillomavirus oncoproteins E6 and E7 have been recalcitrant to high-resolution structure analysis. However, in the last decade a wealth of three-dimensional information has been gained on both proteins whether free or complexed to host target proteins. Here, we first summarize the diverse activities of these small multifunctional oncoproteins. Next, we review the available structural data and the new insights they provide about the evolution of E6 and E7, their multiple interactions and their functional variability across human papillomavirus (HPV) species.
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18
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Zhao J, Guo Z, Wang Q, Si T, Pei S, Wang C, Qu H, Zhong J, Ma Y, Nie C, Zhang D. Human papillomavirus genotypes associated with cervical precancerous lesions and cancer in the highest area of cervical cancer mortality, Longnan, China. Infect Agent Cancer 2017; 12:8. [PMID: 28138337 PMCID: PMC5264338 DOI: 10.1186/s13027-017-0116-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/04/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The mortality of cervical cancer in Longnan is as high as 39/10 million, ranking first in China. METHODS Between 2012 to 2016, 329 samples with cervicitis, cervical intraepithelial neoplasia grade 1 to 3 (CINI to III), and invasive squamous cell carcinoma (SCC) were collected. HPV genotypes were examined with a validated kit for 23 different HPV subtypes. RESULTS Compared to cervicitis, the HPV positivity is significantly higher in CINI, CIN II/III, and SCC (38.60%, 74.60%, 87.50% and 89.05%, P < 0.001) and the positivity is also higher in SCC compared to CINI (P < 0.01). The most frequently detected genotypes were HPV16 in cervicitis, HPV16, 58 and 52 in CINI and CIN II/III, and HPV16, 58 and 18 in SCC groups. HPV16 positivity in cervicitis, CINI, CIN II/III, and SCC patients were 45.46%, 46.81%, 60.32% and 78.69%, respectively. Compared to cervicitis and CINI, the odds ratios (OR) for SCC in HPV16 positive patients were 2.96 (95% confidence interval [CI]: 1.09-8.00, P < 0.05) and 4.20 (95% confidence interval [CI]: 2.05-8.61, P < 0.001), respectively. In addition, the multiple infections in cervicitis, CINI, CINII/III and SCC group are 9.09%, 27.66%, 26.98% and 25.41% and HPV16 + 58 was the most common combinations. CONCLUSION These findings highlight the key role of HPV16, 58, 52 and 18 in the development of CIN and SCC in Longnan women and a fully aware of regional differences in HPV genotype distribution are tasks for cervical cancer control and prevention.
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Affiliation(s)
- Jin Zhao
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Zhong Guo
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Qiang Wang
- No.1 Hospital of Longnan City, Longnan, 746000 People’s Republic of China
| | - Tianbin Si
- Gansu Provincial Cancer Hospital, Lanzhou, 730050 People’s Republic of China
| | - Shuyan Pei
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Chenjing Wang
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Hongmei Qu
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Jianbin Zhong
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Ying Ma
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Cong Nie
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
| | - Dan Zhang
- Medical College of Northwest University for Nationalities, Lanzhou, 730030 People’s Republic of China
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19
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Gil da Costa RM, Aragão S, Moutinho M, Alvarado A, Carmo D, Casaca F, Silva S, Ribeiro J, Sousa H, Ferreira R, Nogueira-Ferreira R, Pires MJ, Colaço B, Medeiros R, Venâncio C, Oliveira MM, Bastos MM, Lopes C, Oliveira PA. HPV16 induces a wasting syndrome in transgenic mice: Amelioration by dietary polyphenols via NF-κB inhibition. Life Sci 2017; 169:11-19. [DOI: 10.1016/j.lfs.2016.10.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/04/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
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20
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Molecular archeological evidence in support of the repeated loss of a papillomavirus gene. Sci Rep 2016; 6:33028. [PMID: 27604338 PMCID: PMC5015084 DOI: 10.1038/srep33028] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/16/2016] [Indexed: 11/08/2022] Open
Abstract
It is becoming clear that, in addition to gene gain, the loss of genes may be an important evolutionary mechanism for many organisms. However, gene loss is often associated with an increased mutation rate, thus quickly erasing evidence from the genome. The analysis of evolutionarily related sequences can provide empirical evidence for gene loss events. This paper analyzes the sequences of over 300 genetically distinct papillomaviruses and provides evidence for a role of gene loss during the evolution of certain papillomavirus genomes. Phylogenetic analysis suggests that the viral E6 gene was lost at least twice. Despite belonging to distant papillomaviral genera, these viruses lacking a canonical E6 protein may potentially encode a highly hydrophobic protein from an overlapping open reading frame, which we designate E10. Evolutionary pressure working on this alternative frame, may explain why, despite having lost the E6 open reading frame between 20 and 60 million years ago, evidence of an E6-like protein is conserved.
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21
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Mengual-Chuliá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG. Assessing parallel gene histories in viral genomes. BMC Evol Biol 2016; 16:32. [PMID: 26847371 PMCID: PMC4743424 DOI: 10.1186/s12862-016-0605-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/29/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followed the same evolutionary path due to events such as incomplete lineage sorting, horizontal gene transfer, gene duplication and deletion, or recombination. Considering conflicts between gene trees as an obstacle, numerous methods have been developed to deal with these incongruences and to reconstruct consensus evolutionary histories of species despite the heterogeneity in the history of their genes. However, inconsistencies can also be seen as a source of information about the specific evolutionary processes that have shaped genomes. RESULTS The goal of the approach here proposed is to exploit this conflicting information: we have compiled eleven variables describing phylogenetic relationships and evolutionary pressures and submitted them to dimensionality reduction techniques to identify genes with similar evolutionary histories. To illustrate the applicability of the method, we have chosen two viral datasets, namely papillomaviruses and Turnip mosaic virus (TuMV) isolates, largely dissimilar in genome, evolutionary distance and biology. Our method pinpoints viral genes with common evolutionary patterns. In the case of papillomaviruses, gene clusters match well our knowledge on viral biology and life cycle, illustrating the potential of our approach. For the less known TuMV, our results trigger new hypotheses about viral evolution and gene interaction. CONCLUSIONS The approach here presented allows turning phylogenetic inconsistencies into evolutionary information, detecting gene assemblies with similar histories, and could be a powerful tool for comparative pathogenomics.
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Affiliation(s)
- Beatriz Mengual-Chuliá
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain
| | - Stéphanie Bedhomme
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain.,Bellvitge Institute of Biomedical Research (IDIBELL), Barcelona, Spain.,Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France
| | - Guillaume Lafforgue
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR CNRS 5175, Montpellier, France.,Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain.,I2SysBio, Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, NM, USA
| | - Ignacio G Bravo
- Infections and Cancer Laboratory, Catalan Institute of Oncology (ICO), Barcelona, Spain. .,MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France. .,National Center for Scientific Research (CNRS), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR CNRS 5290, IRD 224, UM, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, Cedex 5, France.
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22
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Bergner S, Halec G, Schmitt M, Aubin F, Alonso A, Auvinen E. Individual and Complementary Effects of Human Papillomavirus Oncogenes on Epithelial Cell Proliferation and Differentiation. Cells Tissues Organs 2015; 201:97-108. [PMID: 26636751 DOI: 10.1159/000441716] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2015] [Indexed: 11/19/2022] Open
Abstract
Previous studies on human papillomavirus (HPV) type 16 protein functions have established the oncogenic nature of three viral proteins: E5, E6 and E7. Here we have studied the functions of these proteins by functional deletion of the individual E5, E6 or E7, or both E6 and E7 oncogenes in the context of the whole viral genome. These mutants, or the intact wild-type genome, were expressed from the natural viral promoters along with differentiation of epithelial HaCaT cells in three-dimensional collagen raft cultures. High episomal viral copy numbers were obtained using a transfection-based loxp-HPV16-eGFP-N1 vector system. All epithelial equivalents carrying the different HPV type 16 genomes showed pronounced hyperplastic and dysplastic morphology. Particularly the E7 oncogene, with contribution of E6, was shown to enhance cell proliferation. Specifically, the crucial role of E7 in HPV-associated hyperproliferation was clearly manifested. Based on morphological characteristics, immunohistochemical staining for differentiation and proliferation markers, and low expression of E1^E4, we propose that our raft culture models produce cervical intraepithelial neoplasia (CIN)1 and CIN2-like tissue. Our experimental setting provides an alternative tool to study concerted functions of HPV proteins in the development of epithelial dysplasia.
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Affiliation(s)
- Sven Bergner
- Research Program in Infection and Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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23
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Doorbar J, Egawa N, Griffin H, Kranjec C, Murakami I. Human papillomavirus molecular biology and disease association. Rev Med Virol 2015; 25 Suppl 1:2-23. [PMID: 25752814 PMCID: PMC5024016 DOI: 10.1002/rmv.1822] [Citation(s) in RCA: 530] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/12/2014] [Accepted: 06/25/2014] [Indexed: 12/27/2022]
Abstract
Human papillomaviruses (HPVs) have evolved over millions of years to propagate themselves in a range of different animal species including humans. Viruses that have co‐evolved slowly in this way typically cause chronic inapparent infections, with virion production in the absence of apparent disease. This is the case for many Beta and Gamma HPV types. The Alpha papillomavirus types have however evolved immunoevasion strategies that allow them to cause persistent visible papillomas. These viruses activate the cell cycle as the infected epithelial cell differentiates in order to create a replication competent environment that allows viral genome amplification and packaging into infectious particles. This is mediated by the viral E6, E7, and E5 proteins. High‐risk E6 and E7 proteins differ from their low‐risk counterparts however in being able to drive cell cycle entry in the upper epithelial layers and also to stimulate cell proliferation in the basal and parabasal layers. Deregulated expression of these cell cycle regulators underlies neoplasia and the eventual progression to cancer in individuals who cannot resolve high‐risk HPV infection. Most work to date has focused on the study of high‐risk HPV types such as HPV 16 and 18, which has led to an understanding of the molecular pathways subverted by these viruses. Such approaches will lead to the development of better strategies for disease treatment, including targeted antivirals and immunotherapeutics. Priorities are now focused toward understanding HPV neoplasias at sites other than the cervix (e.g. tonsils, other transformation zones) and toward understanding the mechanisms by which low‐risk HPV types can sometimes give rise to papillomatosis and under certain situations even cancers. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, UK
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24
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Oštrbenk A, Kocjan BJ, Hošnjak L, Li J, Deng Q, Šterbenc A, Poljak M. Identification of a Novel Human Papillomavirus, Type HPV199, Isolated from a Nasopharynx and Anal Canal, and Complete Genomic Characterization of Papillomavirus Species Gamma-12. PLoS One 2015; 10:e0138628. [PMID: 26375679 PMCID: PMC4574437 DOI: 10.1371/journal.pone.0138628] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/31/2015] [Indexed: 01/04/2023] Open
Abstract
The novel human papillomavirus type 199 (HPV199) was initially identified in a nasopharyngeal swab sample obtained from a 25 year-old immunocompetent male. The complete genome of HPV199 is 7,184 bp in length with a GC content of 36.5%. Comparative genomic characterization of HPV199 and its closest relatives showed the classical genomic organization of Gammapapillomaviruses (Gamma-PVs). HPV199 has seven major open reading frames (ORFs), encoding five early (E1, E2, E4, E6, and E7) and two late (L1 and L2) proteins, while lacking the E5 ORF. The long control region (LCR) of 513 bp is located between the L1 and E6 ORFs. Phylogenetic analysis additionally confirmed that HPV-199 clusters into the Gamma-PV genus, species Gamma-12, additionally containing HPV127, HV132, HPV148, HPV165, and three putative HPV types: KC5, CG2 and CG3. HPV199 is most closely related to HPV127 (nucleotide identity 77%). The complete viral genome sequence of additional HPV199 isolate was determined from anal canal swab sample. Two HPV199 complete viral sequences exhibit 99.4% nucleotide identity. To the best of our knowledge, this is the first member of Gamma-PV with complete nucleotide sequences determined from two independent clinical samples. To evaluate the tissue tropism of the novel HPV type, 916 clinical samples were tested using HPV199 type-specific real-time PCR: HPV199 was detected in 2/76 tissue samples of histologically confirmed common warts, 2/108 samples of eyebrow hair follicles, 2/137 anal canal swabs obtained from individuals with clinically evident anal pathology, 4/184 nasopharyngeal swabs and 3/411 cervical swabs obtained from women with normal cervical cytology. Although HPV199 was found in 1.4% of cutaneous and mucosal samples only, it exhibits dual tissue tropism. According to the results of our study and literature data, dual tropism of all Gamma-12 members is highly possible.
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Affiliation(s)
- Anja Oštrbenk
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Lea Hošnjak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jingjing Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Qiuju Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Anja Šterbenc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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25
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Chen J. Signaling pathways in HPV-associated cancers and therapeutic implications. Rev Med Virol 2015; 25 Suppl 1:24-53. [DOI: 10.1002/rmv.1823] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 10/15/2014] [Accepted: 12/27/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Jiezhong Chen
- School of Biomedical Sciences and Australian Institute for Bioengineering and Nanotechnology; The University of Queensland; Brisbane Queensland Australia
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26
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Abstract
The oncogenic, anogenital types of human papillomavirus (HPV) are established as causing about 4.8% of all human cancers worldwide, particularly cervical, anal, vulvar, vaginal, penile, and oropharyngeal cancers. Quantitative knowledge of the HPV type-specific risks for these cancers, as well as for the different cervical cancer precursors (cervical intraepithelial neoplasias, CINs), is useful for estimating the effect of elimination of specific HPV types and clinical benefits of screening for specific HPV types. The present review summarizes both the worldwide presence of specific HPV types in cervical cancer precursors and in invasive cervical cancers, and also the long-term follow-up data from a large randomized clinical trial of HPV-based cervical cancer screening. All 12 HPV types classified as class I (established) carcinogens (HPV types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59) were more common in cervical cancers than among women without cervical lesions. A few rare HPV types also were more common in cervical cancers (eg, HPV26, 67, 68, 69, 73, 82). The follow-up studies found increased long-term risks particularly for HPV types 16, 18, 31, and 33, which had 14-year cumulative incidences for CIN3+above 28%, while HPV35, 45, 52, and 58 had 14-year risks between 14%-18% and HPV39, 51, 56, 59, 66, and 68 had risks<10%. HPV16 contributed to the greatest proportion of CIN2+(first-round population attributable proportion [PAR] 36%), followed by types 31, 52, 45, and 58 (7%-11%). HPV16, 18, 31, 33, 45, 52, and 58 together contributed 73.9% of CIN2+lesions and all high-risk types contributed 86.9%.In summary, the different oncogenic HPV types have substantial differences in their oncogenic potential. These differences are relevant for the design and evaluation of cervical screening tests and programs, as well as for studying the effect of vaccination programs using different HPV vaccines.
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Affiliation(s)
- Joakim Dillner
- International HPV Reference Center, Department of Laboratory Medicine, and Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden.
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27
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Warren CJ, Van Doorslaer K, Pandey A, Espinosa JM, Pyeon D. Role of the host restriction factor APOBEC3 on papillomavirus evolution. Virus Evol 2015; 1. [PMID: 27570633 PMCID: PMC4999249 DOI: 10.1093/ve/vev015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
More than 270 different types of papillomaviruses have been discovered in a wide array of animal species. Despite the great diversity of papillomaviruses, little is known about the evolutionary processes that drive host tropism and the emergence of oncogenic genotypes. Although host defense mechanisms have evolved to interfere with various aspects of a virus life cycle, viruses have also coevolved copious strategies to avoid host antiviral restriction. Our and other studies have shown that the cytidine deaminase APOBEC3 family members edit HPV genomes and restrict virus infectivity. Thus, we hypothesized that host restriction by APOBEC3 served as selective pressure during papillomavirus evolution. To test this hypothesis, we analyzed the relative abundance of all dinucleotide sequences in full-length genomes of 274 papillomavirus types documented in the Papillomavirus Episteme database (PaVE). Here, we report that TC dinucleotides, the preferred target sequence of several human APOBEC3 proteins (hA3A, hA3B, hA3F, and hA3H), are highly depleted in papillomavirus genomes. Given that HPV infection is highly tissue-specific, the expression levels of APOBEC3 family members were analyzed. The basal expression levels of all APOBEC3 isoforms, excluding hA3B, are significantly higher in mucosal skin compared with cutaneous skin. Interestingly, we reveal that Alphapapillomaviruses (alpha-PVs), a majority of which infects anogenital mucosa, display the most dramatic reduction in TC dinucleotide content. Computer modeling and reconstruction of ancestral alpha-PV genomes suggest that TC depletion occurred after the alpha-PVs diverged from their most recent common ancestor. In addition, we found that TC depletion in alpha-PVs is greatly affected by protein coding potential. Taken together, our results suggest that PVs replicating in tissues with high APOBEC3 levels may have evolved to evade restriction by selecting for variants that contain reduced APOBEC3 target sites in their genomes.
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Affiliation(s)
- Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ahwan Pandey
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA; Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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28
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Accardi R, Gheit T. Cutaneous HPV and skin cancer. Presse Med 2014; 43:e435-43. [DOI: 10.1016/j.lpm.2014.08.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/25/2014] [Indexed: 12/31/2022] Open
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29
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Ure AE, Forslund O. Characterization of human papillomavirus type 154 and tissue tropism of gammapapillomaviruses. PLoS One 2014; 9:e89342. [PMID: 24551244 PMCID: PMC3923884 DOI: 10.1371/journal.pone.0089342] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/19/2014] [Indexed: 11/19/2022] Open
Abstract
The novel human papillomavirus type 154 (HPV154) was characterized from a wart on the crena ani of a three-year-old boy. It was previously designated as the putative HPV type FADI3 by sequencing of a subgenomic FAP amplicon. We obtained the complete genome by combined methods including rolling circle amplification (RCA), genome walking through an adapted method for detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR), long-range PCR, and finally by cloning of four overlapping amplicons. Phylogenetically, the HPV154 genome clustered together with members of the proposed species Gammapapillomavirus 11, and demonstrated the highest identity in L1 to HPV136 (68.6%). The HPV154 was detected in 3% (2/62) of forehead skin swabs from healthy children. In addition, the different detection sites of 62 gammapapillomaviruses were summarized in order to analyze their tissue tropism. Several of these HPV types have been detected from multiple sources such as skin, oral, nasal, and genital sites, suggesting that the gammapapillomaviruses are generalists with a broader tissue tropism than previously appreciated. The study expands current knowledge concerning genetic diversity and tropism among HPV types in the rapidly growing gammapapillomavirus genus.
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Affiliation(s)
- Agustín Enrique Ure
- Department of Laboratory Medicine, Section of Medical Microbiology, Lund University, Malmö, Sweden
| | - Ola Forslund
- Department of Laboratory Medicine, Section of Medical Microbiology, Lund University, Malmö, Sweden
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30
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Tommasino M. The human papillomavirus family and its role in carcinogenesis. Semin Cancer Biol 2013; 26:13-21. [PMID: 24316445 DOI: 10.1016/j.semcancer.2013.11.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/22/2013] [Accepted: 11/27/2013] [Indexed: 01/17/2023]
Abstract
Human papillomaviruses (HPVs) are a family of small double-stranded DNA viruses that have a tropism for the epithelia of the genital and upper respiratory tracts and for the skin. Approximately 150 HPV types have been discovered so far, which are classified into several genera based on their DNA sequence. Approximately 15 high-risk mucosal HPV types are clearly associated with cervical cancer; HPV16 and HPV18 are the most carcinogenic since they are responsible for approximately 50% and 20% of all cervical cancers worldwide, respectively. It is now also clear that these viruses are linked to a subset of other genital cancers, as well as head and neck cancers. Due to their high level of carcinogenic activity, HPV16 and HPV18 are the most studied HPV types so far. Biological studies have highlighted the key roles in cellular transformation of the products of two viral early genes, E6 and E7. Many of the mechanisms of E6 and E7 in subverting the regulation of fundamental cellular events have been fully characterized, contributing not only to our knowledge of how the oncogenic viruses promote cancer development but also to our understanding of basic cell biology. Despite HPV research resulting in extraordinary achievements in the last four decades, significantly improving the screening and prophylaxis of HPV-induced lesions, additional research is necessary to characterize the biology and epidemiology of the vast number of HPV types that have been poorly investigated so far, with a final aim of clarifying their potential roles in other human diseases.
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Affiliation(s)
- Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer - World Health Organization, 150 Cours Albert-Thomas, 69372 Lyon cedex 08, France.
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31
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Diversity of human papillomaviruses in skin lesions. Virology 2013; 447:300-11. [PMID: 24210127 DOI: 10.1016/j.virol.2013.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/27/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
Abstract
Pools of frozen biopsies from patients with squamous cell carcinoma (SCC) (n=29) actinic keratosis (AK) (n=31), keratoacanthoma (n=91) and swab samples from 84 SCCs and 91 AKs were analysed with an extended HPV general primer PCR and high-throughput sequencing of amplimers. We found 273 different HPV isolates (87 known HPV types, 139 previously known HPV sequences (putative types) and 47 sequences from novel putative HPV types). Among the new sequences, five clustered in genus Betapapillomavirus and 42 in genus Gammapapillomavirus. Resequencing of the three pools between 21 to 70 times resulted in the detection of 283 different known or putative HPV types, with 156 different sequences found in only one of the pools. Type-specific PCRs for 37 putative types from an additional 296 patients found only two of these putative types. In conclusion, skin lesions contain a large diversity of HPV types, but most appeared to be rare infections.
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32
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Bzhalava D, Guan P, Franceschi S, Dillner J, Clifford G. A systematic review of the prevalence of mucosal and cutaneous human papillomavirus types. Virology 2013; 445:224-31. [PMID: 23928291 DOI: 10.1016/j.virol.2013.07.015] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 07/08/2013] [Accepted: 07/16/2013] [Indexed: 01/19/2023]
Abstract
Systematic reviews of the prevalence of different types of Human Papillomavirus (HPV) across a broad range of disease grades from normal to cancer are essential to gain basic knowledge of how widespread infections with the different HPV types are, and to provide information on the possible carcinogenicity of different HPV types. For HPV types that infect human mucosa, of which 12 are established causes of cervical cancer, we present the results of a systematic review and meta-analysis of 47 HPV types in cervical samples across the entire range of cervical diagnoses from normal to cervical cancer, restricted to studies using a number of well characterized PCR assays. For the cutaneous HPV types, which have been linked to the development of squamous cell carcinoma of the skin, their presence has been measured in a variety of different sample types and by assays with variable performance. Therefore, we restricted a systematic review of their prevalence to studies that assayed for cutaneous HPV infection in a case-control format.
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Affiliation(s)
- Davit Bzhalava
- International HPV Reference Center, Deptartment of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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33
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Bzhalava D, Johansson H, Ekström J, Faust H, Möller B, Eklund C, Nordin P, Stenquist B, Paoli J, Persson B, Forslund O, Dillner J. Unbiased approach for virus detection in skin lesions. PLoS One 2013; 8:e65953. [PMID: 23840382 PMCID: PMC3696016 DOI: 10.1371/journal.pone.0065953] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 05/01/2013] [Indexed: 01/28/2023] Open
Abstract
To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.
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Affiliation(s)
- Davit Bzhalava
- Departments of Laboratory Medicine, Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Clinical Microbiology and Pathology, Karolinska Hospital, Stockholm, Sweden
| | - Hanna Johansson
- Department of Medical Microbiology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Johanna Ekström
- Departments of Laboratory Medicine, Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Clinical Microbiology and Pathology, Karolinska Hospital, Stockholm, Sweden
- Department of Medical Microbiology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Helena Faust
- Department of Medical Microbiology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Birgitta Möller
- Departments of Laboratory Medicine, Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Clinical Microbiology and Pathology, Karolinska Hospital, Stockholm, Sweden
| | - Carina Eklund
- Departments of Laboratory Medicine, Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Clinical Microbiology and Pathology, Karolinska Hospital, Stockholm, Sweden
| | - Peter Nordin
- Dermatology Clinic, Läkarhuset, Gothenburg, Sweden
| | - Bo Stenquist
- Department of Dermatology and Venereology, Sahlgrenska University Hospital, Institute of Clinical Sciences at the Sahlgrenska Academy, University of Gothenburg, Sweden
| | - John Paoli
- Department of Dermatology and Venereology, Sahlgrenska University Hospital, Institute of Clinical Sciences at the Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Bengt Persson
- IFM Bioinformatics and Swedish e-Science Research Centre, Linköping University, Linköping, Sweden
| | - Ola Forslund
- Department of Medical Microbiology, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Joakim Dillner
- Departments of Laboratory Medicine, Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Clinical Microbiology and Pathology, Karolinska Hospital, Stockholm, Sweden
- Department of Medical Microbiology, Skåne University Hospital, Lund University, Malmö, Sweden
- * E-mail:
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34
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Abstract
E7 is an accessory protein that is not encoded by all papillomaviruses. The E7 amino terminus contains two regions of similarity to conserved regions 1 and 2 of the adenovirus E1A protein, which are also conserved in the simian vacuolating virus 40 large tumor antigen. The E7 carboxyl terminus consists of a zinc-binding motif, which is related to similar motifs in E6 proteins. E7 proteins play a central role in the human papillomavirus life cycle, reprogramming the cellular environment to be conducive to viral replication. E7 proteins encoded by the cancer-associated alpha human papillomaviruses have potent transforming activities, which together with E6, are necessary but not sufficient to render their host squamous epithelial cell tumorigenic. This article strives to provide a comprehensive summary of the published research studies on human papillomavirus E7 proteins.
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35
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de Villiers EM. Cross-roads in the classification of papillomaviruses. Virology 2013; 445:2-10. [PMID: 23683837 DOI: 10.1016/j.virol.2013.04.023] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/02/2013] [Accepted: 04/25/2013] [Indexed: 01/22/2023]
Abstract
Acceptance of an official classification for the family Papillomaviridae based purely on DNA sequence relatedness, was achieved as late as 2003. The rate of isolation and characterization of new papillomavirus types has greatly depended on and subjected to the development of new laboratory techniques. Introduction of every new technique led to a temporarily burst in the number of new isolates. In the following, the bumpy road towards achieving a classification system combined with the controversies of implementing and accepting new techniques will be summarized. An update of the classification of the 170 human papillomavirus (HPV) types presently known is presented. Arguments towards the implementation of metagenomic sequencing for this rapidly growing family will be presented.
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Affiliation(s)
- Ethel-Michele de Villiers
- Division for the Characterization of Papillomaviruses, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
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36
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Doorbar J, Quint W, Banks L, Bravo IG, Stoler M, Broker TR, Stanley MA. The biology and life-cycle of human papillomaviruses. Vaccine 2012; 30 Suppl 5:F55-70. [PMID: 23199966 DOI: 10.1016/j.vaccine.2012.06.083] [Citation(s) in RCA: 878] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/04/2012] [Accepted: 06/05/2012] [Indexed: 12/20/2022]
Abstract
Human papillomaviruses (HPVs) comprise a diverse group, and have different epithelial tropisms and life-cycle strategies. Many HPVs are classified as low-risk, as they are only very rarely associated with neoplasia or cancer in the general population. These HPVs typically cause inapparent/inconspicuous infections, or benign papillomas, which can persist for months or years, but which are eventually resolved by the host's immune system. Low-risk HPVs are difficult to manage in immunosuppressed people and in individuals with genetic predispositions, and can give rise to papillomatosis, and in rare instances, to cancer. The high-risk HPV types are, by contrast, a cause of several important human cancers, including almost all cases of cervical cancer, a large proportion of other anogenital cancers and a growing number of head and neck tumours. The high-risk HPV types constitute a subset of the genus Alphapapillomavirus that are prevalent in the general population, and in most individuals cause only inconspicuous oral and genital lesions. Cancer progression is associated with persistent high-risk HPV infection and with deregulated viral gene expression, which leads to excessive cell proliferation, deficient DNA repair, and the accumulation of genetic damage in the infected cell. Although their life-cycle organisation is broadly similar to that of the low-risk HPV types, the two groups differ significantly in their capacity to drive cell cycle entry and cell proliferation in the basal/parabasal cell layers. This is thought to be linked, at least in part, to different abilities of the high- and low-risk E6 proteins to modulate the activity of p53 and PDZ-domain proteins, and the differential ability of the E7 proteins to target the several different members of the retinoblastoma protein family. This article forms part of a special supplement entitled "Comprehensive Control of HPV Infections and Related Diseases" Vaccine Volume 30, Supplement 5, 2012.
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Affiliation(s)
- John Doorbar
- Division of Virology, National Institute for Medical Research, London, United Kingdom.
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37
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Differential regulation of cutaneous oncoprotein HPVE6 by wtp53, mutant p53R248W and ΔNp63α is HPV type dependent. PLoS One 2012; 7:e35540. [PMID: 22530045 PMCID: PMC3329482 DOI: 10.1371/journal.pone.0035540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 03/19/2012] [Indexed: 11/19/2022] Open
Abstract
UV exposure and p53 mutations are major factors in non-melanoma skin cancer, whereas a role for HPV infections has not been defined. Previous data demonstrated the wtp53-mediated degradation of cutaneous HPV20E6 by caspase-3. ΔNp63α and hot-spot mutant p53R248W conveyed a protective effect on HPV20E6 under these conditions. We demonstrate a differential regulation by wtp53 of the E6 genes of cutaneous types HPV4, HPV5, HPV7, HPV27, HPV38, HPV48, HPV60 and HPV77. Caspase- or proteasome-mediated down-regulation was HPV type dependent. Mutant p53R248W up-regulated expression of all these E6 proteins as did ΔNp63α except for HPV38E6 which was down-regulated by the latter. None of these cellular proteins affected HPV41E6 expression. Ectopic expression of both mutp53R248W and ΔNp63α in the normal NIKS keratinocyte cell line harbouring endogenous p53 and p63however led to a down-regulation of HPV20E6. We demonstrate that HPV20E6 expression in these cells is modulated by additional, yet unidentified, cellular protein(s), which are not necessarily involved in apoptosis or autophagy. We further demonstrate proliferation of HPV20E6-expressing keratinocytes. Levels of proteins involved in cell cycle control, cyclin-D1, cdk6 and p16INK4a, phosphorylated pRB, as well as c-Jun and p-c-Jun, were all increased in these cells. HPV20E6 did not compete for the interaction between p16INK4a with cyclin-D1 or cdk6. Phosphorylation of pRB in the HPV20E6 expressing cells seems to be sufficient to override the cytokenetic block induced by the p16INK4a/pRB pathway. The present study demonstrates the diverse influence of p53 family members on individual cutaneous HPVE6 proteins. HPV20E6 expression also resulted in varying protein levels of factors involved in proliferation and differentiation.
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38
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Ekström J, Bzhalava D, Svenback D, Forslund O, Dillner J. High throughput sequencing reveals diversity of Human Papillomaviruses in cutaneous lesions. Int J Cancer 2011; 129:2643-50. [PMID: 21630257 DOI: 10.1002/ijc.26204] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 05/16/2011] [Indexed: 11/06/2022]
Abstract
There are at least 120 completely characterized human papillomavirus (HPV) types and putative new types are continuously found. Both squamous cell carcinoma of the skin (SCC) and other skin lesions commonly contain multiple cutaneous HPV types. The objective of this study was to achieve an improved resolution of the diversity of HPV types in lesions such as SCCs, actinic keratoses (AKs) and keratoacanthomas (KAs). Fresh frozen biopsies from 37 SCC lesions, 36 AK lesions and 92 KA lesions and swab samples from the top of the lesion from 86 SCCs and 92 AKs were amplified using the general HPV primers FAP and mixed to three pools followed by high throughput sequencing. We obtained 2196 reads with homology to HPV. In the pool of SCC/AK biopsies 48 different HPV types were found. Eighty-three types were found in the pool of SCC/AK swab samples and 64 types in the KA biopsies, respectively. For 9 novel putative HPV types most of the amplimer sequence was obtained, whereas for an additional 35 novel putative HPV types only partial amplimer sequences were obtained. Most of the novel putative types belonged to the genus Gamma. In conclusion, high throughput sequencing was an effective means to identify both known and previously unknown HPV types in putatively HPV-associated lesions and has revealed an extended diversity of HPV types.
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Affiliation(s)
- Johanna Ekström
- Division of Medical Microbiology, Department of Laboratory Medicine, Lund University, Skånes Universitetssjukhus, Malmö, Sweden
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39
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Nobre RJ, Cruz E, Real O, de Almeida LP, Martins TC. Characterization of common and rare human papillomaviruses in Portuguese women by the polymerase chain reaction, restriction fragment length polymorphism and sequencing. J Med Virol 2010; 82:1024-32. [PMID: 20419818 DOI: 10.1002/jmv.21756] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The present study aimed to provide additional information on the prevalence of mucosal human papillomavirus (HPV) types in Portuguese women by using polymerase chain reaction, restriction fragment length polymorphism and sequencing. HPV was detected in 15.5% (15/97) of the control samples, 23.5% (12/51) of atypical squamous cells of undetermined significance, 52.8% (28/53) of low-grade lesions, 82.4% (28/34) of high-grade lesions, and 100% (44/44) of carcinomas. Overall, 28 HPV types were detected: 11 high-risk (HPV 16, 18, 31, 33, 35, 39, 45, 52, 56, 58, and 59), 3 probable high-risk (HPV 53, 66, and 73), 6 low-risk (HPV 6, 11, 44, 61, 70, and 81), and 8 unknown-risk types (HPV 34, 62, 67, 71, 83, 84, 102, and 108). The most prevalent type was HPV 16, detected in 33.8% of women infected with HPV, followed by HPV 58 (9.2%), HPV 33 (7.0%), HPV 18 (6.3%), HPV 53 (5.6%), HPV 31 and 56 (4.9% each), HPV 6 (3.5%), and HPV 66 and 81 (2.8% each). Of 44 cervical carcinoma samples, 71% were associated with HPV 16 (60%) and HPV 18 (11.1%), followed by the high-risk types 33 (11.1%), 35 (4.4%), 45 (4.4%), and 56 (2.2%), the probable high-risk type 53 (4.4%) and the unknown-risk type 67 (2.2%). This study provides information on the most common HPV types in Portuguese women and suggests that the current prophylactic HPV 16/18 vaccine may be useful for the prevention of cervical cancer in this population.
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Affiliation(s)
- Rui Jorge Nobre
- Molecular Pathology Laboratory, Portuguese Institute for Oncology at Coimbra Francisco Gentil, EPE, Coimbra, Portugal.
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40
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Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010; 401:70-9. [PMID: 20206957 DOI: 10.1016/j.virol.2010.02.002] [Citation(s) in RCA: 1098] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/27/2010] [Accepted: 02/03/2010] [Indexed: 10/19/2022]
Abstract
We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time.
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Three novel papillomaviruses (HPV109, HPV112 and HPV114) and their presence in cutaneous and mucosal samples. Virology 2010; 397:331-6. [DOI: 10.1016/j.virol.2009.11.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 10/30/2009] [Accepted: 11/17/2009] [Indexed: 12/31/2022]
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Chouhy D, Gorosito M, Sánchez A, Serra EC, Bergero A, Fernandez Bussy R, Giri AA. New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3. Virology 2009; 397:205-16. [PMID: 19948351 DOI: 10.1016/j.virol.2009.11.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 10/06/2009] [Accepted: 11/10/2009] [Indexed: 01/06/2023]
Abstract
We explored the cutaneotropic HPV genetic diversity in 71 subjects from Argentina. New generic primers (CUT) targeting 88 mucosal/cutaneous HPV were designed and compared to FAP primers. Overall, 69 different HPV types/putative types were identified, being 17 of them novel putative types. Phylogenetic analysis of partial L1 sequences grouped 2 novel putative types in the Beta-PV, 14 in the Gamma-PV and 1 in the Mu-PV genera. CUT primers showed broader capacity than FAP primers in detecting different genera/species and novel putative types (p<0.01). Using overlapping PCR, the full-length genome of a Beta-PV putative type was amplified and cloned. The new virus, designated HPV 115, encodes five early genes and two late genes. Phylogenetic analysis indicated HPV 115 as the most divergent type within the genus Beta-PV species 3. This report is the first providing data on cutaneous HPVs circulating in South America and expands our knowledge of the Papillomaviridae family.
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Affiliation(s)
- Diego Chouhy
- Area Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Argentina
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Ghittoni R, Accardi R, Hasan U, Gheit T, Sylla B, Tommasino M. The biological properties of E6 and E7 oncoproteins from human papillomaviruses. Virus Genes 2009; 40:1-13. [PMID: 19838783 DOI: 10.1007/s11262-009-0412-8] [Citation(s) in RCA: 215] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 10/05/2009] [Indexed: 02/07/2023]
Abstract
More than 100 different human papillomavirus (HPV) types have been isolated so far, and they can be sub-grouped in cutaneous or mucosal according to their ability to infect the skin or the mucosa of the genital or upper-respiratory tracts. A sub-group of human mucosal HPVs, referred to as high-risk HPV types, is responsible for approximately 5% of all human cancers, which represents one-third of all the tumours induced by viruses. Epidemiological and biological studies have shown that HPV16 is the most oncogenic type within the high-risk group. Emerging lines of evidence suggest that, in addition to the high-risk mucosal HPV types, certain cutaneous HPVs are involved in skin cancer. HPV-associated cancers are intimately linked to HPV persistence and the accumulation of chromosomal rearrangements. The products of the early genes, E6 and E7, of the high-risk mucosal HPV types play a key role in both events. Indeed, these proteins have developed a number of strategies to evade host immuno-surveillance allowing viral persistence, and to alter cell cycle and apoptosis control, facilitating the accumulation of DNA damage/mutations. Often, the two oncoproteins target the same cellular pathways with different mechanisms, showing a strong synergism in promoting cellular transformation and neutralizing the immune response. Here, we review most of the findings on the biological properties and molecular mechanisms of the oncoproteins E6 and E7 from mucosal and cutaneous HPV types.
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Affiliation(s)
- Raffaella Ghittoni
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69008 Lyon, France.
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