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Chitsazzadeh V, Coarfa C, Drummond JA, Nguyen T, Joseph A, Chilukuri S, Charpiot E, Adelmann CH, Ching G, Nguyen TN, Nicholas C, Thomas VD, Migden M, MacFarlane D, Thompson E, Shen J, Takata Y, McNiece K, Polansky MA, Abbas HA, Rajapakshe K, Gower A, Spira A, Covington KR, Xiao W, Gunaratne P, Pickering C, Frederick M, Myers JN, Shen L, Yao H, Su X, Rapini RP, Wheeler DA, Hawk ET, Flores ER, Tsai KY. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates. Nat Commun 2016; 7:12601. [PMID: 27574101 PMCID: PMC5013636 DOI: 10.1038/ncomms12601] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 07/18/2016] [Indexed: 01/21/2023] Open
Abstract
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible.
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Affiliation(s)
- Vida Chitsazzadeh
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer A Drummond
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tri Nguyen
- Northwest Diagnostic Clinic, Houston, Texas 77090, USA
| | - Aaron Joseph
- Skin and Laser Surgery Associates, Pasadena, Texas 77505, USA
| | | | | | - Charles H Adelmann
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Grace Ching
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Tran N Nguyen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Courtney Nicholas
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Valencia D Thomas
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Michael Migden
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Deborah MacFarlane
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Erika Thompson
- Sequencing and Microarray Facility, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Jianjun Shen
- Next Generation Sequencing Facility, Smithville, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Yoko Takata
- Next Generation Sequencing Facility, Smithville, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kayla McNiece
- Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Maxim A Polansky
- Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - Hussein A Abbas
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Adam Gower
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02215, USA
| | - Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02215, USA
| | - Kyle R Covington
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Weimin Xiao
- Department of Biology and Biochemistry University of Houston, Houston, Texas 77204, USA
| | - Preethi Gunaratne
- Department of Biology and Biochemistry University of Houston, Houston, Texas 77204, USA
| | - Curtis Pickering
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Mitchell Frederick
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Jeffrey N Myers
- Department of Head &Neck Surgery, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Li Shen
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Hui Yao
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Xiaoping Su
- Department of Bioinformatics &Computational Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Ronald P Rapini
- Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas Medical School at Houston, Houston, Texas 77030, USA
| | - David A Wheeler
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ernest T Hawk
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Elsa R Flores
- Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
| | - Kenneth Y Tsai
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA.,Department of Dermatology, University of Texas MD Anderson Cancer Center Houston, Houston, Texas 77030, USA
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52
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Nunes EM, Sudenga SL, Gheit T, Tommasino M, Baggio ML, Ferreira S, Galan L, Silva RC, Pierce Campbell CM, Lazcano-Ponce E, Giuliano AR, Villa LL, Sichero L. Diversity of beta-papillomavirus at anogenital and oral anatomic sites of men: The HIM Study. Virology 2016; 495:33-41. [PMID: 27161202 PMCID: PMC4949595 DOI: 10.1016/j.virol.2016.04.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 11/22/2022]
Abstract
Our goal was to describe prevalence of β-HPVs at three anatomic sites among 717 men from Brazil, Mexico and US enrolled in the HPV Infection in Men (HIM) Study. β-HPVs were genotyped using Luminex technology. Overall, 77.7%, 54.3% and 29.3% men were positive for any β-HPV at the genitals, anal canal, and oral cavity, respectively. Men from US and Brazil were significantly less likely to have β-HPV at the anal canal than men from Mexico. Older men were more likely to have β-HPV at the anal canal compared to younger men. Prevalence of β-HPV at the oral cavity was significantly associated with country of origin and age. Current smokers were significantly less likely to have β-HPV in the oral cavity than men who never smoked. Lack of associations between β-HPV and sexual behaviors may suggest other routes of contact such as autoinoculation which need to be explored further.
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Affiliation(s)
- Emily Montosa Nunes
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Staci L Sudenga
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Cancer Research (IARC), Lyon, France
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Cancer Research (IARC), Lyon, France
| | - Maria Luiza Baggio
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Silvaneide Ferreira
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lenice Galan
- Ludwig Institute for Cancer Research, São Paulo branch, São Paulo, Brazil
| | - Roberto C Silva
- Centro de Referência e Treinamento DST/Aids, São Paulo, Brazil
| | | | - Eduardo Lazcano-Ponce
- Centro de Investigación en Salud Poblacional, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Anna R Giuliano
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Luisa L Villa
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Department of Radiology and Oncology, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Laura Sichero
- Molecular Biology Laboratory, Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
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53
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Network Analysis Identifies Mitochondrial Regulation of Epidermal Differentiation by MPZL3 and FDXR. Dev Cell 2016; 35:444-57. [PMID: 26609959 DOI: 10.1016/j.devcel.2015.10.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/19/2015] [Accepted: 10/26/2015] [Indexed: 01/07/2023]
Abstract
Current gene expression network approaches commonly focus on transcription factors (TFs), biasing network-based discovery efforts away from potentially important non-TF proteins. We developed proximity analysis, a network reconstruction method that uses topological constraints of scale-free, small-world biological networks to reconstruct relationships in eukaryotic systems, independent of subcellular localization. Proximity analysis identified MPZL3 as a highly connected hub that is strongly induced during epidermal differentiation. MPZL3 was essential for normal differentiation, acting downstream of p63, ZNF750, KLF4, and RCOR1, each of which bound near the MPZL3 gene and controlled its expression. MPZL3 protein localized to mitochondria, where it interacted with FDXR, which was itself also found to be essential for differentiation. Together, MPZL3 and FDXR increased reactive oxygen species (ROS) to drive epidermal differentiation. ROS-induced differentiation is dependent upon promotion of FDXR enzymatic activity by MPZL3. ROS induction by the MPZL3 and FDXR mitochondrial proteins is therefore essential for epidermal differentiation.
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54
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McDowell LJ, Young RJ, Johnston ML, Tan TJ, Kleid S, Liu CS, Bressel M, Estall V, Rischin D, Solomon B, Corry J. p16-positive lymph node metastases from cutaneous head and neck squamous cell carcinoma: No association with high-risk human papillomavirus or prognosis and implications for the workup of the unknown primary. Cancer 2016; 122:1201-8. [PMID: 26881928 DOI: 10.1002/cncr.29901] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/18/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND The incidence of p16 overexpression and the role of human papillomavirus (HPV) in cutaneous head and neck squamous cell carcinoma (cHNSCC) are unclear. METHODS One hundred forty-three patients with cHNSCC lymph node metastases involving the parotid gland were evaluated for p16 expression by immunohistochemistry. The detection of 18 high-risk HPV subtypes was performed with HPV RNA in situ hybridization for a subset of 59 patients. The results were correlated with clinicopathological features and outcomes. RESULTS The median follow-up time was 5.3 years. No differences were observed in clinicopathological factors with respect to the p16 status. p16 was positive, weak, and negative in 45 (31%), 21 (15%), and 77 cases (54%), respectively. No high-risk HPV subtypes were identified, regardless of the p16 status. The p16 status was not prognostic for overall (hazard ratio, 1.08; 95% confidence interval [CI], 0.85-1.36; P = .528), cancer-specific (hazard ratio, 1.12; 95% CI, 0.77-1.64; P = .542), or progression-free survival (hazard ratio, 1.03; 95% CI, 0.83-1.29; P = .783). Distant metastasis-free survival, freedom from locoregional failure, and freedom from local failure were also not significantly associated with the p16 status. CONCLUSIONS p16 positivity is common but not prognostic in cHNSCC lymph node metastases. High-risk HPV subtypes are not associated with p16 positivity and do not appear to play a role in this disease. HPV testing, in addition to the p16 status in the unknown primary setting, may provide additional information for determining a putative primary site.
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Affiliation(s)
- Lachlan J McDowell
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Richard J Young
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Meredith L Johnston
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Tze-Jian Tan
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Stephen Kleid
- Division of Surgical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Chen S Liu
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Mathias Bressel
- Centre for Biostatistics and Clinical Trials, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Vanessa Estall
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Parkville, Australia
| | - Danny Rischin
- University of Melbourne, Parkville, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Benjamin Solomon
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Parkville, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - June Corry
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Parkville, Australia
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55
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Tufaro AP, Azoury SC, Crompton JG, Straughan DM, Reddy S, Prasad NB, Shi G, Fischer AC. Rising incidence and aggressive nature of cutaneous malignancies after transplantation: An update on epidemiology, risk factors, management and surveillance. Surg Oncol 2015; 24:345-52. [DOI: 10.1016/j.suronc.2015.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/16/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023]
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56
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Histopathologic Variants of Cutaneous Squamous Cell Carcinoma In Situ With Analysis of Multicentric Subtypes. Am J Dermatopathol 2015; 37:680-5. [DOI: 10.1097/dad.0000000000000354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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57
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Beta genus papillomaviruses and skin cancer. Virology 2015; 479-480:290-6. [PMID: 25724416 DOI: 10.1016/j.virol.2015.02.004] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/20/2015] [Accepted: 02/05/2015] [Indexed: 11/23/2022]
Abstract
A role for the beta genus HPVs in keratinocyte carcinoma (KC) remains to be established. In this article we examine the potential role of the beta HPVs in cancer revealed by the epidemiology associating these viruses with KC and supported by oncogenic properties of the beta HPV proteins. Unlike the cancer associated alpha genus HPVs, in which transcriptionally active viral genomes are invariably found associated with the cancers, that is not the case for the beta genus HPVs and keratinocyte carcinomas. Thus a role for the beta HPVs in KC would necessarily be in the carcinogenesis initiation and not in the maintenance of the tumor.
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58
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Abstract
Human papillomaviruses (HPVs) infect the squamous epithelium and can induce benign and malignant lesions. To date, more than 200 different HPV types have been identified and classified into five genera, α, β, γ, μ, and ν. While high-risk α mucosal HPVs have a well-established role in cervical carcinoma and a significant percentage of other anogenital tract and oral carcinomas, the biology of the cutaneous β HPVs and their contribution to non-melanoma skin cancer (NMSC) has been less studied. Although the association of β HPV infection with NMSC in patients with a rare, genetically determined condition, epidermodysplasia verruciformis has been well established, the role of β HPV infection with NMSC in the normal population remains controversial. In stark contrast to α HPV-associated cancers, the presence of the β HPV genome does not appear to be mandatory for the maintenance of the malignant phenotype. Moreover, the mechanism of action of the β HPV E6 and E7 oncoproteins differs from the β HPV oncoproteins.
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Affiliation(s)
- Margaret E McLaughlin-Drubin
- Division of Infectious Diseases, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA.
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59
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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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Evaluation of specific humoral and cellular immune responses against the major capsid L1 protein of cutaneous wart-associated alpha-Papillomaviruses in solid organ transplant recipients. J Dermatol Sci 2014; 77:37-45. [PMID: 25439730 DOI: 10.1016/j.jdermsci.2014.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/07/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND Infection with different species of cutaneous human papillomaviruses (cHPV) of genus alpha (cαHPVs) and associated skin disease are highly prevalent in solid organ transplant recipients (OTR), documenting the importance of the immunological control of HPV infection. OBJECTIVES To investigate the natural course of cαHPV-specific cellular and humoral immune responses during systemic long-term immunosuppression. METHODS Integrating bead-based multiplex serology and flow cytometry we analyzed natural cαHPV-specific antibodies and T(H) cell responses against the major capsid protein L1 of HPV types 2, 27, 57 (species 4) and 3, 10 and 77 (species 2) in sera and blood of OTR before and after initiation of iatrogenic immunosuppression and in comparison to immunocompetent individuals (IC). RESULTS Among OTR we observed an overall 42% decrease in humoral L1-specific immune responses during the course of iatrogenic immunosuppression, comparing median values 30 d before and 30 d after initiation of immunosuppressive therapy (p < 0.05). This difference disappeared after long-term (>1 year) immunosuppression. The predominant cellular L1-specific immune response was of type T(H)1 (CD4(+)CD40L(+)IL-2(+)IFN-γ(+)). Consistent with the detected L1-specific antibody titers, L1-specific T(H)1 responses were unchanged in long-term immunosuppressed OTR compared to IC. Notably, cαHPV-L1-specific IL-2(+)/CD40L(+)CD4(+) or IFN-γ(+)/CD40L(+) CD4(+) T(H) cell responses against any of the cαHPV-L1 types were significantly higher in OTR with clinically apparent common warts. CONCLUSION The systemic humoral immune response against cαHPV may reflect the individual degree of iatrogenic immunosuppression indicating a higher susceptibility for cαHPV infection among OTR during the early phase after organ transplantation. Humoral cαHPV-specific immune responses may show a reconstitution to pre-transplantation levels despite continuous potent immunosuppression.
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Schrama D, Groesser L, Ugurel S, Hafner C, Pastrana DV, Buck CB, Cerroni L, Theiler A, Becker JC. Presence of human polyomavirus 6 in mutation-specific BRAF inhibitor-induced epithelial proliferations. JAMA Dermatol 2014; 150:1180-6. [PMID: 24943872 PMCID: PMC8369517 DOI: 10.1001/jamadermatol.2014.1116] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
IMPORTANCE A frequent adverse effect of mutation-specific BRAF inhibitor therapy is the induction of epithelial proliferations including cutaneous squamous cell carcinomas. To date, the only factor identified contributing to their development is the activation of the mitogen-activated signal transduction cascade by mutations in the RAS genes. However, these mutations explain only 60% of the tumors; hence, it is important to identify what is causing the remaining tumors. OBJECTIVE To test for the presence of human papillomaviruses (HPVs) and the recently identified human polyomaviruses (HPyVs), Merkel cell polyomavirus (MCPyV), and trichodysplasia spinulosa-associated polyomavirus (TSPyV), as well as HPyV-6, HPyV-7, HPyV-9, and HPyV-10, in epithelial proliferations occurring after BRAF inhibitor therapy to determine whether these oncogenic viruses may contribute to BRAF inhibitor-induced skin tumors. DESIGN, SETTING, AND PARTICIPANTS Retrospective study at a university hospital in Austria of epithelial proliferations that developed in patients with melanoma after initiation of treatment with the BRAF inhibitor vemurafenib. Samples were analyzed for (1) presence of the most frequently observed RAS mutations by SNaPshot technology, (2) detection of the viruses by real-time polymerase chain reaction, and (3) presence of capsid proteins of the most abundantly detected virus by immunohistochemical analysis. MAIN OUTCOMES AND MEASURES RAS mutational status, as well as HPV and HPyV presence, in BRAF inhibitor-induced epithelial proliferations. RESULTS Eighteen biopsy samples from 6 patients were retrieved from our hospital's archive. We identified RAS mutations in 10 (62%) of the 16 samples with clear results. DNA of HPyV-9, HPyV-10, and TSPyV were virtually absent in the samples. MCPyV DNA was present in 13 of 18 samples, and HPV, HPyV-6, and HPyV-7 DNA were present in all samples. In general, the amount of DNA encoding the latter viruses was rather low, with the exception of HPyV-6 in several samples of 1 individual patient. Notably, the relevance of the presence of HPyV-6 in the epithelial proliferation was underlined by immunohistochemical detection of the core protein VP1 of HPyV-6. CONCLUSIONS AND RELEVANCE The presence of both high HPyV-6 DNA load and VP1 protein suggests that polyomaviruses may contribute to the epithelial proliferations observed in patients receiving BRAF inhibitor therapy, albeit the relative impact as compared with that of RAS mutations appears circumstantial.
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Affiliation(s)
- David Schrama
- Department of Dermatology, Medical University of Graz, Graz, Austria2Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Leopold Groesser
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Christian Hafner
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Anna Theiler
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jürgen C Becker
- Department of Dermatology, Medical University of Graz, Graz, Austria
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63
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Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N. Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke. Head Neck 2014; 37:1642-9. [PMID: 24954188 DOI: 10.1002/hed.23807] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 04/19/2014] [Accepted: 06/18/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Evidence suggests the incidence of oral tongue squamous cell carcinoma is increasing in young patients, many who have no history of tobacco use. METHODS We clinically reviewed 89 patients with oral tongue cancer. Exomic sequencing of tumor DNA from 6 nonsmokers was performed and compared to previously sequenced cases. RNA from 20 tumors was evaluated by massively parallel sequencing to search for potentially oncogenic viruses. RESULTS Non-smokers (53 of 89) were younger than smokers (36 of 89; mean, 50.4 vs 61.9 years; p < .001), and seemed more likely to be women (58.5% vs 38.9%; p = .069). Nonsmokers had fewer TP53 mutations (p = .02) than smokers. No tumor-associated viruses were detected. CONCLUSION The young age of nonsmoking patients with oral tongue cancer and fewer TP53 mutations suggest a viral role in this disease. Our efforts to identify such a virus were unsuccessful. Further studies are warranted to elucidate the drivers of carcinogenesis in these patients.
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Affiliation(s)
- Ryan Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Carole Fakhry
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Chaz Langelier
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Yuchen Jiao
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Yuxuan Wang
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Matthew D Wilkerson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - Chandra Sekhar Pedamallu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew Old
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, Ohio
| | - James Lang
- Department of Otolaryngology-Head and Neck Surgery, Ohio State University, Columbus, Ohio
| | - Myriam Loyo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sun Mi Ahn
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marietta Tan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhen Gooi
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jason Chan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeremy Richmon
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura D Wood
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Justin Bishop
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - William H Westra
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Christine H Chung
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph Califano
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Christine G Gourin
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew Meyerson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Nickolas Papadopoulos
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Kenneth W Kinzler
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Bert Vogelstein
- The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Joseph L DeRisi
- Howard Hughes Medical Institute, Chevy Chase, Maryland.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nishant Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.,The Ludwig Center and the Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
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64
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Improved detection reveals active β-papillomavirus infection in skin lesions from kidney transplant recipients. Mod Pathol 2014; 27:1101-15. [PMID: 24390217 DOI: 10.1038/modpathol.2013.240] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 11/21/2013] [Accepted: 11/26/2013] [Indexed: 01/10/2023]
Abstract
The aim of this study was to determine whether detection of β-HPV gene products, as defined in epidermodysplasia verruciformis skin cancer, could also be observed in lesions from kidney transplant recipients alongside the viral DNA. A total of 111 samples, corresponding to 79 skin lesions abscised from 17 kidney transplant recipients, have been analyzed. The initial PCR analysis demonstrated that β-HPV-DNA was highly present in our tumor series (85%). Using a combination of antibodies raised against the E4 and L1 proteins of the β-genotypes, we were able to visualize productive infection in 4 out of 19 actinic keratoses, and in the pathological borders of 1 out of 14 squamous cell carcinomas and 1 out of 31 basal cell carcinomas. Increased expression of the cellular proliferation marker minichromosome maintenance protein 7 (MCM7), that extended into the upper epithelial layers, was a common feature of all the E4-positive areas, indicating that cells were driven into the cell cycle in areas of productive viral infections. Although the present study does not directly demonstrate a causal role of these viruses, the detection of E4 and L1 positivity in actinic keratosis and the adjacent pathological epithelium of skin cancer, clearly shows that β-HPV are actively replicating in the intraepidermal precursor lesions of kidney transplant recipients and can therefore cooperate with other carcinogenic agents, such as UVB, favoring skin cancer promotion.
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65
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Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression. Virology 2014; 462-463:14-24. [PMID: 25092457 DOI: 10.1016/j.virol.2014.05.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/02/2014] [Accepted: 05/16/2014] [Indexed: 01/15/2023]
Abstract
Two classes of Human papillomaviruses (HPV) infect the anogenital track: high risk viruses that are associated with risk of cervical cancer and low risk types that drive development of benign lesions, such as condylomas. In the present study, we established quantitative transcriptional maps of the viral genome in clinical lesions associated with high risk HPV16 or low risk HPV6b. Marked qualitative and quantitative changes in the HPV16 transcriptome were associated with progression from low to high grade lesions. Specific transcripts encoding essential regulatory proteins such as E7, E2, E1^E4 and E5 were identified. We also identified intrinsic differences between the HPV6b-associated condyloma transcript map and that of the HPV16-associated low grade CIN specifically regarding promoter usage. Characterization and quantification of HPV transcripts in patient samples thus establish the impact of viral transcriptional regulation on the status of HPV-associated lesions and may therefore help in defining new biologically-relevant prognosis markers.
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66
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Madeleine MM, Carter JJ, Johnson LG, Wipf GC, Davis C, Berg D, Nelson K, Daling JR, Schwartz SM, Galloway DA. Risk of squamous cell skin cancer after organ transplant associated with antibodies to cutaneous papillomaviruses, polyomaviruses, and TMC6/8 (EVER1/2) variants. Cancer Med 2014; 3:1440-7. [PMID: 24913986 PMCID: PMC4302694 DOI: 10.1002/cam4.280] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/21/2022] Open
Abstract
Squamous cell skin cancer (SCSC) disproportionately affects organ transplant recipients, and may be related to increased viral replication in the setting of immune suppression. We conducted a nested case–control study among transplant recipients to determine whether SCSC is associated with antibodies to cutaneous human papillomaviruses (HPV), to genes associated with a rare genetic susceptibility to HPV (TMC6/TMC8), or to human polyomaviruses (HPyV). Cases (n = 149) had histologically confirmed SCSC, and controls (n = 290) were individually matched to cases on time since transplant, type of transplant, gender, and race. All subjects had serum drawn immediately prior to transplant surgery. Antibodies to 25 cutaneous HPVs and six HPyVs were assayed by detection of binding to virus-like particles, and 11 TMC6/8 variants were genotyped. After correction for multiple comparisons, only antibodies to HPV37 were associated with SCSC (OR 2.0, 95% CI 1.2–3.4). Common genetic variants of TMC6/8 were not associated with SCSC, but three variants in TMC8 (rs12452890, rs412611, and rs7208422) were associated with greater seropositivity for species 2 betapapillomaviruses among controls. This study suggests that some betaHPVs, but not polyomaviruses, may play a role in the excess risk of SCSC among transplant recipients.
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Affiliation(s)
- Margaret M Madeleine
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington, Seattle, Washington
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67
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Genus beta human papillomavirus E6 proteins vary in their effects on the transactivation of p53 target genes. J Virol 2014; 88:8201-12. [PMID: 24850740 DOI: 10.1128/jvi.01197-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED The genus beta human papillomaviruses (beta HPVs) cause cutaneous lesions and are thought to be involved in the initiation of some nonmelanoma skin cancers (NMSCs), particularly in patients with the genetic disorder epidermodysplasia verruciformis (EV). We have previously reported that at least two of the genus beta HPV E6 proteins bind to and/or increase the steady-state levels of p53 in squamous epithelial cells. This is in contrast to a well-characterized ability of the E6 proteins of cancer-associated HPVs of genus alpha HPV, which inactivate p53 by targeting its ubiquitin-mediated proteolysis. In this study, we have investigated the ability of genus beta E6 proteins from eight different HPV types to block the transactivation of p53 target genes following DNA damage. We find that the E6 proteins from diverse beta HPV species and types vary in their capacity to block the induction of MDM2, p21, and proapoptotic genes after genotoxic stress. We conclude that some genus beta HPV E6 proteins inhibit at least some p53 target genes, although perhaps not by the same mechanism or to the same degree as the high-risk genus alpha HPV E6 proteins. IMPORTANCE This study addresses the ability of various human papillomavirus E6 proteins to block the activation of p53-responsive cellular genes following DNA damage in human keratinocytes, the normal host cell for HPVs. The E6 proteins encoded by the high-risk, cancer-associated HPV types of genus alpha HPV have a well-established activity to target p53 degradation and thereby inhibit the response to DNA damage. In this study, we have investigated the ability of genus beta HPV E6 proteins from eight different HPV types to block the ability of p53 to transactivate downstream genes following DNA damage. We find that some, but not all, genus beta HPV E6 proteins can block the transactivation of some p53 target genes. This differential response to DNA damage furthers the understanding of cutaneous HPV biology and may help to explain the potential connection between some beta HPVs and cancer.
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68
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Wang J, Aldabagh B, Yu J, Arron ST. Role of human papillomavirus in cutaneous squamous cell carcinoma: a meta-analysis. J Am Acad Dermatol 2014; 70:621-629. [PMID: 24629358 DOI: 10.1016/j.jaad.2014.01.857] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND The role of human papillomavirus (HPV) in cutaneous squamous cell carcinoma (cuSCC) is not well defined, with past studies showing conflicting results. OBJECTIVE We sought to determine if there is a significant association between HPV and cuSCC and whether cuSCC from immunosuppressed patients are more likely to carry HPV than cuSCC from immunocompetent patients. METHODS We performed a systematic review and abstracted data from articles that included: skin samples by biopsy, HPV detection by polymerase chain reaction, and a minimum of 10 cases and 10 controls. Pooled effect size and 95% confidence intervals were calculated using random effects meta-analysis using the inverse variance method. RESULTS cuSCC were more likely to carry HPV than normal-appearing skin (pooled effect size [ES] 3.43, 95% confidence interval 1.97-5.98, P < .0001) in all patients. An increase in HPV prevalence was found in tumors from immunosuppressed patients compared with immunocompetent patients (pooled ES 3.01, 95% confidence interval 2.00-4.52, P < .0001). LIMITATIONS The greatest limitation is the heterogeneity of the studies included. The association of higher HPV prevalence in squamous cell carcinoma compared with normal-appearing skin does not imply causality. CONCLUSION These results contribute to evidence that HPV is associated with cuSCC. Higher HPV burden in tumors from immunosuppressed patients compared with immunocompetent patients may have therapeutic implications.
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Affiliation(s)
- Jennifer Wang
- Department of Dermatology, New York Medical College, Valhalla, New York
| | - Bishr Aldabagh
- Department of Dermatology, University of California, San Francisco, California
| | - Justin Yu
- Department of Dermatology, St Louis University, St Louis, Missouri
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69
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Bernat-García J, Morales Suárez-Varela M, Vilata-Corell J, Marquina-Vila A. Detection of Human Papillomavirus in Nonmelanoma Skin Cancer Lesions and Healthy Perilesional Skin in Kidney Transplant Recipients and Immunocompetent Patients. ACTA ACUST UNITED AC 2014; 105:286-94. [DOI: 10.1016/j.adengl.2013.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/27/2013] [Indexed: 01/20/2023]
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70
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Detección del virus del papiloma humano en muestras de cáncer cutáneo no melanoma y piel sana perilesional en pacientes trasplantados renales y pacientes inmunocompetentes. ACTAS DERMO-SIFILIOGRAFICAS 2014. [DOI: 10.1016/j.ad.2013.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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71
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Holderfield M, Lorenzana E, Weisburd B, Lomovasky L, Boussemart L, Lacroix L, Tomasic G, Favre M, Vagner S, Robert C, Ghoddusi M, Daniel D, Pryer N, McCormick F, Stuart D. Vemurafenib cooperates with HPV to promote initiation of cutaneous tumors. Cancer Res 2014; 74:2238-45. [PMID: 24523442 DOI: 10.1158/0008-5472.can-13-1065-t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Treatment with RAF inhibitors such as vemurafenib causes the development of cutaneous squamous cell carcinomas (cSCC) or keratoacanthomas as a side effect in 18% to 30% of patients. It is known that RAF inhibitors activate the mitogen-activated protein kinase (MAPK) pathway and stimulate growth of RAS-mutated cells, possibly accounting for up to 60% of cSCC or keratoacanthoma lesions with RAS mutations, but other contributing events are obscure. To identify such events, we evaluated tumors from patients treated with vemurafenib for the presence of human papilloma virus (HPV) DNA and identified 13% to be positive. Using a transgenic murine model of HPV-driven cSCC (K14-HPV16 mice), we conducted a functional test to determine whether administration of RAF inhibitors could promote cSCC in HPV-infected tissues. Vemurafenib treatment elevated MAPK markers and increased cSCC incidence from 22% to 70% in this model. Furthermore, 55% of the cSCCs arising in vemurafenib-treated mice exhibited a wild-type Ras genotype, consistent with the frequency observed in human patients. Our results argue that HPV cooperates with vemurafenib to promote tumorigenesis, in either the presence or absence of RAS mutations.
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Affiliation(s)
- Matthew Holderfield
- Authors' Affiliations: Novartis Institutes for Biomedical Research, Emeryville; UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California; Dermatology Unit and INSERM U 981; Department of Medical Biology and Pathology; Laboratory and Biobank; INSERM U 981, Institut Gustave Roussy, Villejuif Paris-Sud; and Unité de Génétique, Papillomavirus et Cancer Humain, Institut Pasteur, Paris, France
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72
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Dimon MT, Wood HM, Rabbitts PH, Liao W, Cho RJ, Arron ST. No evidence for integrated viral DNA in the genome sequence of cutaneous squamous cell carcinoma. J Invest Dermatol 2014; 134:2055-2057. [PMID: 24480882 PMCID: PMC4057961 DOI: 10.1038/jid.2014.52] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michelle T Dimon
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Henry M Wood
- Pre-Cancer Genomics, Leeds Institute of Cancer Studies and Pathology, Leeds, UK
| | - Pamela H Rabbitts
- Pre-Cancer Genomics, Leeds Institute of Cancer Studies and Pathology, Leeds, UK
| | - Wilson Liao
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Raymond J Cho
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
| | - Sarah T Arron
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA.
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73
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Marcuzzi GP, Awerkiew S, Hufbauer M, Schädlich L, Gissmann L, Eming S, Pfister H. Tumor prevention in HPV8 transgenic mice by HPV8-E6 DNA vaccination. Med Microbiol Immunol 2014; 203:155-63. [PMID: 24446083 DOI: 10.1007/s00430-014-0327-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/09/2014] [Indexed: 12/11/2022]
Abstract
The genus beta human papillomavirus 8 (HPV8) is involved in the development of cutaneous squamous cell carcinomas (SCCs) in individuals with epidermodysplasia verruciformis. Immunosuppressed transplant recipients are prone to harbor particularly high betapapillomavirus DNA loads, which may contribute to their highly increased risk of SCC. Tumor induction in HPV8 transgenic mice correlates with increased expression of viral oncogenes E6 and E2. In an attempt to prevent skin tumor development, we evaluated an HPV8-E6-DNA vaccine, which was able to stimulate a detectable HPV8-E6-specific cell-mediated immune response in 8/15 immunized mice. When skin of HPV8 transgenic mice was grafted onto non-transgenic littermates, the grafted HPV8 transgenic tissue was not rejected and papillomas started to grow within 14 days all over the transplant of 9/9 non-vaccinated and 7/15 not successfully vaccinated mice. In contrast, no papillomas developed in 6/8 successfully vaccinated mice. In the other two of these eight mice, a large ulcerative lesion developed within the initial papilloma growth or papilloma development was highly delayed. As the vaccine completely or partially prevented papilloma development without rejecting the transplanted HPV8 positive skin, the immune system appears to attack only keratinocytes with increased levels of E6 protein, which would give rise to papillomas.
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Affiliation(s)
- Gian Paolo Marcuzzi
- Institute of Virology, University of Cologne, Fuerst-Pueckler-Str. 56, 50935, Cologne, Germany
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74
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Bruegger C, Kempf W, Spoerri I, Arnold AW, Itin PH, Burger B. MicroRNA expression differs in cutaneous squamous cell carcinomas and healthy skin of immunocompetent individuals. Exp Dermatol 2014; 22:426-8. [PMID: 23711067 DOI: 10.1111/exd.12153] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2013] [Indexed: 12/11/2022]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is one of the most common skin cancers, but the influence of microRNA (miRNA) expression has only been sporadically analysed. We hypothesized that miRNAs are differentially expressed in cSCC and hence influence its development. We therefore isolated total miRNA from well-differentiated cSCCs and from controls without SCC. Expression analyses of 12 miRNAs showed three significantly differentially expressed miRNAs. We identified a significant upregulation of the miR-21 and the miR-31, a proto-oncogene like miR-21. While the upregulated expression of miR-21 has been known for some time, the increased expression of miR-31 was never shown so clearly. Furthermore, we showed the upregulation of miRNA-205, which has never been described before. The miR-205 induces specific keratinocyte migration and could be a characteristic marker for cSCC. It has to be determined in following studies whether these upregulated expressions are specific for cSCC and if so, for which cSCC stages.
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75
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Abstract
Over the past two decades, advances in the fields of cancer genetics and molecular biology have elucidated molecular pathways that cause numerous cutaneous malignancies. This in turn has spurred the rational design of molecularly targeted therapies. In this review, we discuss the molecular pathways critical to the development of nonmelanoma skin cancers and the novel pharmacologic agents that target them. Included is a review of vismodegib for basal cell carcinoma, cetuximab for squamous cell carcinomas, imatinib for dermatofibrosarcoma protuberans, and sirolimus for Kaposi's sarcoma.
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Affiliation(s)
- Lucinda S Liu
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520-8059, USA
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76
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Batrani M, Mahalingam M. Human papillomavirus and cutaneous squamous cell carcinoma: the dilemma continues. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/edm.12.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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77
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Palyca P, Koshenkov VP, Mehnert JM. Developments in the treatment of locally advanced and metastatic squamous cell carcinoma of the skin: a rising unmet need. Am Soc Clin Oncol Educ Book 2014:e397-e404. [PMID: 24857130 PMCID: PMC5216418 DOI: 10.14694/edbook_am.2014.34.e397] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Squamous cell carcinoma of the skin (SCCS) is a common malignancy with potentially devastating consequences in patients with locally advanced or metastatic disease. Its rising incidence, primarily a result of an aging population and increased ultraviolet (UV) radiation exposure, characterize an emerging unmet need. A firm understanding of the biology of this disease, likely distinct from that of other squamous malignancies because of the influence of UV radiation, is necessary in the evaluation of treatment paradigms. Careful recognition of high-risk features pertaining to tumor and host characteristics is paramount to proper management. However, a lack of standardization in guidelines in this regard creates a challenge for physicians. Questions persist regarding additional evaluation and treatment for advanced disease such as the roles for sentinel lymph node biopsy and the adjuvant use of radiation and chemotherapy. With respect to advanced disease, multiple combinations of chemotherapy have been tested with variable success, but no rigorous randomized studies have been conducted. In addition, EGFR inhibitors such as cetuximab and erlotinib have displayed antitumor activity and as such, warrant further investigation. In sum, the treatment of locally advanced and metastatic SCCS is a ripe area for clinical investigation. This article summarizes the current understanding of disease biology and emerging questions in the management of this disease.
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Affiliation(s)
- Paul Palyca
- From the Rutgers Cancer Institute of New Jersey/Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Vadim P Koshenkov
- From the Rutgers Cancer Institute of New Jersey/Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Janice M Mehnert
- From the Rutgers Cancer Institute of New Jersey/Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
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78
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Sampaio FMS, Miller MDB, Gualberto GV, Galhardo MCG, Valle ACFD, Souza PRCD. Use of the bilobed flap in the pubic region after tumoral lesion excision. An Bras Dermatol 2013; 88:224-6. [PMID: 24346926 PMCID: PMC3875974 DOI: 10.1590/abd1806-4841.20132762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/04/2013] [Indexed: 11/22/2022] Open
Abstract
Reconstruction of surgical defects in the pubic region is a challenge to any surgeon.
Our goal was to demonstrate the use of the bilobed flap to reconstruct the pubic
region skin after the excision of a recurrent HPV lesion, resistant to conventional
treatments. In spite of its classical use in nasal reconstructions, the bilobed flap
has applications in extranasal defects, with excellent functional and aesthetic
results.
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Affiliation(s)
| | | | | | - Maria Clara Gutierrez Galhardo
- Oswaldo Cruz Foundation, Evandro Chagas Research Institute, Laboratory of Dermatology in Infectious Diseases, Rio de JaneiroRJ, Brazil
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79
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Salyakina D, Tsinoremas NF. Viral expression associated with gastrointestinal adenocarcinomas in TCGA high-throughput sequencing data. Hum Genomics 2013; 7:23. [PMID: 24279398 PMCID: PMC3906926 DOI: 10.1186/1479-7364-7-23] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/07/2013] [Indexed: 12/15/2022] Open
Abstract
Background Up to 20% of cancers worldwide are thought to be associated with microbial pathogens, including bacteria and viruses. The widely used methods of viral infection detection are usually limited to a few a priori suspected viruses in one cancer type. To our knowledge, there have not been many broad screening approaches to address this problem more comprehensively. Methods In this study, we performed a comprehensive screening for viruses in nine common cancers using a multistep computational approach. Tumor transcriptome and genome sequencing data were available from The Cancer Genome Atlas (TCGA). Nine hundred fifty eight primary tumors in nine common cancers with poor prognosis were screened against a non-redundant database of virus sequences. DNA sequences from normal matched tissue specimens were used as controls to test whether each virus is associated with tumors. Results We identified human papilloma virus type 18 (HPV-18) and four human herpes viruses (HHV) types 4, 5, 6B, and 8, also known as EBV, CMV, roseola virus, and KSHV, in colon, rectal, and stomach adenocarcinomas. In total, 59% of screened gastrointestinal adenocarcinomas (GIA) were positive for at least one virus: 26% for EBV, 21% for CMV, 7% for HHV-6B, and 20% for HPV-18. Over 20% of tumors were co-infected with multiple viruses. Two viruses (EBV and CMV) were statistically significantly associated with colorectal cancers when compared to the matched healthy tissues from the same individuals (p = 0.02 and 0.03, respectively). HPV-18 was not detected in DNA, and thus, no association testing was possible. Nevertheless, HPV-18 expression patterns suggest viral integration in the host genome, consistent with the potentially oncogenic nature of HPV-18 in colorectal adenocarcinomas. The estimated counts of viral copies were below one per cell for all identified viruses and approached the detection limit. Conclusions Our comprehensive screening for viruses in multiple cancer types using next-generation sequencing data clearly demonstrates the presence of viral sequences in GIA. EBV, CMV, and HPV-18 are potentially causal for GIA, although their oncogenic role is yet to be established.
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Affiliation(s)
- Daria Salyakina
- Center for Computational Science, University of Miami, 1120 NW 14 St, Miami, FL 33136, USA.
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80
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Mapping of betapapillomavirus human papillomavirus 5 transcription and characterization of viral-genome replication function. J Virol 2013; 88:961-73. [PMID: 24198410 DOI: 10.1128/jvi.01841-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Betapapillomavirus replication and transcription have not been studied in detail because of a lack of suitable cellular systems supporting human papillomavirus (HPV) genome replication. We have recently shown that the human osteosarcoma cell line U2OS provides a useful environment for the genome replication of many different HPVs, including the betapapillomaviruses HPV5 and HPV8. Using mutational analysis and complementation assay, we demonstrated herein that the viral early proteins E1 and E2 are viral transfactors that are necessary and sufficient for HPV5 genome replication. We also identified four HPV5 early promoter regions with transcription start sites (TSSs) at nucleotides (nt) 184/191, 460, 840, and 1254, respectively, and the HPV late promoter with a TSS at nt 7640. In addition, we mapped the HPV5 early polyadenylation cleavage sites via 3' rapid amplification of cDNA ends (3'RACE) to nt 4457 and 4475. In total, 14 different viral mRNA species, originating from the HPV5 genome, were mapped in U2OS cells during transient and stable replication. The main splicing donor and acceptor sites identified herein are consistent with the data previously obtained in HPV5-positive skin lesions. In addition, we identified novel E8 open reading frame (ORF)-containing transcripts (E8^E1C and E8^E2C) expressed from the HPV5 genome. Similar to several other papillomaviruses, the product of the E8^E2C mRNA acts as a repressor of viral genome replication.
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81
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Ganzenmueller T, Hage E, Yakushko Y, Kluba J, Woltemate S, Schacht V, Schulz TF, Gutzmer R. No human virus sequences detected by next-generation sequencing in benign verrucous skin tumors occurring in BRAF-inhibitor-treated patients. Exp Dermatol 2013; 22:725-9. [DOI: 10.1111/exd.12249] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2013] [Indexed: 12/13/2022]
Affiliation(s)
| | - Elias Hage
- Institute of Virology; Hannover Medical School; Hannover Germany
| | - Yuri Yakushko
- Institute of Virology; Hannover Medical School; Hannover Germany
| | - Jeanette Kluba
- Institute of Virology; Hannover Medical School; Hannover Germany
| | - Sabrina Woltemate
- Institute for Medical Microbiology and Hospital Epidemiology; Hannover Medical School; Hannover Germany
| | - Vivien Schacht
- Department of Dermatology and Allergy; Hannover Medical School; Hannover Germany
| | - Thomas F. Schulz
- Institute of Virology; Hannover Medical School; Hannover Germany
| | - Ralf Gutzmer
- Department of Dermatology and Allergy; Hannover Medical School; Hannover Germany
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82
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Sensitive detection of viral transcripts in human tumor transcriptomes. PLoS Comput Biol 2013; 9:e1003228. [PMID: 24098097 PMCID: PMC3789765 DOI: 10.1371/journal.pcbi.1003228] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 06/04/2013] [Indexed: 02/07/2023] Open
Abstract
In excess of % of human cancer incidents have a viral cofactor. Epidemiological studies of idiopathic human cancers indicate that additional tumor viruses remain to be discovered. Recent advances in sequencing technology have enabled systematic screenings of human tumor transcriptomes for viral transcripts. However, technical problems such as low abundances of viral transcripts in large volumes of sequencing data, viral sequence divergence, and homology between viral and human factors significantly confound identification of tumor viruses. We have developed a novel computational approach for detecting viral transcripts in human cancers that takes the aforementioned confounding factors into account and is applicable to a wide variety of viruses and tumors. We apply the approach to conducting the first systematic search for viruses in neuroblastoma, the most common cancer in infancy. The diverse clinical progression of this disease as well as related epidemiological and virological findings are highly suggestive of a pathogenic cofactor. However, a viral etiology of neuroblastoma is currently contested. We mapped transcriptomes of neuroblastoma as well as positive and negative controls to the human and all known viral genomes in order to detect both known and unknown viruses. Analysis of controls, comparisons with related methods, and statistical estimates demonstrate the high sensitivity of our approach. Detailed investigation of putative viral transcripts within neuroblastoma samples did not provide evidence for the existence of any known human viruses. Likewise, de-novo assembly and analysis of chimeric transcripts did not result in expression signatures associated with novel human pathogens. While confounding factors such as sample dilution or viral clearance in progressed tumors may mask viral cofactors in the data, in principle, this is rendered less likely by the high sensitivity of our approach and the number of biological replicates analyzed. Therefore, our results suggest that frequent viral cofactors of metastatic neuroblastoma are unlikely. Many human cancers are caused by infections with tumor viruses and identification of these pathogens is considered a critical contribution to cancer prevention. Deep sequencing enables us to systematically investigate viral nucleotide signatures in order to either verify or exclude the existence of viruses in idiopathic human cancers. We have developed Virana, a novel computational approach for identifying tumor viruses in human cancers that is applicable to a wide variety of tumors and viruses. Virana firstly addresses several important biological confounding factors that may hinder successful detection of these pathogens. We applied our approach in the first systematic search for cancer-causing viruses in metastatic neuroblastoma, the most common form of cancer in infancy. Although the heterogeneous clinical progression of this disease as well as epidemiological and virological findings are suggestive of a pathogenic cofactor, the viral etiology of neuroblastoma is currently contested. We conducted an analysis of experimental controls, comparisons with related approaches, as well as statistical analyses in order to validate our method. In spite of the high sensitivity of our approach, analyses of neuroblastoma transcriptomes did not provide evidence for the existence of any known or unknown human viruses. Our results therefore suggest that frequent viral cofactors of metastatic neuroblastoma are unlikely.
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Farzan SF, Waterboer T, Gui J, Nelson HH, Li Z, Michael KM, Perry AE, Spencer SK, Demidenko E, Green AC, Pawlita M, Karagas MR. Cutaneous alpha, beta and gamma human papillomaviruses in relation to squamous cell carcinoma of the skin: a population-based study. Int J Cancer 2013; 133:1713-20. [PMID: 23536363 PMCID: PMC3713187 DOI: 10.1002/ijc.28176] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/01/2013] [Accepted: 02/18/2013] [Indexed: 12/13/2022]
Abstract
Human papillomavirus (HPV) infection is common worldwide and, in immunodeficient populations, may contribute to the pathogenesis of keratinocyte cancers, particularly squamous cell carcinomas (SCC). However, their role in SCC in the general population is less clear. We conducted a comprehensive analysis to investigate the independent effects of seropositivity for cutaneous alpha, beta and gamma HPV types on risk of SCC, and a meta-analysis of the available literature. In a population-based case-control study from New Hampshire, USA (n = 1,408), histologically confirmed SCC cases and controls were tested for L1 antibodies to alpha, beta and gamma cutaneous HPV types 2-5, 7-10, 15, 17, 20, 23, 24, 27b, 36, 38, 48-50, 57, 65, 75-77, 88, 92, 95, 96, 101, 103 and 107 using multiplex serology. An increasing risk of SCC with number of beta HPVs to which an individual tested positive was observed even among those seronegative for gamma types (p for trend = 0.016) with an odds ratio of 1.95 (95% confidence interval (CI) = 1.07-3.56) for four or more beta types positive. In a meta-analysis of six case-control studies, increased SCC risks in relation to beta HPV seropositivity were found across studies (meta odds ratio = 1.45, CI = 1.27-1.66). While the prevalence of gamma HPVs assayed was somewhat higher among SCC cases than controls, the association was only weakly evident among those seronegative for beta HPVs. Overall, the association between cutaneous HPVs and skin cancers appears to be specific to SCC and to genus beta HPVs in a general US population.
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Affiliation(s)
- Shohreh F Farzan
- Department of Community and Family Medicine and The Norris Cotton Cancer Center, Section of Biostatistics and Epidemiology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH 03756, USA
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84
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DeBoever C, Reid EG, Smith EN, Wang X, Dumaop W, Harismendy O, Carson D, Richman D, Masliah E, Frazer KA. Whole transcriptome sequencing enables discovery and analysis of viruses in archived primary central nervous system lymphomas. PLoS One 2013; 8:e73956. [PMID: 24023918 PMCID: PMC3762708 DOI: 10.1371/journal.pone.0073956] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/24/2013] [Indexed: 11/23/2022] Open
Abstract
Primary central nervous system lymphomas (PCNSL) have a dramatically increased prevalence among persons living with AIDS and are known to be associated with human Epstein Barr virus (EBV) infection. Previous work suggests that in some cases, co-infection with other viruses may be important for PCNSL pathogenesis. Viral transcription in tumor samples can be measured using next generation transcriptome sequencing. We demonstrate the ability of transcriptome sequencing to identify viruses, characterize viral expression, and identify viral variants by sequencing four archived AIDS-related PCNSL tissue samples and analyzing raw sequencing reads. EBV was detected in all four PCNSL samples and cytomegalovirus (CMV), JC polyomavirus (JCV), and HIV were also discovered, consistent with clinical diagnoses. CMV was found to express three long non-coding RNAs recently reported as expressed during active infection. Single nucleotide variants were observed in each of the viruses observed and three indels were found in CMV. No viruses were found in several control tumor types including 32 diffuse large B-cell lymphoma samples. This study demonstrates the ability of next generation transcriptome sequencing to accurately identify viruses, including DNA viruses, in solid human cancer tissue samples.
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Affiliation(s)
- Christopher DeBoever
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, California, United States of America
| | - Erin G. Reid
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Erin N. Smith
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Xiaoyun Wang
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
| | - Wilmar Dumaop
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Olivier Harismendy
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
- Clinical and Translational Research Institute, University of California San Diego, La Jolla, California, United States of America
| | - Dennis Carson
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
| | - Douglas Richman
- VA San Diego Healthcare System and Center for AIDS Research, University of California San Diego, La Jolla, California, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Kelly A. Frazer
- Moores Cancer Center, University of California San Diego, La Jolla, California, United States of America
- Department of Pediatrics and Rady Children’s Hospital, University of California San Diego, La Jolla, California, United States of America
- Clinical and Translational Research Institute, University of California San Diego, La Jolla, California, United States of America
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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85
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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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86
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Oral cavity tumors in younger patients show a poor prognosis and do not contain viral RNA. Oral Oncol 2013; 49:525-33. [DOI: 10.1016/j.oraloncology.2013.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 02/06/2013] [Indexed: 12/12/2022]
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87
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Dimon MT, Wood HM, Rabbitts PH, Arron ST. IMSA: integrated metagenomic sequence analysis for identification of exogenous reads in a host genomic background. PLoS One 2013; 8:e64546. [PMID: 23717627 PMCID: PMC3662787 DOI: 10.1371/journal.pone.0064546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/16/2013] [Indexed: 12/11/2022] Open
Abstract
Metagenomics, the study of microbial genomes within diverse environments, is a rapidly developing field. The identification of microbial sequences within a host organism enables the study of human intestinal, respiratory, and skin microbiota, and has allowed the identification of novel viruses in diseases such as Merkel cell carcinoma. There are few publicly available tools for metagenomic high throughput sequence analysis. We present Integrated Metagenomic Sequence Analysis (IMSA), a flexible, fast, and robust computational analysis pipeline that is available for public use. IMSA takes input sequence from high throughput datasets and uses a user-defined host database to filter out host sequence. IMSA then aligns the filtered reads to a user-defined universal database to characterize exogenous reads within the host background. IMSA assigns a score to each node of the taxonomy based on read frequency, and can output this as a taxonomy report suitable for cluster analysis or as a taxonomy map (TaxMap). IMSA also outputs the specific sequence reads assigned to a taxon of interest for downstream analysis. We demonstrate the use of IMSA to detect pathogens and normal flora within sequence data from a primary human cervical cancer carrying HPV16, a primary human cutaneous squamous cell carcinoma carrying HPV 16, the CaSki cell line carrying HPV16, and the HeLa cell line carrying HPV18.
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Affiliation(s)
- Michelle T. Dimon
- Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America
| | - Henry M. Wood
- Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, United Kingdom
| | - Pamela H. Rabbitts
- Leeds Institute of Molecular Medicine, St James’s University Hospital, Leeds, United Kingdom
| | - Sarah T. Arron
- Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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88
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PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3-GENES GENOMES GENETICS 2013; 3:865-80. [PMID: 23550143 PMCID: PMC3656733 DOI: 10.1534/g3.113.005967] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Low-cost DNA sequencing technologies have expanded the role for direct nucleic acid sequencing in the analysis of genomes, transcriptomes, and the metagenomes of whole ecosystems. Human and machine comprehension of such large datasets can be simplified via synthesis of sequence fragments into long, contiguous blocks of sequence (contigs), but most of the progress in the field of assembly has focused on genomes in isolation rather than metagenomes. Here, we present software for paired-read iterative contig extension (PRICE), a strategy for focused assembly of particular nucleic acid species using complex metagenomic data as input. We describe the assembly strategy implemented by PRICE and provide examples of its application to the sequence of particular genes, transcripts, and virus genomes from complex multicomponent datasets, including an assembly of the BCBL-1 strain of Kaposi's sarcoma-associated herpesvirus. PRICE is open-source and available for free download (derisilab.ucsf.edu/software/price/ or sourceforge.net/projects/pricedenovo/).
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89
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Hameetman L, Commandeur S, Bavinck JNB, Wisgerhof HC, de Gruijl FR, Willemze R, Mullenders L, Tensen CP, Vrieling H. Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients. BMC Cancer 2013; 13:58. [PMID: 23379751 PMCID: PMC3570297 DOI: 10.1186/1471-2407-13-58] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/30/2013] [Indexed: 01/06/2023] Open
Abstract
Background The risk of developing cutaneous squamous cell carcinoma (SCC) is markedly increased in organ transplant recipients (OTRs) compared to the normal population. Next to sun exposure, the immunosuppressive regimen is an important risk factor for the development of SCC in OTRs. Various gene mutations (e.g. TP53) and genetic alterations (e.g. loss of CDKN2A, amplification of RAS) have been found in SCCs. The aim of this genome-wide study was to identify pathways and genomic alterations that are consistently involved in the formation of SCCs and their precursor lesions, actinic keratoses (AKs). Methods To perform the analysis in an isogenic background, RNA and DNA were isolated from SCC, AK and normal (unexposed) epidermis (NS) from each of 13 OTRs. Samples were subjected to genome-wide expression analysis and genome SNP analysis using Illumina’s HumanWG-6 BeadChips and Infinium II HumanHap550 Genotyping BeadChips, respectively. mRNA expression results were verified by quantitative PCR. Results Hierarchical cluster analysis of mRNA expression profiles showed SCC, AK and NS samples to separate into three distinct groups. Several thousand genes were differentially expressed between epidermis, AK and SCC; most upregulated in SCCs were hyperproliferation related genes and stress markers, such as keratin 6 (KRT6), KRT16 and KRT17. Matching to oncogenic pathways revealed activation of downstream targets of RAS and cMYC in SCCs and of NFκB and TNF already in AKs. In contrast to what has been reported previously, genome-wide SNP analysis showed very few copy number variations in AKs and SCCs, and these variations had no apparent relationship with observed changes in mRNA expression profiles. Conclusion Vast differences in gene expression profiles exist between SCC, AK and NS from immunosuppressed OTRs. Moreover, several pathways activated in SCCs were already activated in AKs, confirming the assumption that AKs are the precursor lesions of SCCs. Since the drastic changes in gene expression appeared unlinked to specific genomic gains or losses, the causal events driving SCC development require further investigation. Other molecular mechanisms, such as DNA methylation or miRNA alterations, may affect gene expression in SCCs of OTRs. Further study is required to identify the mechanisms of early activation of NFκB and TNF, and to establish whether these pathways offer a feasible target for preventive intervention among OTRs.
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Affiliation(s)
- Liesbeth Hameetman
- Department of Toxicogenetics, Leiden University Medical Center, PO Box 9600, 2300, RC Leiden, the Netherlands
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90
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White EA, Howley PM. Proteomic approaches to the study of papillomavirus-host interactions. Virology 2013; 435:57-69. [PMID: 23217616 PMCID: PMC3522865 DOI: 10.1016/j.virol.2012.09.046] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 01/22/2023]
Abstract
The identification of interactions between viral and host cellular proteins has provided major insights into papillomavirus research, and these interactions are especially relevant to the role of papillomaviruses in the cancers with which they are associated. Recent advances in mass spectrometry technology and data processing now allow the systematic identification of such interactions. This has led to an improved understanding of the different pathologies associated with the many papillomavirus types, and the diverse nature of these viruses is reflected in the spectrum of interactions with host proteins. Here we review a history of proteomic approaches, particularly as applied to the papillomaviruses, and summarize current techniques. Current proteomic studies on the papillomaviruses use yeast-two-hybrid or affinity purification-mass spectrometry approaches. We detail the advantages and disadvantages of each and describe current examples of papillomavirus proteomic studies, with a particular focus on the HPV E6 and E7 oncoproteins.
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Affiliation(s)
- Elizabeth A. White
- Department of Microbiology and Immunobiology, Harvard Medical School, NRB Room 950, 77 Avenue Louis Pasteur, Boston, MA 02115
| | - Peter M. Howley
- Department of Microbiology and Immunobiology, Harvard Medical School, NRB Room 950, 77 Avenue Louis Pasteur, Boston, MA 02115
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91
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Verhoeven RHA, Aben KKH, van Rossum MM, Reedijk AM, Botterweck AA, Veerbeek L, Visser O, van der Aa MA, Ho VKY, Coebergh JWW, Kiemeney LALM. New insights into the aetiology of scrotal cancer, a nationwide case-control study in the Netherlands. J Eur Acad Dermatol Venereol 2012; 28:65-71. [PMID: 23216598 DOI: 10.1111/jdv.12056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND Although scrotal cancer is traditionally regarded as an occupational disease, there is increasing evidence that factors which are involved in cutaneous and genital carcinogenesis might play a role in the carcinogenesis of scrotal cancer. OBJECTIVE This exploratory study aimed to detect exposures that might have an aetiological relation with scrotal cancer. METHODS A nationwide population-based case-control study was conducted in the Netherlands. The patients were identified through the Netherlands cancer registry. Controls were recruited among acquaintances of the cancer registry registrars. The participants completed a questionnaire that included questions on occupational exposures, naked sunbathing, use of sunbeds, skin diseases and their treatments, treatments for cancer and sexually transmitted diseases. Age-adjusted odds-ratios (ORs) were calculated. RESULTS Forty-seven scrotal cancer patients and 125 controls completed the questionnaire. The patients were categorized according to histology of the scrotal tumours. Having had a skin disease (OR = 6.3, 95% CI = 1.8-22), especially psoriasis (OR = 8.7), increased the risk of squamous cell carcinomas (SCC) of the scrotum. A previous cancer diagnosis may affect the risk of scrotal basal cell carcinomas (BCC; OR = 4.9, 95% CI = 0.9-27.3). Furthermore, an association between the number of sexual partners and the occurrence of scrotal sarcoma was found. CONCLUSION Scrotal SCCs may be related with skin diseases or skin disease treatments. Having had cancer may be a risk factor for a BCC of the scrotum. Scrotal sarcomas seem to be correlated with the number of sexual partners. This study suggests that scrotal cancer has characteristics of both cutaneous and genital carcinogenesis.
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Affiliation(s)
- R H A Verhoeven
- Eindhoven Cancer Registry/Comprehensive Cancer Centre South, EindhovenDepartment of Research & Registration, Comprehensive Cancer Centre The Netherlands, UtrechtDepartment of Health Evidence, Radboud University Medical CentreDepartment of Dermatology, Radboud University Medical Centre, NijmegenDepartment of Public Health, Erasmus University Medical Centre, RotterdamDepartment of Urology, Radboud University Medical Centre, Nijmegen, The Netherlands
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92
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White EA, Kramer RE, Tan MJA, Hayes SD, Harper JW, Howley PM. Comprehensive analysis of host cellular interactions with human papillomavirus E6 proteins identifies new E6 binding partners and reflects viral diversity. J Virol 2012; 86:13174-86. [PMID: 23015706 PMCID: PMC3503137 DOI: 10.1128/jvi.02172-12] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/18/2012] [Indexed: 12/14/2022] Open
Abstract
We have begun to define the human papillomavirus (HPV)-associated proteome for a subset of the more than 120 HPV types that have been identified to date. Our approach uses a mass spectrometry-based platform for the systematic identification of interactions between human papillomavirus and host cellular proteins, and here we report a proteomic analysis of the E6 proteins from 16 different HPV types. The viruses included represent high-risk, low-risk, and non-cancer-associated types from genus alpha as well as viruses from four different species in genus beta. The E6 interaction data set consists of 153 cellular proteins, including several previously reported HPV E6 interactors such as p53, E6AP, MAML1, and p300/CBP and proteins containing PDZ domains. We report the genus-specific binding of E6s to either E6AP or MAML1, define the specific HPV E6s that bind to p300, and demonstrate several new features of interactions involving beta HPV E6s. In particular, we report that several beta HPV E6s bind to proteins containing PDZ domains and that at least two beta HPV E6s bind to p53. Finally, we report the newly discovered interaction of proteins of E6 of beta genus, species 2, with the Ccr4-Not complex, the first report of a viral protein binding to this complex. This data set represents a comprehensive survey of E6 binding partners that provides a resource for the HPV field and will allow continued studies on the diverse biology of the human papillomaviruses.
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Affiliation(s)
- Elizabeth A. White
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rebecca E. Kramer
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Min Jie Alvin Tan
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sebastian D. Hayes
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter M. Howley
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
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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: 866] [Impact Index Per Article: 72.2] [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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94
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Aldabagh B, Angeles JGC, Cardones AR, Arron ST. Cutaneous squamous cell carcinoma and human papillomavirus: is there an association? Dermatol Surg 2012; 39:1-23. [PMID: 22928516 DOI: 10.1111/j.1524-4725.2012.02558.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The role of human papillomavirus (HPV) in the induction and maintenance of cervical, anogenital, and some oropharyngeal carcinomas is well recognized, but its role in cutaneous squamous cell carcinoma (SCC) remains to be elucidated. HPV is thought to act as a possible cocarcinogen in the development of SCC. OBJECTIVE To review the literature assessing the correlation between and possible causation of HPV and cutaneous SCC in immunocompetent and immunocompromised populations. METHODS We reviewed HPV sampling and detection methods, epidemiologic studies examining HPV carriage in immunocompetent and immunosuppressed individuals, and evidence asserting an association between HPV and cutaneous SCC. RESULTS Although an abundant body of evidence points toward a link between HPV and cutaneous SCC, many studies indicate otherwise. Recent studies have focused on viral activity in addition to DNA presence. CONCLUSION The possibility exists that HPV may play a role in the induction but not maintenance of cutaneous SCC.
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Affiliation(s)
- Bishr Aldabagh
- Department of Dermatology, Duke University Medical Center, Durham, North Carolina, USA
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95
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Abstract
Dermatological research has been very active this year. Most of the numerous fields investigated involve the mechanisms of cutaneous regeneration and barrier function. A novel target of early ultraviolet-induced skin photodamage, the Syk kinase, has been recently identified. Synergistic relationship between telomere damage and cutaneous progerin production during cell senescence may also participate in the natural skin aging process. Interestingly, ultraviolet radiation induces an inhibitory effect on subcutaneous lipogenesis. Androgenetic alopecia or common baldness is not characterized by loss of hair follicle stem cells but by a defect in the conversion of hair follicle stem cells into active progenitor cells. It has been shown that the cornified envelope functions not only as a physicomechanical barrier, but also as both a biochemical line of antoxidant defense and an immunological line of defense. Like human papillomaviruses, Merckel cell polyomavirus belongs to the skin microbiome and different studies have demonstrated the protective role of epidermal resident microflora through the activation of innate immunity. Production of antimicrobial peptides and the activation of inflammasome and plasmacytoid dendritic cells are involved in the modulation of the cutaneous barrier function. Results from different studies suggest that IL-22 and IL-36 may be common mediators of both innate and adaptive immune responses. All these pathways interact not only to maintain cutaneous homeostasis and integrity (wound healing) but also to regulate autoinflammatory and autoimmune dermatoses (psoriasis, lupus, rosacea, atopic dermatitis, etc...). In addition, molecular mechanisms that regulate T helper type 2 differentiation and the retention at the site of inflammation of Th2 cells have been identified. New promising therapeutic targets for different chronic dermatosis are thus suggested. Mechanobiology and mechanotransduction are also emerging fields that investigate mechanical interactions between living cells and their environment and the conversion of mechanical cues into biochemical signals. Electronic second skin is now a current concept through bio-integrated epidermal electronics platforms used for different monitoring and stimulations of body functions.
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Affiliation(s)
- F Aubin
- Université de Franche Comté, EA3181, IFR133 et Service de Dermatologie, CHU de Besançon, 2 place Saint-Jacques 25030 Besançon cedex, France.
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96
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Ganzenmueller T, Yakushko Y, Kluba J, Henke-Gendo C, Gutzmer R, Schulz TF. Next-generation sequencing fails to identify human virus sequences in cutaneous squamous cell carcinoma. Int J Cancer 2012; 131:E1173-9. [DOI: 10.1002/ijc.27581] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 03/27/2012] [Indexed: 01/15/2023]
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97
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Loeb KR, Asgari MM, Hawes SE, Feng Q, Stern JE, Jiang M, Argenyi ZB, de Villiers EM, Kiviat NB. Analysis of Tp53 codon 72 polymorphisms, Tp53 mutations, and HPV infection in cutaneous squamous cell carcinomas. PLoS One 2012; 7:e34422. [PMID: 22545084 PMCID: PMC3335843 DOI: 10.1371/journal.pone.0034422] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 02/28/2012] [Indexed: 12/26/2022] Open
Abstract
Background Non-melanoma skin cancers are one of the most common human malignancies accounting for 2–3% of tumors in the US and represent a significant health burden. Epidemiology studies have implicated Tp53 mutations triggered by UV exposure, and human papilloma virus (HPV) infection to be significant causes of non-melanoma skin cancer. However, the relationship between Tp53 and cutaneous HPV infection is not well understood in skin cancers. In this study we assessed the association of HPV infection and Tp53 polymorphisms and mutations in lesional specimens with squamous cell carcinomas. Methods We studied 55 cases of histologically confirmed cutaneous squamous cell carcinoma and 41 controls for the presence of HPV infection and Tp53 genotype (mutations and polymorphism). Results We found an increased number of Tp53 mutations in the squamous cell carcinoma samples compared with perilesional or control samples. There was increased frequency of homozygous Tp53-72R polymorphism in cases with squamous cell carcinomas, while the Tp53-72P allele (Tp53-72R/P and Tp53-72P/P) was more frequent in normal control samples. Carcinoma samples positive for HPV showed a decreased frequency of Tp53 mutations compared to those without HPV infection. In addition, carcinoma samples with a Tp53-72P allele showed an increased incidence of Tp53 mutations in comparison carcinomas samples homozygous for Tp53-72R. Conclusions These studies suggest there are two separate pathways (HPV infection and Tp53 mutation) leading to cutaneous squamous cell carcinomas stratified by the Tp53 codon-72 polymorphism. The presence of a Tp53-72P allele is protective against cutaneous squamous cell carcinoma, and carcinoma specimens with Tp53-72P are more likely to have Tp53 mutations. In contrast Tp53-72R is a significant risk factor for cutaneous squamous cell carcinoma and is frequently associated with HPV infection instead of Tp53 mutations. Heterozygosity for Tp53-72R/P is protective against squamous cell carcinomas, possibly reflecting a requirement for both HPV infection and Tp53 mutations.
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Affiliation(s)
- Keith R. Loeb
- Divisions of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Maryam M. Asgari
- Department of Epidemiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stephen E. Hawes
- Department of Epidemiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Qinghua Feng
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Joshua E. Stern
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Mingjun Jiang
- Institute of Dermatology, National Academy of Medical Sciences, Nanjing, People’s Republic of China
| | - Zsolt B. Argenyi
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Division of Dermatology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ethel-Michele de Villiers
- Division for the Characterization of Tumorviruses, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Nancy B. Kiviat
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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98
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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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99
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Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL. Virus identification in unknown tropical febrile illness cases using deep sequencing. PLoS Negl Trop Dis 2012; 6:e1485. [PMID: 22347512 PMCID: PMC3274504 DOI: 10.1371/journal.pntd.0001485] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 12/07/2011] [Indexed: 02/06/2023] Open
Abstract
Dengue virus is an emerging infectious agent that infects an estimated 50–100 million people annually worldwide, yet current diagnostic practices cannot detect an etiologic pathogen in ∼40% of dengue-like illnesses. Metagenomic approaches to pathogen detection, such as viral microarrays and deep sequencing, are promising tools to address emerging and non-diagnosable disease challenges. In this study, we used the Virochip microarray and deep sequencing to characterize the spectrum of viruses present in human sera from 123 Nicaraguan patients presenting with dengue-like symptoms but testing negative for dengue virus. We utilized a barcoding strategy to simultaneously deep sequence multiple serum specimens, generating on average over 1 million reads per sample. We then implemented a stepwise bioinformatic filtering pipeline to remove the majority of human and low-quality sequences to improve the speed and accuracy of subsequent unbiased database searches. By deep sequencing, we were able to detect virus sequence in 37% (45/123) of previously negative cases. These included 13 cases with Human Herpesvirus 6 sequences. Other samples contained sequences with similarity to sequences from viruses in the Herpesviridae, Flaviviridae, Circoviridae, Anelloviridae, Asfarviridae, and Parvoviridae families. In some cases, the putative viral sequences were virtually identical to known viruses, and in others they diverged, suggesting that they may derive from novel viruses. These results demonstrate the utility of unbiased metagenomic approaches in the detection of known and divergent viruses in the study of tropical febrile illness. Dengue virus infection is a global health concern, affecting as many as 100 million people annually worldwide. A critical first step to proper treatment and control of any virus infection is a correct diagnosis. Traditional diagnostic tests for viruses depend on amplification of conserved portions of the viral genome, detection of the binding of antibodies to viral proteins, or replication of the virus in cell cultures. These methods have a major shortcoming: they are unable to detect divergent or novel viruses for which a priori sequence, serological, or cellular tropism information is not known. In our study, we use two approaches, microarrays and deep sequencing, to virus identification that are less susceptible to such shortcomings. We used these unbiased tools to search for viruses in blood collected from Nicaraguan children with clinical symptoms indicating dengue virus infection, but for whom current dengue virus detection assays yielded negative results. We were able to identify both known and divergent viruses in about one third of previously negative samples, demonstrating the utility of these approaches to detect viruses in cases of unknown dengue-like illness.
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Affiliation(s)
- Nathan L. Yozwiak
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Peter Skewes-Cox
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, California, United States of America
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Mark D. Stenglein
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Angel Balmaseda
- Departamento de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Joseph L. DeRisi
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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100
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Abstract
Over the past several decades, there has been increasing interest in understanding the roles of the immune system in the development and progression of cancer. The importance of the immune system in human skin cancer has been long recognized based primarily upon the increased incidence of skin cancers in organ transplant recipients and mechanisms of ultraviolet (UV) radiation-mediated immunomodulation. In this review, we integrate multiple lines of evidence highlighting the roles of the immune system in skin cancer. First, we discuss the concepts of cancer immunosurveillance and immunoediting as they might relate to human skin cancers. We then describe the clinical and molecular mechanisms of skin cancer development and progression in the contexts of therapeutic immunosuppression in organ transplant recipients, viral oncogenesis, and UV radiation-induced immunomodulation with a primary focus on basal cell carcinoma and squamous cell carcinoma. The clinical evidence supporting expanding roles for immunotherapy is also described. Finally, we discuss recent research examining the functions of particular immune cell subsets in skin cancer and how they might contribute to both antitumour and protumour effects. A better understanding of the biological mechanisms of cancer immunosurveillance holds the promise of enabling better therapies.
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Affiliation(s)
- S Rangwala
- Baylor College of Medicine, Houston, TX, USA
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