1
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Lim YX, D'Silva NJ. HPV-associated oropharyngeal cancer: in search of surrogate biomarkers for early lesions. Oncogene 2024; 43:543-554. [PMID: 38191674 PMCID: PMC10873204 DOI: 10.1038/s41388-023-02927-9] [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: 09/29/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024]
Abstract
The incidence of oropharyngeal cancer (OPSCC) has escalated in the past few decades; this has largely been triggered by high-risk human papillomavirus (HPV). Early cancer screening is needed for timely clinical intervention and may reduce mortality and morbidity, but the lack of knowledge about premalignant lesions for OPSCC poses a significant challenge to early detection. Biomarkers that identify individuals at high risk for OPSCC may act as surrogate markers for precancer but these are limited as only a few studies decipher the multistep progression from HPV infection to OPSCC development. Here, we summarize the current literature describing the multistep progression from oral HPV infection, persistence, and tumor development in the oropharynx. We also examine key challenges that hinder the identification of premalignant lesions in the oropharynx and discuss potential biomarkers for oropharyngeal precancer. Finally, we evaluate novel strategies to improve investigations of the biological process that drives oral HPV persistence and OPSCC, highlighting new developments in the establishment of a genetic progression model for HPV + OPSCC and in vivo models that mimic HPV + OPSCC pathogenesis.
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Affiliation(s)
- Yvonne X Lim
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
| | - Nisha J D'Silva
- Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, USA.
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2
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Aghbash PS, Hemmat N, Fathi H, Baghi HB. Monoclonal antibodies in cervical malignancy-related HPV. Front Oncol 2022; 12:904790. [PMID: 36276117 PMCID: PMC9582116 DOI: 10.3389/fonc.2022.904790] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Despite many efforts to treat HPV infection, cervical cancer survival is still poor for several reasons, including resistance to chemotherapy and relapse. Numerous treatments such as surgery, radiation therapy, immune cell-based therapies, siRNA combined with various drugs, and immunotherapy are being studied and performed to provide the best treatment. Depending on the stage and size of the tumor, methods such as radical hysterectomy, pelvic lymphadenectomy, or chemotherapy can be utilized to treat cervical cancer. While accepted, these treatments lead to interruptions in cellular pathways and immune system homeostasis. In addition to a low survival rate, cervical neoplasm incidence has been rising significantly. However, new strategies have been proposed to increase patient survival while reducing the toxicity of chemotherapy, including targeted therapy and monoclonal antibodies. In this article, we discuss the types and potential therapeutic roles of monoclonal antibodies in cervical cancer.
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Affiliation(s)
- Parisa Shiri Aghbash
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nima Hemmat
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Drug Applied Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamidreza Fathi
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- *Correspondence: Hossein Bannazadeh Baghi, ;
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3
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Genetic variability of the HPV16 early genes and LCR. Present and future perspectives. Expert Rev Mol Med 2021; 23:e19. [PMID: 34847982 DOI: 10.1017/erm.2021.18] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Human papillomavirus 16 (HPV16) infection is the aetiologic factor for the development of cervical dysplasia and is regarded as highly carcinogen, because it is implicated in more than 50% of cervical cancer cases, worldwide. The tumourigenic potential of HPV16 has triggered the extensive sequence analysis of viral genome in order to identify nucleotide variations and amino acid substitutions that influence viral oncogenicity and subsequently the initiation and progression of cervical cancer. Nowadays, specific mutations of HPV16 DNA have been associated with an increased risk of high-grade squamous intraepithelial lesions and invasive cervical cancer (ICC) development, including E6: Q14H, H78Y, L83V, Ε7: N29S, S63F, E2: H35Q, P219S, T310K, E5: I65V, whereas highly conserved regions of viral DNA have been extensively characterised. In addition, numerous novel HPV16 mutations are observed among the studied populations from various geographic regions, hence advocating that different HPV16 strains seem to emerge with different tumourigenic capacities. The present review focuses on the variability of the early genes and the long control region, emphasising on the association of specific mutations with the development of severe dysplasia. Finally, it evaluates whether specific regions of HPV16 DNA are able to serve as valuable biomarkers for cervical cancer risk.
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4
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Jak HPV wysokiego ryzyka indukuje optymalne środowisko dla własnej replikacji w różnicującym się nabłonku. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstrakt
Wirusy brodawczaka ludzkiego (HPV) są często czynnikami wywołującymi niegroźne dla człowieka infekcje, ale przetrwałe zakażenie niektórymi typami HPV jest poważnym zagrożeniem dla zdrowia, ponieważ jest związane z wieloma nowotworami, w tym z rakiem szyjki macicy oraz rosnącą liczbą nowotworów głowy i szyi. Cykl replikacyjny HPV jest ściśle zależny od różnicowania komórek wielowarstwowego nabłonka, co oznacza, że genom wirusa musi być replikowany za pomocą różnych mechanizmów na różnych etapach różnicowania komórek. Ustanowienie infekcji i utrzymywanie genomu wirusa zachodzi w proliferujących komórkach nabłonka, gdzie dostępność czynników replikacji jest optymalna dla wirusa. Jednak produktywna faza cyklu rozwojowego wirusa, w tym produktywna replikacja, późna ekspresja genów i wytwarzanie wirionów, zachodzi w wyniku różnicowania się nabłonka w komórkach, które prawidłowo opuszczają cykl komórkowy. Wirus wykorzystuje wiele szlaków sygnalizacyjnych komórki, w tym odpowiedź na uszkodzenia DNA (DDR, DNA damage response) do realizacji produktywnej replikacji własnego genomu. Zrozumienie mechanizmów związanych z cyklem replikacyjnym HPV jest potrzebne do ustalenia właściwego podejścia terapeutycznego do zwalczania chorób powodowanych przez HPV.
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5
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Pavesi A. Origin, Evolution and Stability of Overlapping Genes in Viruses: A Systematic Review. Genes (Basel) 2021; 12:genes12060809. [PMID: 34073395 PMCID: PMC8227390 DOI: 10.3390/genes12060809] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
During their long evolutionary history viruses generated many proteins de novo by a mechanism called “overprinting”. Overprinting is a process in which critical nucleotide substitutions in a pre-existing gene can induce the expression of a novel protein by translation of an alternative open reading frame (ORF). Overlapping genes represent an intriguing example of adaptive conflict, because they simultaneously encode two proteins whose freedom to change is constrained by each other. However, overlapping genes are also a source of genetic novelties, as the constraints under which alternative ORFs evolve can give rise to proteins with unusual sequence properties, most importantly the potential for novel functions. Starting with the discovery of overlapping genes in phages infecting Escherichia coli, this review covers a range of studies dealing with detection of overlapping genes in small eukaryotic viruses (genomic length below 30 kb) and recognition of their critical role in the evolution of pathogenicity. Origin of overlapping genes, what factors favor their birth and retention, and how they manage their inherent adaptive conflict are extensively reviewed. Special attention is paid to the assembly of overlapping genes into ad hoc databases, suitable for future studies, and to the development of statistical methods for exploring viral genome sequences in search of undiscovered overlaps.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, I-43124 Parma, Italy
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6
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Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene 2020; 39:6327-6339. [PMID: 32848210 PMCID: PMC7529583 DOI: 10.1038/s41388-020-01431-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/19/2020] [Accepted: 08/13/2020] [Indexed: 12/26/2022]
Abstract
The dominant paradigm for HPV carcinogenesis includes integration into the host genome followed by expression of E6 and E7 (E6/E7). We explored an alternative carcinogenic pathway characterized by episomal E2, E4, and E5 (E2/E4/E5) expression. Half of HPV positive cervical and pharyngeal cancers comprised a subtype with increase in expression of E2/E4/E5, as well as association with lack of integration into the host genome. Models of the E2/E4/E5 carcinogenesis show p53 dependent enhanced proliferation in vitro, as well as increased susceptibility to induction of cancer in vivo. Whole genomic expression analysis of the E2/E4/E5 pharyngeal cancer subtype is defined by activation of the fibroblast growth factor receptor (FGFR) pathway and this subtype is susceptible to combination FGFR and mTOR inhibition, with implications for targeted therapy.
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Affiliation(s)
- Shuling Ren
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Department of Otolaryngology-Head and Neck Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Alexander V Favorov
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elana J Fertig
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Juan Luis Callejas-Valera
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Cancer Biology and Immunotherapies group, Sanford Research, Sioux Falls, SD, USA
| | - Mike Allevato
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Mara Gilardi
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Jessica Santos
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Takahito Fukusumi
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Akihiro Sakai
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Mizuo Ando
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Sayed Sadat
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Chao Liu
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Guorong Xu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zhiyong Wang
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Alfredo A Molinolo
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Joseph A Califano
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA. .,Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, CA, USA.
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7
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Khan A, Liu Q, Chen X, Stucky A, Sedghizadeh PP, Adelpour D, Zhang X, Wang K, Zhong JF. Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect. Mol Oncol 2019; 13:829-839. [PMID: 30597724 PMCID: PMC6441885 DOI: 10.1002/1878-0261.12435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/13/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing provides an opportunity to detect viral species from RNA-seq data of human tissues, but existing computational approaches do not perform optimally on clinical samples. We developed a bioinformatic method called VirTect for detecting viruses in neoplastic human tissues using RNA-seq data. Here, we used VirTect to analyze RNA-seq data from 363 head and neck squamous cell carcinoma (HNSCC) patients and identified 22 human papillomavirus (HPV)-induced HNSCCs. These predictions were validated by manual review of pathology reports on histopathologic specimens. VirTect showed better performance in recall and accuracy compared to the two existing prediction methods, VirusFinder and VirusSeq, in identifying viral sequences from RNA-seq data. The majority of HPV carcinogenesis studies thus far have been performed on cervical cancer and generalized to HNSCC. Our results suggest that carcinogenesis of HPV-induced HNSCC and other cases of HNSCC involve different genes, so understanding the underlying molecular mechanisms will have a significant impact on therapeutic approaches and outcomes. In summary, RNA-seq together with VirTect can be an effective solution for the detection of viruses from tumor samples and can facilitate the clinicopathologic characterization of various types of cancers with broad applications for oncology.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xuelian Chen
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Andres Stucky
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Parish P Sedghizadeh
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Daniel Adelpour
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Xi Zhang
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jiang F Zhong
- Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA.,Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
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8
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Gleber-Netto FO, Rao X, Guo T, Xi Y, Gao M, Shen L, Erikson K, Kalu NN, Ren S, Xu G, Fisch KM, Akagi K, Seiwert T, Gillison M, Frederick MJ, Johnson FM, Wang J, Myers JN, Califano J, Skinner HD, Pickering CR. Variations in HPV function are associated with survival in squamous cell carcinoma. JCI Insight 2019; 4:124762. [PMID: 30626753 DOI: 10.1172/jci.insight.124762] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/27/2018] [Indexed: 12/25/2022] Open
Abstract
Incidence of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) has been increasing dramatically. Although long-term survival rates for these patients are high, they often suffer from permanent radiotherapy-related morbidity. This has prompted the development of de-escalation clinical protocols to reduce morbidity. However, a subset of patients do not respond even to standard therapy and have poor outcomes. It is unclear how to properly identify and treat the high- and low-risk HPV+ OPSCC patients. Since HPV positivity drives radiotherapy sensitivity, we hypothesized that variations in HPV biology may cause differences in treatment response and outcome. By analyzing gene expression data, we identified variations in HPV-related molecules among HPV+ OPSCC. A subset of tumors presented a molecular profile distinct from that of typical HPV+ tumors and exhibited poor treatment response, indicating molecular and clinical similarities with HPV- tumors. These molecular changes were also observed in vitro and correlated with radiation sensitivity. Finally, we developed a prognostic biomarker signature for identification of this subgroup of HPV+ OPSCC and validated it in independent cohorts of oropharyngeal and cervical carcinomas. These findings could translate to improved patient stratification for treatment deintensification and new therapeutic approaches for treatment-resistant HPV-related cancer.
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Affiliation(s)
| | - Xiayu Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. USA
| | - Theresa Guo
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. USA
| | - Meng Gao
- Department of Head and Neck Surgery and
| | - Li Shen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. USA
| | | | - Nene N Kalu
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shuling Ren
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Guorong Xu
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, California. USA
| | - Keiko Akagi
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tanguy Seiwert
- Department of Medicine and Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Maura Gillison
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Faye M Johnson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas. USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery and.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Joseph Califano
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
| | - Heath D Skinner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery and.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
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9
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Pavesi A, Vianelli A, Chirico N, Bao Y, Blinkova O, Belshaw R, Firth A, Karlin D. Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes. PLoS One 2018; 13:e0202513. [PMID: 30339683 PMCID: PMC6195259 DOI: 10.1371/journal.pone.0202513] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/03/2018] [Indexed: 11/19/2022] Open
Abstract
Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a high-quality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them.
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Affiliation(s)
- Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alberto Vianelli
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Nicola Chirico
- Department of Theoretical and Applied Sciences, University of Insubria, Varese, Italy
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Olga Blinkova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America
| | - Robert Belshaw
- School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry (PUPSMD), Plymouth, United Kingdom
| | - Andrew Firth
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - David Karlin
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Division of Structural Biology, University of Oxford, Oxford, United Kingdom
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10
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The human papillomavirus replication cycle, and its links to cancer progression: a comprehensive review. Clin Sci (Lond) 2017; 131:2201-2221. [DOI: 10.1042/cs20160786] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 12/21/2022]
Abstract
HPVs (human papillomaviruses) infect epithelial cells and their replication cycle is intimately linked to epithelial differentiation. There are over 200 different HPV genotypes identified to date and each displays a strict tissue specificity for infection. HPV infection can result in a range of benign lesions, for example verrucas on the feet, common warts on the hands, or genital warts. HPV infects dividing basal epithelial cells where its dsDNA episomal genome enters the nuclei. Upon basal cell division, an infected daughter cell begins the process of keratinocyte differentiation that triggers a tightly orchestrated pattern of viral gene expression to accomplish a productive infection. A subset of mucosal-infective HPVs, the so-called ‘high risk’ (HR) HPVs, cause cervical disease, categorized as low or high grade. Most individuals will experience transient HR-HPV infection during their lifetime but these infections will not progress to clinically significant cervical disease or cancer because the immune system eventually recognizes and clears the virus. Cancer progression is due to persistent infection with an HR-HPV. HR-HPV infection is the cause of >99.7% cervical cancers in women, and a subset of oropharyngeal cancers, predominantly in men. HPV16 (HR-HPV genotype 16) is the most prevalent worldwide and the major cause of HPV-associated cancers. At the molecular level, cancer progression is due to increased expression of the viral oncoproteins E6 and E7, which activate the cell cycle, inhibit apoptosis, and allow accumulation of DNA damage. This review aims to describe the productive life cycle of HPV and discuss the roles of the viral proteins in HPV replication. Routes to viral persistence and cancer progression are also discussed.
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11
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Egawa N, Wang Q, Griffin HM, Murakami I, Jackson D, Mahmood R, Doorbar J. HPV16 and 18 genome amplification show different E4-dependence, with 16E4 enhancing E1 nuclear accumulation and replicative efficiency via its cell cycle arrest and kinase activation functions. PLoS Pathog 2017; 13:e1006282. [PMID: 28306742 PMCID: PMC5371391 DOI: 10.1371/journal.ppat.1006282] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/29/2017] [Accepted: 03/08/2017] [Indexed: 12/03/2022] Open
Abstract
To clarify E1^E4’s role during high-risk HPV infection, the E4 proteins of HPV16 and 18 were compared side by side using an isogenic keratinocyte differentiation model. While no effect on cell proliferation or viral genome copy number was observed during the early phase of either virus life cycle, time-course experiments showed that viral genome amplification and L1 expression were differently affected upon differentiation, with HPV16 showing a much clearer E4 dependency. Although E4 loss never completely abolished genome amplification, its more obvious contribution in HPV16 focused our efforts on 16E4. As previously suggested, in the context of the virus life cycle, 16E4s G2-arrest capability was found to contribute to both genome amplification success and L1 accumulation. Loss of 16E4 also lead to a reduced maintenance of ERK, JNK and p38MAPK activity throughout the genome amplifying cell layers, with 16E4 (but not 18E4) co-localizing precisely with activated cytoplasmic JNK in both wild type raft tissue, and HPV16-induced patient biopsy tissue. When 16E1 was co-expressed with E4, as occurs during genome amplification in vivo, the E1 replication helicase accumulated preferentially in the nucleus, and in transient replication assays, E4 stimulated viral genome amplification. Interestingly, a 16E1 mutant deficient in its regulatory phosphorylation sites no longer accumulated in the nucleus following E4 co-expression. E4-mediated stabilisation of 16E2 was also apparent, with E2 levels declining in organotypic raft culture when 16E4 was absent. These results suggest that 16E4-mediated enhancement of genome amplification involves its cell cycle inhibition and cellular kinase activation functions, with E4 modifying the activity and function of viral replication proteins including E1. These activities of 16E4, and the different kinase patterns seen here with HPV18, 31 and 45, may reflect natural differences in the biology and tropisms of these viruses, as well as differences in E4 function. In HPV induced lesions, the most abundant protein expressed in the productive stage of viral life cycle is E1^E4 (E4), with its expression being coincident with viral genome amplification. To clarify the role of E4 in the high-risk HPV life cycle, we carried out a comparative analysis of E4 function in HPV16 and 18 using an isogenic keratinocyte cell-line background. Our results show that E1^E4 contributes to virus genome replication efficiency and life cycle completion rather than being essential. These effects were seen more dramatically with HPV16. The difference between HPV16 and HPV18 in our system suggests important tropism differences between these viruses. HPV16 E4’s contribution to the virus life cycle is mediated by several activities, including its G2 arrest function, as well as its role in activating members of the MAPK pathway, including ERK, p38, and most notably pJNK. These 16 E4 functions facilitated the nuclear localization of the E1 virus helicase and enhanced E1/E2 dependent viral genome amplification as well as stabilising E2. We suspect that the massive accumulation of E4 in the upper epithelial layers may however underlie a more critical role for E4 post-genome amplification.
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Affiliation(s)
- Nagayasu Egawa
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Qian Wang
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Heather M. Griffin
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Isao Murakami
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Deborah Jackson
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Radma Mahmood
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
- * E-mail:
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12
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Phosphorylation of the Bovine Papillomavirus E2 Protein on Tyrosine Regulates Its Transcription and Replication Functions. J Virol 2017; 91:JVI.01854-16. [PMID: 27807239 DOI: 10.1128/jvi.01854-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/30/2016] [Indexed: 12/21/2022] Open
Abstract
Papillomaviruses are small, double-stranded DNA viruses that encode the E2 protein, which controls transcription, replication, and genome maintenance in infected cells. Posttranslational modifications (PTMs) affecting E2 function and stability have been demonstrated for multiple types of papillomaviruses. Here we describe the first phosphorylation event involving a conserved tyrosine (Y) in the bovine papillomavirus 1 (BPV-1) E2 protein at amino acid 102. While its phosphodeficient phenylalanine (F) mutant activated both transcription and replication in luciferase reporter assays, a mutant that may act as a phosphomimetic, with a Y102-to-glutamate (E) mutation, lost both activities. The E2 Y102F protein interacted with cellular E2-binding factors and the viral helicase E1; however, in contrast, the Y102E mutant associated with only a subset and was unable to bind to E1. While the Y102F mutant fully supported transient viral DNA replication, BPV genomes encoding this mutation as well as Y102E were not maintained as stable episomes in murine C127 cells. These data imply that phosphorylation at Y102 disrupts the helical fold of the N-terminal region of E2 and its interaction with key cellular and viral proteins. We hypothesize that the resulting inhibition of viral transcription and replication in basal epithelial cells prevents the development of a lytic infection. IMPORTANCE Papillomaviruses (PVs) are small, double-stranded DNA viruses that are responsible for cervical, oropharyngeal, and various genitourinary cancers. Although vaccines against the major oncogenic human PVs are available, there is no effective treatment for existing infections. One approach to better understand the viral replicative cycle, and potential therapies to target it, is to examine the posttranslational modification of viral proteins and its effect on function. Here we have discovered that the bovine papillomavirus 1 (BPV-1) transcription and replication regulator E2 is phosphorylated at residue Y102. While a phosphodeficient mutant at this site was fully functional, a phosphomimetic mutant displayed impaired transcription and replication activity as well as a lack of an association with certain E2-binding proteins. This study highlights the influence of posttranslational modifications on viral protein function and provides additional insight into the complex interplay between papillomaviruses and their hosts.
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13
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The Cellular DNA Helicase ChlR1 Regulates Chromatin and Nuclear Matrix Attachment of the Human Papillomavirus 16 E2 Protein and High-Copy-Number Viral Genome Establishment. J Virol 2016; 91:JVI.01853-16. [PMID: 27795438 PMCID: PMC5165203 DOI: 10.1128/jvi.01853-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/07/2016] [Indexed: 01/13/2023] Open
Abstract
In papillomavirus infections, the viral genome is established as a double-stranded DNA episome. To segregate the episomes into daughter cells during mitosis, they are tethered to cellular chromatin by the viral E2 protein. We previously demonstrated that the E2 proteins of diverse papillomavirus types, including bovine papillomavirus (BPV) and human papillomavirus 16 (HPV16), associate with the cellular DNA helicase ChlR1. This virus-host interaction is important for the tethering of BPV E2 to mitotic chromatin and the stable maintenance of BPV episomes. The role of the association between E2 and ChlR1 in the HPV16 life cycle is unresolved. Here we show that an HPV16 E2 Y131A mutant (E2Y131A) had significantly reduced binding to ChlR1 but retained transcriptional activation and viral origin-dependent replication functions. Subcellular fractionation of keratinocytes expressing E2Y131A showed a marked change in the localization of the protein. Compared to that of wild-type E2 (E2WT), the chromatin-bound pool of E2Y131A was decreased, concomitant with an increase in nuclear matrix-associated protein. Cell cycle synchronization indicated that the shift in subcellular localization of E2Y131A occurred in mid-S phase. A similar alteration between the subcellular pools of the E2WT protein occurred upon ChlR1 silencing. Notably, in an HPV16 life cycle model in primary human keratinocytes, mutant E2Y131A genomes were established as episomes, but at a markedly lower copy number than that of wild-type HPV16 genomes, and they were not maintained upon cell passage. Our studies indicate that ChlR1 is an important regulator of the chromatin association of E2 and of the establishment and maintenance of HPV16 episomes.
IMPORTANCE Infections with high-risk human papillomaviruses (HPVs) are a major cause of anogenital and oropharyngeal cancers. During infection, the circular DNA genome of HPV persists within the nucleus, independently of the host cell chromatin. Persistence of infection is a risk factor for cancer development and is partly achieved by the attachment of viral DNA to cellular chromatin during cell division. The HPV E2 protein plays a critical role in this tethering by binding simultaneously to the viral genome and to chromatin during mitosis. We previously showed that the cellular DNA helicase ChlR1 is required for loading of the bovine papillomavirus E2 protein onto chromatin during DNA synthesis. Here we identify a mutation in HPV16 E2 that abrogates interaction with ChlR1, and we show that ChlR1 regulates the chromatin association of HPV16 E2 and that this virus-host interaction is essential for viral episome maintenance.
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14
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The CXCL12/CXCR4 Signaling Pathway: A New Susceptibility Factor in Human Papillomavirus Pathogenesis. PLoS Pathog 2016; 12:e1006039. [PMID: 27918748 PMCID: PMC5138052 DOI: 10.1371/journal.ppat.1006039] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022] Open
Abstract
The productive human papillomavirus (HPV) life cycle is tightly linked to the differentiation and cycling of keratinocytes. Deregulation of these processes and stimulation of cell proliferation by the action of viral oncoproteins and host cell factors underlies HPV-mediated carcinogenesis. Severe HPV infections characterize the wart, hypogammaglobulinemia, infection, and myelokathexis (WHIM) immunodeficiency syndrome, which is caused by gain-of-function mutations in the CXCR4 receptor for the CXCL12 chemokine, one of which is CXCR41013. We investigated whether CXCR41013 interferes in the HPV18 life cycle in epithelial organotypic cultures. Expression of CXCR41013 promoted stabilization of HPV oncoproteins, thus disturbing cell cycle progression and proliferation at the expense of the ordered expression of the viral genes required for virus production. Conversely, blocking CXCR41013 function restored virus production and limited HPV-induced carcinogenesis. Thus, CXCR4 and its potential activation by genetic alterations in the course of the carcinogenic process can be considered as an important host factor for HPV carcinogenesis. Human papillomaviruses (HPV) are epitheliotropic tumor viruses causing mostly benign warts but that have developed strategies to establish persistent infections. Although host immune responses clear most infections, persistence of some HPV types causes ~5% of human cancers and severe pathogenesis in immunosuppressed individuals. How early events in HPV infection, determined by the interaction between viral and host proteins, might lead to viral persistence and pathogenesis is unknown. Here, we thought to investigate this issue by providing mechanistic insights into the selective susceptibility to HPV pathogenesis displayed by patients who are immunosuppressed as a consequence of mutations in the CXCR4 gene encoding for the receptor of the CXCL12 chemokine (WHIM syndrome). We previously unraveled the existence of a general interplay between the CXCL12/CXCR4 axis and HPV, which is hijacked toward cell transformation upon expression of the CXCR4 mutant. Here, using three dimensional epithelial cell cultures to analyze the HPV life cycle, we found that the CXCR4 mutant promotes cell hyperproliferation and stabilization of viral oncoprotein expression at the expense of virus production. Our results, which identify CXCR4 as an important gatekeeper of keratinocyte proliferation and as a new susceptibility factor in HPV pathogenesis, may be translated into anti-viral and anti-cancer strategies.
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15
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Human Papillomavirus E2 Protein: Linking Replication, Transcription, and RNA Processing. J Virol 2016; 90:8384-8. [PMID: 27412596 DOI: 10.1128/jvi.00502-16] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The human papillomavirus (HPV) life cycle is tightly linked to differentiation of the infected epithelium. This means that viral proteins must exert control over epithelial gene expression in order to optimize viral production. The HPV E2 protein controls replication, transcription, and viral genome partitioning during the viral infectious life cycle. It consists of a nucleic acid-binding domain and a protein-protein interaction domain separated by a flexible serine and arginine-rich hinge region. Over the last few years, mounting evidence has uncovered an important new role for E2 in viral and cellular RNA processing. This Gem discusses the role of E2 in controlling the epithelial cellular environment and how E2 might act to coordinate late events in the viral replication cycle.
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16
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Siddiqa A, Léon KC, James CD, Bhatti MF, Roberts S, Parish JL. The human papillomavirus type 16 L1 protein directly interacts with E2 and enhances E2-dependent replication and transcription activation. J Gen Virol 2015; 96:2274-2285. [PMID: 25911730 PMCID: PMC4681068 DOI: 10.1099/vir.0.000162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human papillomavirus (HPV) E2 protein is a multifunctional protein essential for the control of virus gene expression, genome replication and persistence. E2 is expressed throughout the differentiation-dependent virus life cycle and is functionally regulated by association with multiple viral and cellular proteins. Here, we show for the first time to our knowledge that HPV16 E2 directly associates with the major capsid protein L1, independently of other viral or cellular proteins. We have mapped the L1 binding region within E2 and show that the α-2 helices within the E2 DNA-binding domain mediate L1 interaction. Using cell-based assays, we show that co-expression of L1 and E2 results in enhanced transcription and virus origin-dependent DNA replication. Upon co-expression in keratinocytes, L1 reduces nucleolar association of E2 protein, and when co-expressed with E1 and E2, L1 is partially recruited to viral replication factories. Furthermore, co-distribution of E2 and L1 was detected in the nuclei of upper suprabasal cells in stratified epithelia of HPV16 genome-containing primary human keratinocytes. Taken together, our findings suggest that the interaction between E2 and L1 is important for the regulation of E2 function during the late events of the HPV life cycle.
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Affiliation(s)
- Abida Siddiqa
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.,Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Kashmir Highway, Islamabad 44000, Pakistan
| | - Karen Campos Léon
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Claire D James
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Kashmir Highway, Islamabad 44000, Pakistan
| | - Sally Roberts
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Joanna L Parish
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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17
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Prescott EL, Brimacombe CL, Hartley M, Bell I, Graham S, Roberts S. Human papillomavirus type 1 E1^E4 protein is a potent inhibitor of the serine-arginine (SR) protein kinase SRPK1 and inhibits phosphorylation of host SR proteins and of the viral transcription and replication regulator E2. J Virol 2014; 88:12599-611. [PMID: 25142587 PMCID: PMC4248925 DOI: 10.1128/jvi.02029-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/13/2014] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED The serine-arginine-specific protein kinase SRPK1 is a common binding partner of the E1^E4 protein of diverse human papillomavirus types. We show here for the first time that the interaction between HPV1 E1^E4 and SRPK1 leads to potent inhibition of SRPK1 phosphorylation of host serine-arginine (SR) proteins that have critical roles in mRNA metabolism, including pre-mRNA processing, mRNA export, and translation. Furthermore, we show that SRPK1 phosphorylates serine residues of SR/RS dipeptides in the hinge region of the HPV1 E2 protein in in vitro kinase assays and that HPV1 E1^E4 inhibits this phosphorylation. After mutation of the putative phosphoacceptor serine residues, the localization of the E2 protein was altered in primary human keratinocytes; with a significant increase in the cell population showing intense E2 staining of the nucleolus. A similar effect was observed following coexpression of E2 and E1^E4 that is competent for inhibition of SRPK1 activity, suggesting that the nuclear localization of E2 is sensitive to E1^E4-mediated SRPK1 inhibition. Collectively, these data suggest that E1^E4-mediated inhibition of SRPK1 could affect the functions of host SR proteins and those of the virus transcription/replication regulator E2. We speculate that the novel E4 function identified here is involved in the regulation of E2 and SR protein function in posttranscriptional processing of viral transcripts. IMPORTANCE The HPV life cycle is tightly linked to the epithelial terminal differentiation program, with the virion-producing phase restricted to differentiating cells. While the most abundant HPV protein expressed in this phase is the E4 protein, we do not fully understand the role of this protein. Few E4 interaction partners have been identified, but we had previously shown that E4 proteins from diverse papillomaviruses interact with the serine-arginine-specific protein kinase SRPK1, a kinase important in the replication cycles of a diverse range of DNA and RNA viruses. We show that HPV1 E4 is a potent inhibitor of this host cell kinase. We show that E4 inhibits SRPK1 phosphorylation, not only of cellular SR proteins involved in regulating alternative splicing of RNA but also the viral transcription/replication regulator E2. Our findings reveal a potential E4 function in regulation of viral late gene expression through the inhibition of a host cell kinase.
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Affiliation(s)
- Emma L Prescott
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claire L Brimacombe
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Margaret Hartley
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ian Bell
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sheila Graham
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity, and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sally Roberts
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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18
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The role of ubiquitin and ubiquitin-like modification systems in papillomavirus biology. Viruses 2014; 6:3584-611. [PMID: 25254385 PMCID: PMC4189040 DOI: 10.3390/v6093584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Human papillomaviruses (HPVs) are small DNA viruses that are important etiological agents of a spectrum of human skin lesions from benign to malignant. Because of their limited genome coding capacity they express only a small number of proteins, only one of which has enzymatic activity. Additionally, the HPV productive life cycle is intimately tied to the epithelial differentiation program and they must replicate in what are normally non-replicative cells, thus, these viruses must reprogram the cellular environment to achieve viral reproduction. Because of these limitations and needs, the viral proteins have evolved to co-opt cellular processes primarily through protein-protein interactions with critical host proteins. The ubiquitin post-translational modification system and the related ubiquitin-like modifiers constitute a widespread cellular regulatory network that controls the levels and functions of thousands of proteins, making these systems an attractive target for viral manipulation. This review describes the interactions between HPVs and the ubiquitin family of modifiers, both to regulate the viral proteins themselves and to remodel the host cell to facilitate viral survival and reproduction.
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19
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Abstract
The papillomavirus E2 proteins are pivotal to the viral life cycle and have well characterized functions in transcriptional regulation, initiation of DNA replication and partitioning the viral genome. The E2 proteins also function in vegetative DNA replication, post-transcriptional processes and possibly packaging. This review describes structural and functional aspects of the E2 proteins and their binding sites on the viral genome. It is intended to be a reference guide to this viral protein.
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Affiliation(s)
- Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892, USA.
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20
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Doorbar J. The E4 protein; structure, function and patterns of expression. Virology 2013; 445:80-98. [PMID: 24016539 DOI: 10.1016/j.virol.2013.07.008] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/08/2013] [Indexed: 01/05/2023]
Abstract
The papillomavirus E4 open reading frame (ORF) is contained within the E2 ORF, with the primary E4 gene-product (E1^E4) being translated from a spliced mRNA that includes the E1 initiation codon and adjacent sequences. E4 is located centrally within the E2 gene, in a region that encodes the E2 protein's flexible hinge domain. Although a number of minor E4 transcripts have been reported, it is the product of the abundant E1^E4 mRNA that has been most extensively analysed. During the papillomavirus life cycle, the E1^E4 gene products generally become detectable at the onset of vegetative viral genome amplification as the late stages of infection begin. E4 contributes to genome amplification success and virus synthesis, with its high level of expression suggesting additional roles in virus release and/or transmission. In general, E4 is easily visualised in biopsy material by immunostaining, and can be detected in lesions caused by diverse papillomavirus types, including those of dogs, rabbits and cattle as well as humans. The E4 protein can serve as a biomarker of active virus infection, and in the case of high-risk human types also disease severity. In some cutaneous lesions, E4 can be expressed at higher levels than the virion coat proteins, and can account for as much as 30% of total lesional protein content. The E4 proteins of the Beta, Gamma and Mu HPV types assemble into distinctive cytoplasmic, and sometimes nuclear, inclusion granules. In general, the E4 proteins are expressed before L2 and L1, with their structure and function being modified, first by kinases as the infected cell progresses through the S and G2 cell cycle phases, but also by proteases as the cell exits the cell cycle and undergoes true terminal differentiation. The kinases that regulate E4 also affect other viral proteins simultaneously, and include protein kinase A, Cyclin-dependent kinase, members of the MAP Kinase family and protein kinase C. For HPV16 E1^E4, these kinases regulate one of the E1^E4 proteins main functions, the association with the cellular keratin network, and eventually also its cleavage by the protease calpain which allows assembly into amyloid-like fibres and reorganisation of the keratin network. Although the E4 proteins of different HPV types appear divergent at the level of their primary amino acid sequence, they share a recognisable modular organisation and pattern of expression, which may underlie conserved functions and regulation. Assembly into higher-order multimers and suppression of cell proliferation are common to all E4 proteins examined. Although not yet formally demonstrated, a role in virus release and transmission remains a likely function for E4.
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Affiliation(s)
- John Doorbar
- Division of Virology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom.
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21
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Yuan CH, Filippova M, Duerksen-Hughes P. Modulation of apoptotic pathways by human papillomaviruses (HPV): mechanisms and implications for therapy. Viruses 2012; 4:3831-50. [PMID: 23250450 PMCID: PMC3528293 DOI: 10.3390/v4123831] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 12/14/2022] Open
Abstract
The ability of the host to trigger apoptosis in infected cells is perhaps the most powerful tool by which viruses can be cleared from the host organism. To avoid elimination by this mechanism, human papillomaviruses (HPV) have developed several mechanisms that enable the cells they infect to elude both extrinsic and intrinsic apoptosis. In this manuscript, we review the current literature regarding how HPV-infected cells avoid apoptosis and the molecular mechanisms involved in these events. In particular, we will discuss the modifications in intrinsic and extrinsic apoptotic pathways caused by proteins encoded by HPV early genes. Many of the current efforts regarding anti-cancer drug development are focused on directing tumor cells to undergo apoptosis. However, the ability of HPV-infected cells to resist apoptotic signals renders such therapies ineffective. Possible mechanisms for overcoming the resistance of HPV-infected tumor cells to anticancer drugs will be discussed.
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Affiliation(s)
- Chung-Hsiang Yuan
- Department of Basic Sciences, Loma Linda University School of Medicine, 11085 Campus St., Loma Linda, CA 92354, USA.
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22
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Pang CL, Thierry F. Human papillomavirus proteins as prospective therapeutic targets. Microb Pathog 2012; 58:55-65. [PMID: 23164805 DOI: 10.1016/j.micpath.2012.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 11/07/2012] [Accepted: 11/07/2012] [Indexed: 01/01/2023]
Abstract
Human papillomaviruses (HPV) are the causative agents of a subset of cervical cancers that are associated with persistent viral infection. The HPV genome is an ∼8 kb circle of double-stranded DNA that encodes eight viral proteins, among which the products of the E6 and E7 open reading frames are recognized as being the primary HPV oncogenes. E6 and E7 are expressed in pre-malignant lesions as well as in cervical cancers; hence these proteins have been extensively studied as potential targets for HPV therapies and novel vaccines. Here we review the expression and functions of E6 and E7 in the viral vegetative cycle and in oncogenesis. We also explore the expression and functions of other HPV proteins, including those with oncogenic properties, and discuss the potential of these molecules as alternative therapeutic targets.
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Affiliation(s)
- Chai Ling Pang
- Singapore Immunology Network, 8A Biomedical Grove, #4-06 Immunos, A*STAR, Singapore 138648, Singapore
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23
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Abstract
Persistent infection with cancer risk-related viruses leads to molecular, cellular and immune response changes in host organisms that in some cases direct cellular transformation. Alternative splicing is a conserved cellular process that increases the coding complexity of genomes at the pre-mRNA processing stage. Human and other animal tumour viruses use alternative splicing as a process to maximize their transcriptomes and proteomes. Medical therapeutics to clear persistent viral infections are still limited. However, specific lessons learned in some viruses [e.g. HIV and HCV (hepatitis C virus)] suggest that drug-directed inhibition of alternative splicing could be useful for this purpose. The present review describes the basic mechanisms of constitutive and alternative splicing in a cellular context and known splicing patterns and the mechanisms by which these might be achieved for the major human infective tumour viruses. The roles of splicing-related proteins expressed by these viruses in cellular and viral gene regulation are explored. Moreover, we discuss some currently available drugs targeting SR (serine/arginine-rich) proteins that are the main regulators of constitutive and alternative splicing, and their potential use in treatment for so-called persistent viral infections.
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Tsakogiannis D, Ruether IGA, Kyriakopoulou Z, Pliaka V, Skordas V, Gartzonika C, Levidiotou-Stefanou S, Markoulatos P. Molecular and phylogenetic analysis of the HPV 16 E4 gene in cervical lesions from women in Greece. Arch Virol 2012; 157:1729-39. [DOI: 10.1007/s00705-012-1356-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/23/2012] [Indexed: 01/23/2023]
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25
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Ekeowa-Anderson AL, Purdie KJ, Gibbon K, Byrne CR, Arbeit JM, Harwood CA, O'Shaughnessy RFL. AKT1 loss correlates with episomal HPV16 in vulval intraepithelial neoplasia. PLoS One 2012; 7:e38608. [PMID: 22685591 PMCID: PMC3369856 DOI: 10.1371/journal.pone.0038608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 05/08/2012] [Indexed: 11/23/2022] Open
Abstract
Anogenital malignancy has a significant association with high-risk mucosal alpha-human papillomaviruses (alpha-PV), particularly HPV 16 and 18 whereas extragenital SCC has been linked to the presence of cutaneous beta and gamma–HPV types. Vulval skin may be colonised by both mucosal and cutaneous (beta-, mu-, nu- and gamma-) PV types, but there are few systematic studies investigating their presence and their relative contributions to vulval malignancy. Dysregulation of AKT, a serine/threonine kinase, plays a significant role in several cancers. Mucosal HPV types can increase AKT phosphorylation and activity whereas cutaneous HPV types down-regulate AKT1 expression, probably to weaken the cornified envelope to promote viral release. We assessed the presence of mucosal and cutaneous HPV in vulval malignancy and its relationship to AKT1 expression in order to establish the corresponding HPV and AKT1 profile of normal vulval skin, vulval intraepithelial neoplasia (VIN) and vulval squamous cell carcinoma (vSCC). We show that HPV16 is the principle HPV type present in VIN, there were few detectable beta types present and AKT1 loss was not associated with the presence of these cutaneous HPV. We show that HPV16 early gene expression reduced AKT1 expression in transgenic mouse epidermis. AKT1 loss in our VIN cohort correlated with presence of high copy number, episomal HPV16. Maintained AKT1 expression correlated with low copy number, an increased frequency of integration and increased HPV16E7 expression, a finding we replicated in another untyped cohort of vSCC. Since expression of E7 reflects tumour progression, these findings suggest that AKT1 loss associated with episomal HPV16 may have positive prognostic implications in vulval malignancy.
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Affiliation(s)
- Arucha L. Ekeowa-Anderson
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Department of Dermatology, Whipps Cross University Hospital, London, United Kingdom
| | - Karin J. Purdie
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Karen Gibbon
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Department of Dermatology, Whipps Cross University Hospital, London, United Kingdom
| | - Carolyn R. Byrne
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jeffrey M. Arbeit
- Division of Urologic Surgery, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Catherine A. Harwood
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Ryan F. L. O'Shaughnessy
- Centre for Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- Departments of Immunobiology and Dermatology, Institute of Child Health, University College London, London, United Kingdom
- * E-mail:
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26
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HPV-16 E2 contributes to induction of HPV-16 late gene expression by inhibiting early polyadenylation. EMBO J 2012; 31:3212-27. [PMID: 22617423 DOI: 10.1038/emboj.2012.147] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 04/24/2012] [Indexed: 11/08/2022] Open
Abstract
We provide evidence that the human papillomavirus (HPV) E2 protein regulates HPV late gene expression. High levels of E2 caused a read-through at the early polyadenylation signal pAE into the late region of the HPV genome, thereby inducing expression of L1 and L2 mRNAs. This is a conserved property of E2 of both mucosal and cutaneous HPV types. Induction could be reversed by high levels of HPV-16 E1 protein, or by the polyadenylation factor CPSF30. HPV-16 E2 inhibited polyadenylation in vitro by preventing the assembly of the CPSF complex. Both the N-terminal and hinge domains of E2 were required for induction of HPV late gene expression in transfected cells as well as for inhibition of polyadenylation in vitro. Finally, overexpression of HPV-16 E2 induced late gene expression from a full-length genomic clone of HPV-16. We speculate that the accumulation of high levels of E2 during the viral life cycle, not only turns off the expression of the pro-mitotic viral E6 and E7 genes, but also induces the expression of the late HPV genes L1 and L2.
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27
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HPV-18 E2^E4 chimera: 2 new spliced transcripts and proteins induced by keratinocyte differentiation. Virology 2012; 429:47-56. [PMID: 22541938 DOI: 10.1016/j.virol.2012.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 02/09/2012] [Accepted: 03/30/2012] [Indexed: 11/20/2022]
Abstract
The Human Papillomavirus (HPV) E4 is known to be synthesized as an E1^E4 fusion resulting from splice donor and acceptor sites conserved across HPV types. Here we demonstrate the existence of 2 HPV-18 E2^E4 transcripts resulting from 2 splice donor sites in the 5' part of E2, while the splice acceptor site is the one used for E1^E4. Both E2^E4 transcripts are up-regulated by keratinocyte differentiation in vitro and can be detected in clinical samples containing low-grade HPV-18-positive cells from Pap smears. They give rise to two fusion proteins in vitro, E2^E4-S and E2^E4-L. Whereas we could not differentiate E2^E4-S from E1^E4 in vivo, E2^E4-L could be formally identified as a 23 kDa protein in raft cultures in which the corresponding transcript was also found, and in a biopsy from a patient with cervical intraepithelial neoplasia stage I-II (CINI-II) associated with HPV-18, demonstrating the physiological relevance of E2^E4 products.
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28
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Role of calpain in the formation of human papillomavirus type 16 E1^E4 amyloid fibers and reorganization of the keratin network. J Virol 2011; 85:9984-97. [PMID: 21752901 DOI: 10.1128/jvi.02158-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human papillomavirus (HPV) type 16 E1^E4 (16E1^E4) protein is expressed in the middle to upper layers of infected epithelium and has several roles within the virus life cycle. It is apparent that within the epithelium there are multiple species of 16E1^E4 that differ in length and/or degree of phosphorylation and that some or all of these can associate with the cellular keratin networks, leading to network disruption. We show here that the cellular cysteine protease calpain cleaves the 16E1^E4 protein after amino acid 17 to generate species that lack the N terminus. These C-terminal fragments are able to multimerize and form amyloid-like fibers. This can lead to accumulation of 16E1^E4 and disruption of the normal dynamics of the keratin networks. The cleavage of E1^E4 proteins by calpain may be a common strategy used by α-group viruses, since we show that cleavage of type 18 E1^E4 in raft culture is also dependent on calpain. Interestingly, the cleavage of 16E1^E4 by calpain appears to be highly regulated as differentiation of HPV genome-containing cells by methylcellulose is insufficient to induce cleavage. We hypothesize that this is important since it ensures that the formation of the amyloid fibers is not prematurely triggered in the lower layers and is restricted to the upper layers, where calpain is active and where disruption of the keratin networks may aid virus release.
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29
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King LE, Dornan ES, Donaldson MM, Morgan IM. Human papillomavirus 16 E2 stability and transcriptional activation is enhanced by E1 via a direct protein-protein interaction. Virology 2011; 414:26-33. [PMID: 21458836 DOI: 10.1016/j.virol.2011.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 12/13/2010] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
Human papillomavirus 16 E1 and E2 interact with cellular factors to replicate the viral genome. E2 forms homodimers and binds to 12 bp palindromic sequences adjacent to the viral origin and recruits E1 to the origin. E1 forms a di-hexameric helicase complex that replicates the viral genome. This manuscript demonstrates that E1 stabilises the E2 protein, increasing the half life in both C33a and 293 T cells respectively. This stabilisation requires a direct protein--protein interaction. In addition, the E1 protein enhances E2 transcription function in a manner that suggests the E1 protein itself can contribute to transcriptional regulation not simply by E2 stabilisation but by direct stimulation of transcription. This activation of E2 transcription is again dependent upon an interaction with E1. Overall the results suggest that in the viral life cycle, co-expression of E1 with E2 can increase E2 stability and enhance E2 function.
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Affiliation(s)
- Lauren E King
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK
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