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Pinatti LM, Gu W, Wang Y, Elhossiny A, Bhangale AD, Brummel CV, Carey TE, Mills RE, Brenner JC. SearcHPV: A novel approach to identify and assemble human papillomavirus-host genomic integration events in cancer. Cancer 2021; 127:3531-3540. [PMID: 34160069 DOI: 10.1002/cncr.33691] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/15/2021] [Accepted: 05/03/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Human papillomavirus (HPV) is a well-established driver of malignant transformation at a number of sites, including head and neck, cervical, vulvar, anorectal, and penile squamous cell carcinomas; however, the impact of HPV integration into the host human genome on this process remains largely unresolved. This is due to the technical challenge of identifying HPV integration sites, which includes limitations of existing informatics approaches to discovering viral-host breakpoints from low-read-coverage sequencing data. METHODS To overcome this limitation, the authors developed SearcHPV, a new HPV detection pipeline based on targeted capture technology, and applied the algorithm to targeted capture data. They performed an integrated analysis of SearcHPV-defined breakpoints with genome-wide linked-read sequencing to identify potential HPV-related structural variations. RESULTS Through an analysis of HPV+ models, the authors showed that SearcHPV detected HPV-host integration sites with a higher sensitivity and specificity than 2 other commonly used HPV detection callers. SearcHPV uncovered HPV integration sites adjacent to known cancer-related genes, including TP63, MYC, and TRAF2, and near regions of large structural variation. The authors further validated the junction contig assembly feature of SearcHPV, which helped to accurately identify viral-host junction breakpoint sequences. They found that viral integration occurred through a variety of DNA repair mechanisms, including nonhomologous end joining, alternative end joining, and microhomology-mediated repair. CONCLUSIONS In summary, SearcHPV is a new optimized tool for the accurate detection of HPV-human integration sites from targeted capture DNA sequencing data.
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Affiliation(s)
- Lisa M Pinatti
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan.,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Wenjin Gu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Yifan Wang
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Ahmed Elhossiny
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Apurva D Bhangale
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Collin V Brummel
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan
| | - Thomas E Carey
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan.,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, Michigan Medicine, Ann Arbor, Michigan.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - J Chad Brenner
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan.,Rogel Cancer Center, Michigan Medicine, Ann Arbor, Michigan.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
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52
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Aldersley J, Lorenz DR, Mouw KW, D'Andrea AD, Gabuzda D. Genomic Landscape of Primary and Recurrent Anal Squamous Cell Carcinomas in Relation to HPV Integration, Copy-Number Variation, and DNA Damage Response Genes. Mol Cancer Res 2021; 19:1308-1321. [PMID: 33883185 DOI: 10.1158/1541-7786.mcr-20-0884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/02/2021] [Accepted: 04/16/2021] [Indexed: 12/26/2022]
Abstract
The incidence of anal squamous cell carcinoma (ASCC) has been increasing, particularly in populations with HIV. Human papillomavirus (HPV) is the causal factor in 85% to 90% of ASCCs, but few studies evaluated HPV genotypes and integrations in relation to genomic alterations in ASCC. Using whole-exome sequence data for primary (n = 56) and recurrent (n = 31) ASCC from 72 patients, we detected HPV DNA in 87.5% of ASCC, of which HPV-16, HPV-18, and HPV-6 were detected in 56%, 22%, and 33% of HIV-positive (n = 9) compared with 83%, 3.2%, and 1.6% of HIV-negative cases (n = 63), respectively. Recurrent copy-number variations (CNV) involving genes with documented roles in cancer included amplification of PI3KCA and deletion of APC in primary and recurrent tumors; amplifications of CCND1, MYC, and NOTCH1 and deletions of BRCA2 and RB1 in primary tumors; and deletions of ATR, FANCD2, and FHIT in recurrent tumors. DNA damage response genes were enriched among recurrently deleted genes in recurrent ASCCs (P = 0.001). HPV integrations were detected in 29 of 76 (38%) ASCCs and were more frequent in stage III-IV versus stage I-II tumors. HPV integrations were detected near MYC and CCND1 amplifications and recurrent targets included NFI and MUC genes. These results suggest HPV genotypes in ASCC differ by HIV status, HPV integration is associated with ASCC progression, and DNA damage response genes are commonly disrupted in recurrent ASCCs. IMPLICATIONS: These data provide the largest whole-exome sequencing study of the ASCC genomic landscape to date and identify HPV genotypes, integrations, and recurrent CNVs in primary or recurrent ASCCs.
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Affiliation(s)
- Jordan Aldersley
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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53
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Pathogenic Role of Immune Evasion and Integration of Human Papillomavirus in Oropharyngeal Cancer. Microorganisms 2021; 9:microorganisms9050891. [PMID: 33919460 PMCID: PMC8143538 DOI: 10.3390/microorganisms9050891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
The incidence of oropharyngeal cancer (OPC) is increasing remarkably among all head and neck cancers, mainly due to its association with the human papillomavirus (HPV). Most HPVs are eliminated by the host’s immune system; however, because HPV has developed an effective immune evasion mechanism to complete its replication cycle, a small number of HPVs are not eliminated, leading to persistent infection. Moreover, during the oncogenic process, the extrachromosomal HPV genome often becomes integrated into the host genome. Integration involves the induction and high expression of E6 and E7, leading to cell cycle activation and increased genomic instability in the host. Therefore, integration is an important event in oncogenesis, although the associated mechanism remains unclear, especially in HPV-OPC. In this review, we summarize the current knowledge on HPV-mediated carcinogenesis, with special emphasis on immune evasion and integration mechanisms, which are crucial for oncogenesis.
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54
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Garza-Rodríguez ML, Oyervides-Muñoz MA, Pérez-Maya AA, Sánchez-Domínguez CN, Berlanga-Garza A, Antonio-Macedo M, Valdés-Chapa LD, Vidal-Torres D, Vidal-Gutiérrez O, Pérez-Ibave DC, Treviño V. Analysis of HPV Integrations in Mexican Pre-Tumoral Cervical Lesions Reveal Centromere-Enriched Breakpoints and Abundant Unspecific HPV Regions. Int J Mol Sci 2021; 22:ijms22063242. [PMID: 33810183 PMCID: PMC8005155 DOI: 10.3390/ijms22063242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 01/11/2023] Open
Abstract
Human papillomavirus (HPV) DNA integration is a crucial event in cervical carcinogenesis. However, scarce studies have focused on studying HPV integration (HPVint) in early-stage cervical lesions. Using HPV capture followed by sequencing, we investigated HPVint in pre-tumor cervical lesions. Employing a novel pipeline, we analyzed reads containing direct evidence of the integration breakpoint. We observed multiple HPV infections in most of the samples (92%) with a median integration rate of 0.06% relative to HPV mapped reads corresponding to two or more sequence breakages. Unlike cancer studies, most integrations events were unique (supported by one read), consistent with the lack of clonal selection. Congruent to other studies, we found that breakpoints could occur, practically, in any part of the viral genome. We noted that L1 had a higher frequency of rupture integration (25%). Based on host genome integration frequencies, we found previously reported integration sites in cancer for genes like FHIT, CSMD1, and LRP1B and putatively many new ones such as those exemplified in CSMD3, ROBO2, and SETD3. Similar host integrations regions and genes were observed in diverse HPV types within many genes and even equivalent integration positions in different samples and HPV types. Interestingly, we noted an enrichment of integrations in most centromeres, suggesting a possible mechanism where HPV exploits this structural machinery to facilitate integration. Supported by previous findings, overall, our analysis provides novel information and insights about HPVint.
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Affiliation(s)
- María Lourdes Garza-Rodríguez
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Mariel Araceli Oyervides-Muñoz
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico;
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Antonio Alí Pérez-Maya
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Celia Nohemí Sánchez-Domínguez
- Departamento de Bioquímica y Medicina Molecular, Facultad de Medicina, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro Monterrey, Nuevo León 64460, Mexico; (A.A.P.-M.); (C.N.S.-D.)
| | - Anais Berlanga-Garza
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Mauro Antonio-Macedo
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Lezmes Dionicio Valdés-Chapa
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Diego Vidal-Torres
- Departamento de Ginecología y Obstetricia, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (A.B.-G.); (M.A.-M.); (L.D.V.-C.); (D.V.-T.)
| | - Oscar Vidal-Gutiérrez
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Diana Cristina Pérez-Ibave
- Hospital Universitario “Dr. José Eleuterio González”, Centro Universitario Contra el Cáncer, Universidad Autónoma de Nuevo León, Av. Francisco I. Madero S/N, Mitras Centro, Nuevo León 64460, Mexico; (M.L.G.-R.); (D.C.P.-I.); (O.V.-G.)
| | - Víctor Treviño
- Escuela de Medicina y Ciencias de la Salud, Tecnologico de Monterrey, Av. Morones Prieto 3000, Colonia Los Doctores, Nuevo León 64710, Mexico
- Correspondence:
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Della Fera AN, Warburton A, Coursey TL, Khurana S, McBride AA. Persistent Human Papillomavirus Infection. Viruses 2021; 13:v13020321. [PMID: 33672465 PMCID: PMC7923415 DOI: 10.3390/v13020321] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The success of HPV as an infectious agent lies not within its ability to cause disease, but rather in the adeptness of the virus to establish long-term persistent infection. The ability of HPV to replicate and maintain its genome in a stratified epithelium is contingent on the manipulation of many host pathways. HPVs must abrogate host anti-viral defense programs, perturb the balance of cellular proliferation and differentiation, and hijack DNA damage signaling and repair pathways to replicate viral DNA in a stratified epithelium. Together, these characteristics contribute to the ability of HPV to achieve long-term and persistent infection and to its evolutionary success as an infectious agent. Abstract Persistent infection with oncogenic human papillomavirus (HPV) types is responsible for ~5% of human cancers. The HPV infectious cycle can sustain long-term infection in stratified epithelia because viral DNA is maintained as low copy number extrachromosomal plasmids in the dividing basal cells of a lesion, while progeny viral genomes are amplified to large numbers in differentiated superficial cells. The viral E1 and E2 proteins initiate viral DNA replication and maintain and partition viral genomes, in concert with the cellular replication machinery. Additionally, the E5, E6, and E7 proteins are required to evade host immune responses and to produce a cellular environment that supports viral DNA replication. An unfortunate consequence of the manipulation of cellular proliferation and differentiation is that cells become at high risk for carcinogenesis.
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56
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Karapurkar JK, Antao AM, Kim KS, Ramakrishna S. CRISPR-Cas9 based genome editing for defective gene correction in humans and other mammals. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:185-229. [PMID: 34127194 DOI: 10.1016/bs.pmbts.2021.01.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR/Cas9), derived from bacterial and archean immune systems, has received much attention from the scientific community as a powerful, targeted gene editing tool. The CRISPR/Cas9 system enables a simple, relatively effortless and highly specific gene targeting strategy through temporary or permanent genome regulation or editing. This endonuclease has enabled gene correction by taking advantage of the endogenous homology directed repair (HDR) pathway to successfully target and correct disease-causing gene mutations. Numerous studies using CRISPR support the promise of efficient and simple genome manipulation, and the technique has been validated in in vivo and in vitro experiments, indicating its potential for efficient gene correction at any genomic loci. In this chapter, we detailed various strategies related to gene editing using the CRISPR/Cas9 system. We also outlined strategies to improve the efficiency of gene correction via the HDR pathway and to improve viral and non-viral mediated gene delivery methods, with an emphasis on their therapeutic potential for correcting genetic disorder in humans and other mammals.
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Affiliation(s)
| | - Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
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57
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Abstract
Human Papillomavirus (HPV) is the causative agent in the majority of anal, head and neck, oral, oropharyngeal, penile, vaginal, vulvar, and cervical cancers. Cervical cancer is the fourth most common cancer among women worldwide. Of all diagnosed human malignant neoplasms, approximately 4.5% are attributable to HPV, including cervical, anal cancers, vaginal, vulvar, penile, and oropharyngeal cancers. Over 182 HPV types have been identified and sequenced to date however, only certain types of HPV are more frequent in malignant lesions and considered to be a major risk factor in the development of some cancers. Because most HPV infections are transient, and an individual's immunocompetent may clear the infection, HPV infection has received little attention from clinicians, the general public, or policy makers. This lack of attention may underpin a deadly and increasing problem because each newly acquired infection has the potential to persist and become an incurable, lifelong affliction. In addition, no successful treatment of HPV infection currently exists despite the great strides toward understanding the mechanisms underlying HPV pathogenesis. Moreover, ample research has proven that the use of prophylactic vaccines, such as Gardasil and Cervarix, have led to documented progress in decreasing the burden of HPV infection, however not all countries introduced a government-funded National HPV Vaccination Program to protect young men and women. This chapter summarizes the HPV infection, detection and prevention. We also shed light on non-cervical HPV-related cancers, which is rapidly increasing in more developed countries toward cervical cancer.
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58
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Pinatti LM, Sinha HN, Brummel CV, Goudsmit CM, Geddes TJ, Wilson GD, Akervall JA, Brenner CJ, Walline HM, Carey TE. Association of human papillomavirus integration with better patient outcomes in oropharyngeal squamous cell carcinoma. Head Neck 2020; 43:544-557. [PMID: 33073473 DOI: 10.1002/hed.26501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The molecular drivers of human papillomavirus-related head and neck squamous cell carcinoma (HPV + HNSCC) are not entirely understood. This study evaluated the relationship between HPV integration, expression of E6/E7, and patient outcomes in p16+ HNSCCs. METHODS HPV type was determined by HPV PCR-MassArray, and integration was called using detection of integrated papillomavirus sequences polymerase chain reaction (PCR). We investigated whether fusion transcripts were produced by reverse transcriptase polymerase chain reaction (RT-PCR). E6/E7 expression was assessed by quantitative RT-PCR. We assessed if there was a relationship between integration and E6/E7 expression, clinical variables, or patient outcomes. RESULTS Most samples demonstrated HPV integration, which sometimes resulted in a fusion transcript. HPV integration was positively correlated with age at diagnosis and E6/E7 expression. There was a significant difference in survival between patients with vs without integration. CONCLUSIONS Contrary to previous reports, HPV integration was associated with improved patient survival. Therefore, HPV integration may act as a molecular marker of good prognosis.
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Affiliation(s)
- Lisa M Pinatti
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan, USA.,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Hana N Sinha
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Collin V Brummel
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine M Goudsmit
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | | | - George D Wilson
- Beaumont BioBank, Beaumont Hospital, Royal Oak, Michigan, USA.,Department of Radiation Oncology, Beaumont Hospital, Royal Oak, Michigan, USA
| | - Jan A Akervall
- Beaumont BioBank, Beaumont Hospital, Royal Oak, Michigan, USA.,Department of Otolaryngology, Saint Joseph Mercy Hospital, Ypsilanti, Michigan, USA
| | - Chad J Brenner
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Heather M Walline
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
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59
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Tian R, Zhou P, Li M, Tan J, Cui Z, Xu W, Wei J, Zhu J, Jin Z, Cao C, Fan W, Xie W, Huang Z, Xie H, You Z, Niu G, Wu C, Guo X, Weng X, Tian X, Yu F, Yu Z, Liang J, Hu Z. DeepHPV: a deep learning model to predict human papillomavirus integration sites. Brief Bioinform 2020; 22:5924410. [PMID: 33059369 DOI: 10.1093/bib/bbaa242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 01/09/2023] Open
Abstract
Human papillomavirus (HPV) integrating into human genome is the main cause of cervical carcinogenesis. HPV integration selection preference shows strong dependence on local genomic environment. Due to this theory, it is possible to predict HPV integration sites. However, a published bioinformatic tool is not available to date. Thus, we developed an attention-based deep learning model DeepHPV to predict HPV integration sites by learning environment features automatically. In total, 3608 known HPV integration sites were applied to train the model, and 584 reviewed HPV integration sites were used as the testing dataset. DeepHPV showed an area under the receiver-operating characteristic (AUROC) of 0.6336 and an area under the precision recall (AUPR) of 0.5670. Adding RepeatMasker and TCGA Pan Cancer peaks improved the model performance to 0.8464 and 0.8501 in AUROC and 0.7985 and 0.8106 in AUPR, respectively. Next, we tested these trained models on independent database VISDB and found the model adding TCGA Pan Cancer performed better (AUROC: 0.7175, AUPR: 0.6284) than the model adding RepeatMasker peaks (AUROC: 0.6102, AUPR: 0.5577). Moreover, we introduced attention mechanism in DeepHPV and enriched the transcription factor binding sites including BHLHA15, CHR, COUP-TFII, DMRTA2, E2A, HIC1, INR, NPAS, Nr5a2, RARa, SCL, Snail1, Sox10, Sox3, Sox4, Sox6, STAT6, Tbet, Tbx5, TEAD, Tgif2, ZNF189, ZNF416 near attention intensive sites. Together, DeepHPV is a robust and explainable deep learning model, providing new insights into HPV integration preference and mechanism. Availability: DeepHPV is available as an open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepHPV.git, Contact: huzheng1998@163.com, liangjiuxing@m.scnu.edu.cn, lizheyzy@163.com.
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Affiliation(s)
- Rui Tian
- Translational Medicine of the First Affiliated Hospital, Sun Yat-sen University
| | - Ping Zhou
- Dongguan Maternal and Child Health Care Hospital
| | - Mengyuan Li
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jinfeng Tan
- First Affiliated Hospital, Sun Yat-sen University
| | - Zifeng Cui
- First Affiliated Hospital, Sun Yat-sen University
| | - Wei Xu
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jingyue Wei
- Department of Obstetrics and Gynecology at the First Affiliated Hospital, Sun Yat-sen University
| | - Jingjing Zhu
- Department of Obstetrics and Gynecology of the First Affiliated Hospital, Sun Yat-sen University
| | - Zhuang Jin
- First Affiliated Hospital, Sun Yat-sen University
| | - Chen Cao
- Central Hospital of Wuhan, China
| | - Weiwen Fan
- College of Medicine at the Sun Yat-sen University
| | - Weiling Xie
- First Affiliated Hospital, Sun Yat-sen University
| | | | | | - Zeshan You
- First Affiliated Hospital, Sun Yat-sen University
| | - Gang Niu
- Department of Obstetrics and Gynecology of the First Affiliated Hospital, Sun Yat-sen University
| | - Canbiao Wu
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital at the First Affiliated Hospital, Sun Yat-sen University
| | - Xuchu Weng
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | | | - Fubing Yu
- Dongguan Maternal and Child Health Care Hospital
| | - Zhiying Yu
- Department of Gynecology, Shenzhen Second People's Hospital/the First Affiliated Hospital of Shenzhen University Health Science Center
| | - Jiuxing Liang
- Institute for Brain Research and Rehabilitation at the South China Normal University
| | - Zheng Hu
- Gynecological Oncology of the First Affiliated Hospital, Precision Medicine Institute, Sun Yat-sen University
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60
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Pinatti LM, Walline HM, Carey TE, Klussmann JP, Huebbers CU. Viral Integration Analysis Reveals Likely Common Clonal Origin of Bilateral HPV16-Positive, p16-Positive Tonsil Tumors. ACTA ACUST UNITED AC 2020; 4:680-696. [PMID: 32954225 PMCID: PMC7497862 DOI: 10.26502/acmcr.96550248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infections with high-risk human papilloma viruses (HPV) are responsible for a significant number of oropharyngeal squamous cell carcinoma (OPSCC), with infection rates currently rising at epidemic rates in the western world. Synchronous bilateral HPV+ tumors of both tonsils are a very rare event whose understanding, however, could provide important insights into virus-driven tumor development and progression and whether such integration events are of clonal origin. In this study we analyzed a single case of a bilateral tonsillar p16+ HPV+OPSCC. The viral integration status of the various tumor samples was determined by integration-specific PCR methods and sequencing, which identified viral insertion sites and affected host genes. Integration events were further confirmed by transcript analysis. Analysis of the tumors revealed common viral integration events involving the CD36 gene, as well as a unique event in the LAMA3 gene which resulted in loss of LAMA3 exon one in both tissues that had lost the complex viral LAMA3 integration event. In addition, there were several integration events into intergenic regions. This suggests a common origin but individual evolution of the tumors, supporting the single-clone hypothesis of bilateral tumor development. This hypothesis is further supported by the fact that the two cellular genes LAMA3 and CD36 as targets of viral integration are involved in cell migration and ECM-receptor interactions, which provides a possible mechanism for clonal migration from one tonsil to another.
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Affiliation(s)
- Lisa M. Pinatti
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Heather M. Walline
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Thomas E. Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Jens Peter Klussmann
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christian U. Huebbers
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
- Corresponding Author: Dr. Christian U. Huebbers, Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany, Tel: +49221478-97017; Fax +4922147897010;
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Lou H, Boland JF, Torres-Gonzalez E, Albanez A, Zhou W, Steinberg MK, Diaw L, Mitchell J, Roberson D, Cullen M, Garland L, Bass S, Burk RD, Yeager M, Wentzensen N, Schiffman M, Freites EA, Gharzouzi E, Mirabello L, Dean M. The D2 and D3 Sublineages of Human Papilloma Virus 16-Positive Cervical Cancer in Guatemala Differ in Integration Rate and Age of Diagnosis. Cancer Res 2020; 80:3803-3809. [PMID: 32631904 PMCID: PMC7501218 DOI: 10.1158/0008-5472.can-20-0029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/06/2020] [Accepted: 06/29/2020] [Indexed: 01/25/2023]
Abstract
Human papillomavirus (HPV) 16 displays substantial sequence variation; four HPV16 lineages (A, B, C, and D) have been described as well as multiple sublineages. To identify molecular events associated with HPV16 carcinogenesis, we evaluated viral variation, the integration of HPV16, and somatic mutation in 96 cervical cancer samples from Guatemala. A total of 65% (62/96) of the samples had integrated HPV16 sequences and integration was associated with an earlier age of diagnosis and premenopausal disease. HPV16 integration sites were broadly distributed in the genome, but in one tumor, HPV16 integrated into the promoter of the IFN regulatory factor 4 (IRF4) gene, which plays an important role in the regulation of the IFN response to viral infection. The HPV16 D2 and D3 sublineages were found in 23% and 30% of the tumors, respectively, and were significantly associated with adenocarcinoma. D2-positive tumors had a higher rate of integration, earlier age of diagnosis, and a lower rate of somatic mutation, whereas D3-positive tumors were less likely to integrate, had later age of diagnosis, and exhibited a higher rate of somatic mutation. In conclusion, Guatemalan cervical tumors have a high frequency of very high-risk HPV16 D2 and D3 sublineages harboring distinct histology, which may help guide future therapeutic strategies to target the tumor and reduce recurrence. SIGNIFICANCE: This study details the biological and molecular properties of the most pathogenic forms of HPV16, the cause of the majority of cervical cancers.
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Affiliation(s)
- Hong Lou
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Joseph F Boland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Edmundo Torres-Gonzalez
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland
| | | | - Weiyin Zhou
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Mia K Steinberg
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Lena Diaw
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland
| | - Jason Mitchell
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - David Roberson
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Michael Cullen
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Lisa Garland
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Sara Bass
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, New York
| | - Meredith Yeager
- Cancer Genetics Research Laboratory, Division of Cancer Epidemiology and Genetics, Leidos Biomedical Research Inc., National Laboratory for Cancer Research, Gaithersburg, Maryland
| | - Nicolas Wentzensen
- Laboratory of Cancer Genetics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland
| | - Mark Schiffman
- Laboratory of Cancer Genetics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland
| | - Enrique Alvirez Freites
- Hospital Central Universitario "Dr. Antonio M Pineda," Barquisimeto, Lara State, Venezuela
- Universidad Andina del Cusco, Vicerrectorado de Investigación, Division of Cancer Research, Cusco, Perú
| | | | - Lisa Mirabello
- Laboratory of Cancer Genetics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, NCI, Gaithersburg, Maryland.
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62
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Aguayo F, Muñoz JP, Perez-Dominguez F, Carrillo-Beltrán D, Oliva C, Calaf GM, Blanco R, Nuñez-Acurio D. High-Risk Human Papillomavirus and Tobacco Smoke Interactions in Epithelial Carcinogenesis. Cancers (Basel) 2020; 12:E2201. [PMID: 32781676 PMCID: PMC7465661 DOI: 10.3390/cancers12082201] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Cervical, anogenital, and some head and neck cancers (HNC) are etiologically associated with high-risk human papillomavirus (HR-HPV) infection, even though additional cofactors are necessary. Epidemiological studies have established that tobacco smoke (TS) is a cofactor for cervical carcinogenesis because women who smoke are more susceptible to cervical cancer when compared to non-smokers. Even though such a relationship has not been established in HPV-related HNC, a group of HPV positive patients with this malignancy are smokers. TS is a complex mixture of more than 4500 chemical compounds and approximately 60 of them show oncogenic properties such as benzo[α]pyrene (BaP) and nitrosamines, among others. Some of these compounds have been evaluated for carcinogenesis through experimental settings in collaboration with HR-HPV. Here, we conducted a comprehensive review of the suggested molecular mechanisms involved in cooperation with both HR-HPV and TS for epithelial carcinogenesis. Furthermore, we propose interaction models in which TS collaborates with HR-HPV to promote epithelial cancer initiation, promotion, and progression. More studies are warranted to clarify interactions between oncogenic viruses and chemical or physical environmental factors for epithelial carcinogenesis.
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Affiliation(s)
- Francisco Aguayo
- Universidad de Tarapacá, Arica 1000000, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Medicina, Universidad de Chile, Santiago 8330024, Chile
| | - Juan P. Muñoz
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (J.P.M.); (G.M.C.)
| | - Francisco Perez-Dominguez
- Laboratorio Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile; (F.P.-D.); (D.C.-B.); (C.O.); (R.B.); (D.N.-A.)
| | - Diego Carrillo-Beltrán
- Laboratorio Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile; (F.P.-D.); (D.C.-B.); (C.O.); (R.B.); (D.N.-A.)
| | - Carolina Oliva
- Laboratorio Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile; (F.P.-D.); (D.C.-B.); (C.O.); (R.B.); (D.N.-A.)
| | - Gloria M. Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile; (J.P.M.); (G.M.C.)
- Center for Radiological Research, Columbia University Medical Center, New York, NY 10032, USA
| | - Rances Blanco
- Laboratorio Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile; (F.P.-D.); (D.C.-B.); (C.O.); (R.B.); (D.N.-A.)
| | - Daniela Nuñez-Acurio
- Laboratorio Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile; (F.P.-D.); (D.C.-B.); (C.O.); (R.B.); (D.N.-A.)
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Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker JC, Grundhoff A, Fischer N. High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms. PLoS Pathog 2020; 16:e1008562. [PMID: 32833988 PMCID: PMC7470373 DOI: 10.1371/journal.ppat.1008562] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/03/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022] Open
Abstract
Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.
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Affiliation(s)
- Manja Czech-Sioli
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marlin Therre
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Spohn
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Juliane Theiss
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumorbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Corinna Wülbeck
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Irene Fernandez-Cuesta
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Franziska Esmek
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Jürgen C. Becker
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (AG); (NF)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (AG); (NF)
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64
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Giannuzzi D, Aresu L. A First NGS Investigation Suggests No Association Between Viruses and Canine Cancers. Front Vet Sci 2020; 7:365. [PMID: 32766289 PMCID: PMC7380080 DOI: 10.3389/fvets.2020.00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/26/2020] [Indexed: 12/16/2022] Open
Abstract
Approximately 10–15% of worldwide human cancers are attributable to viral infection. When operating as carcinogenic elements, viruses may act with various mechanisms, but the most important is represented by viral integration into the host genome, causing chromosome instability, genomic mutations, and aberrations. In canine species, few reports have described an association between viral integration and canine cancers, but more comprehensive studies are needed. The advancement of next-generation sequencing and the cost reduction have resulted in a progressive increasing of sequencing data in veterinary oncology offering an opportunity to study virome in canine cancers. In this study, we have performed viral detection and integration analyses using VirusFinder2 software tool on available whole-genome and whole-exome sequencing data of different canine cancers. Several viral sequences were detected in lymphomas, hemangiosarcomas, melanomas, and osteosarcomas, but no reliable integration sites were identified. Even if with some limitations such as the depth and type of sequencing, a restricted number of available nonhuman genomes software, and a limited knowledge on endogenous retroviruses in the canine genome, results are compelling. However, further experiments are needed, and similarly to feline species, dedicated analysis tools for the identification of viral integration sites in canine cancers are required.
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Affiliation(s)
- Diana Giannuzzi
- Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy
| | - Luca Aresu
- Department of Veterinary Science, University of Turin, Grugliasco, Italy
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Yang W, Liu Y, Dong R, Liu J, Lang J, Yang J, Wang W, Li J, Meng B, Tian G. Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. Front Genet 2020; 11:660. [PMID: 32714374 PMCID: PMC7344299 DOI: 10.3389/fgene.2020.00660] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
During the carcinogenesis of cervical cancer, the DNA of human papillomavirus (HPV) is frequently integrated into the human genome, which might be a biomarker for the early diagnosis of cervical cancer. Although the detection sensitivity of virus infection status increased significantly through the Illumina sequencing platform, there were still disadvantages remain for further improvement, including the detection accuracy and the complex integrated genome structure identification, etc. Nanopore sequencing has been proven to be a fast yet accurate technique of detecting pathogens in clinical samples with significant longer sequencing length. However, the identification of virus integration sites, especially HPV integration sites was seldom carried out by using nanopore platform. In this study, we evaluated the feasibility of identifying HPV integration sites by nanopore sequencer. Specifically, we re-sequenced the integration sites of a previously published sample by both nanopore and Illumina sequencing. After analyzing the results, three points of conclusions were drawn: first, 13 out of 19 previously published integration sites were found from all three datasets (i.e., nanopore, Illumina, and the published data), indicating a high overlap rate and comparability among the three platforms; second, our pipeline of nanopore and Illumina data identified 66 unique integration sites compared with previous published paper with 13 of them being verified by Sanger sequencing, indicating the higher integration sites detection sensitivity of our results compared with published data; third, we established a pipeline which could be used in HPV integration site detection by nanopore sequencing data without doing error correction analysis. In summary, a new nanopore data analysis method was tested and proved to be reliable in integration sites detection compared with methods of existing Illumina data analysis pipeline with less sequencing data required. It provides a solid evidence and tool to support the potential application of nanopore in virus status identification.
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Affiliation(s)
| | - Ying Liu
- Laboratory of Genetics, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | | | | | - Jingjing Li
- The Precision Medicine Centre of Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bo Meng
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
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Ishii T, Tamura A, Shibata T, Kuroda K, Kanda T, Sugiyama M, Mizokami M, Moriyama M. Analysis of HBV Genomes Integrated into the Genomes of Human Hepatoma PLC/PRF/5 Cells by HBV Sequence Capture-Based Next-Generation Sequencing. Genes (Basel) 2020; 11:genes11060661. [PMID: 32570699 PMCID: PMC7348787 DOI: 10.3390/genes11060661] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a leading cause of hepatocellular carcinoma (HCC) worldwide. The integration of HBV genomic DNA into the host genome occurs randomly, early after infection, and is associated with hepatocarcinogenesis in HBV-infected patients. Therefore, it is important to analyze HBV genome integration. We analyzed HBV genome integration in human hepatoma PLC/PRF/5 cells by HBV sequence capture-based next-generation sequencing (NGS) methods. We confirmed the results by using Sanger sequencing methods. We observed that HBV genotype A is integrated into the genome of PLC/PRF/5 cells. HBV sequence capture-based NGS is useful for the analysis of HBV genome integrants and their locations in the human genome. Among the HBV genome integrants, we performed functional analysis and demonstrated the automatic expression of some HBV proteins encoded by HBV integrants from chromosomes 3 and 11 in Huh7 cells transfected with these DNA sequences. HBV sequence capture-based NGS may be a useful tool for the assessment of HBV genome integration into the human genome in clinical samples and suggests new strategies for hepatocarcinogenesis in HBV infection.
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Affiliation(s)
- Tomotaka Ishii
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
| | - Akinori Tamura
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
| | - Toshikatsu Shibata
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
| | - Kazumichi Kuroda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
| | - Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
- Correspondence: ; Tel.: +81-3-3972-8111; Fax: +81-3-3956-8496
| | - Masaya Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan; (M.S.); (M.M.)
| | - Masashi Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa 272-8516, Japan; (M.S.); (M.M.)
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo 173-8610, Japan; (T.I.); (A.T.); (T.S.); (K.K.); (M.M.)
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67
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Cao C, Hong P, Huang X, Lin D, Cao G, Wang L, Feng B, Wu P, Shen H, Xu Q, Ren C, Meng Y, Zhi W, Yu R, Wei J, Ding W, Tian X, Zhang Q, Li W, Gao Q, Chen G, Li K, Sung WK, Hu Z, Wang H, Li G, Wu P. HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. J Genet Genomics 2020; 47:437-450. [PMID: 33023834 DOI: 10.1016/j.jgg.2020.05.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Integration of human papillomavirus (HPV) DNA into the human genome is a reputed key driver of cervical cancer. However, the effects of HPV integration on chromatin structural organization and gene expression are largely unknown. We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19. We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome, RNA, chromatin immunoprecipitation and high-throughput chromosome conformation capture (Hi-C) sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis. Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities, with correlation found between three-dimensional (3D) structural change and gene expression. Importantly, HPV integration divided one topologically associated domain (TAD) into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106, with a decrease in PEG3 expression and an increase in CCDC106 expression. This expression dysregulation was further confirmed using 10 samples from our cohort, which exhibited the same HPV-CCDC106 integration. In summary, we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling. Thus, this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.
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Affiliation(s)
- Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingyu Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liming Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bei Feng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Shen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ci Ren
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yifan Meng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenhua Zhi
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ruidi Yu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Juncheng Wei
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Wei Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qinglei Gao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Chen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kezhen Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China; Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Zheng Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Gynecological Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Peng Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Identification of Specific Tumor Markers in Vulvar Carcinoma Through Extensive Human Papillomavirus DNA Characterization Using Next Generation Sequencing Method. J Low Genit Tract Dis 2020; 24:53-60. [PMID: 31860576 DOI: 10.1097/lgt.0000000000000498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES A subset of vulvar carcinomas (VC) are associated with human papillomavirus (HPV) DNA. This trait can be used to identify tumor markers for patient's follow-up. A large diversity of HPV prevalence in VC has been reported, but no data are available concerning the insertional HPV status in this tumor type. Therefore, we have used an innovative next generation sequencing (NGS)-based CaptHPV method able to provide an extensive characterization of HPV DNA in tumors. MATERIAL AND METHODS Tumor tissue specimens from 55 patients with VC were analyzed using p16 immunohistochemistry, in situ hybridization, polymerase chain reaction, and CaptHPV-NGS assays. RESULTS Our analyses showed that 8 (14.5%) of 55 cases were associated with HPV 16 DNA. No other HPV genotypes were identified. The HPV genome was in a free episomal state only in one case and both episomal and integrated into the tumor cell genome in 7. There was a single insertion in 5 cases and multiple sites, scattered at different chromosomal loci in two. ISH data suggest that some of these might reflect tumor heterogeneity. Viral integration targeted cellular genes among which were TP63, CCDC148, LOC100133091, PKP1, and POLA2. Viral integration at the PKP1 locus was associated with partial gene deletion, and no PKP1 protein was detected in tumor tissue. CONCLUSIONS Using the NGS-based innovative capture-HPV approach, we established a cartography of HPV 16 DNA in 8 VC cases and identified novel genes targeted by integration that may be used as specific tumor markers. In addition, we established a rationale strategy for optimal characterization of HPV status in VC.
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Lekoane KMB, Kuupiel D, Mashamba-Thompson TP, Ginindza TG. The interplay of HIV and human papillomavirus-related cancers in sub-Saharan Africa: scoping review. Syst Rev 2020; 9:88. [PMID: 32321580 PMCID: PMC7178989 DOI: 10.1186/s13643-020-01354-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 04/08/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND People living with HIV (PLHIV) are at a high risk of developing HPV-related cancers. HPV-related malignancies occur frequently and/or are high among PLHIV, with cervical cancer as a designated AIDS-defining condition. We aimed to explore the evidence on the interplay of HIV and HPV-related cancers in sub-Saharan Africa (SSA). METHODS The scoping review was guided by Arksey and O'Malley's framework. We searched for literature from the following databases: PubMed; World Health Organization (WHO) Library; Science Direct; Google Scholar and EBSCOhost (Academic search complete, Health Source: Nursing/Academic Edition, CINAHL). Studies reporting on evidence HIV and HPV-related cancers interplay in SSA were eligible for inclusion in this review. The Mixed Methods Appraisal Tool (MMAT) tool was used to assess the risk of bias of the included studies. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) was used for reporting the search results. Thematic analysis used to reveal the emerging themes from the included studies. RESULTS A total of 74 potentially eligible articles were screened. Of these, nine (7 reviews, 1 transversal case controls, and 1 quantitative study) were eligible for data extraction. The studies reported about a total of 16,351 participants in different settings. The nine included studies showed evidence of cervical cancer among HIV-infected women and distribution of HPV infection and cervical abnormalities among HIV-positive individuals. In the four studies generalizing about HIV and anal cancer, only one reported about HPV. Two studies generally reported about HIV and head and neck cancers and one reported about interaction of HIV with vaginal cancer, vulvar cancer, and penile cancer, respectively. CONCLUSION HIV positivity is associated with increased prevalence of HPV infection on different anatomic sites, which will result in increased burden of HPV-related cancers among PLHIV. Furthermore, primary studies with robust study designs aimed at investigating the risk developing HPV-related cancers among PLHIV are recommended. Systematic review registration: PROSPERO CRD42017062403.
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Affiliation(s)
- Kabelo Matjie Bridget Lekoane
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Desmond Kuupiel
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa. .,Department of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa.
| | - Tivani P Mashamba-Thompson
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Themba G Ginindza
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
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Sample KM. DNA repair gene expression is associated with differential prognosis between HPV16 and HPV18 positive cervical cancer patients following radiation therapy. Sci Rep 2020; 10:2774. [PMID: 32066835 PMCID: PMC7026103 DOI: 10.1038/s41598-020-59383-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
Cervical cancers are almost always induced by HPV infections, of which HPV16 and HPV18 are predominant. Cancers associated with these strains are induced through DNA repair factors and have a differential response to radiation therapy. Hence this study focuses on finding DNA repair gene expression differences in HPV16 and HPV18 positive cervical cancers after radiation therapy. A higher number of somatic mutations were observed in HPV16 positive cervical tumours for patients that were disease free when compared to those who recurred/progressed. Moreover, hierarchal clustering of RNAseq data from The Cancer Genome Atlas was conducted to identify groups of DNA repair genes associated with a differential prognosis for cervical cancer following postoperative radiation therapy. TP53BP1, MCM9 (at higher than mean levels), POLR2F and SIRT6 (at lower than mean levels), were associated with an increase in patients experiencing cervical cancer recurrence/progression following postoperative radiation therapy when HPV18 positive, but not HPV16 positive. The expression patterns of these genes provide an explanation for the higher rate of postoperative radiation therapy resistance associated with HPV18 positive cervical cancer patients. Therefore, HPV18 positive cervical tumours may be more likely retain a greater non-homologous end joining and homologous recombination pathway activity, which could dampen the effect of postoperative radiation therapy. Moreover, greater susceptibility to postoperative radiation therapy could be caused by the reliance of cervical cancer cells upon the single-strand annealing and nucleotide excision pathways for repair of DNA damage.
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Affiliation(s)
- Klarke M Sample
- The National Health Commission's Key Laboratory of Immunological Pulmonary Disease, Guizhou Provincial People's Hospital, The Affiliated Hospital of Guizhou University, Guizhou, China.
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71
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Zhou C, Tuong ZK, Frazer IH. Papillomavirus Immune Evasion Strategies Target the Infected Cell and the Local Immune System. Front Oncol 2019; 9:682. [PMID: 31428574 PMCID: PMC6688195 DOI: 10.3389/fonc.2019.00682] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Persistent infection with human papillomavirus (HPV) initiates ~5% of all human cancers, and particularly cervical and oropharyngeal cancers. HPV vaccines prevent HPV infection, but do not eliminate existing HPV infections. Papillomaviruses induce hyperproliferation of epithelial cells. In this review we discuss how hyperproliferation renders epithelial cells less sensitive to immune attack, and impacts upon the efficiency of the local immune system. These observations have significance for the design of therapeutic HPV cancer immunotherapies.
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Affiliation(s)
- Chenhao Zhou
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Zewen Kelvin Tuong
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ian Hector Frazer
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
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72
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Lekoane KMB, Kuupiel D, Mashamba-Thompson TP, Ginindza TG. Evidence on the prevalence, incidence, mortality and trends of human papilloma virus-associated cancers in sub-Saharan Africa: systematic scoping review. BMC Cancer 2019; 19:563. [PMID: 31185951 PMCID: PMC6558783 DOI: 10.1186/s12885-019-5781-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/31/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human papilloma virus (HPV) associated cervical cancer remains a global concern particular, in Sub-Saharan Africa (SSA) where the impact is felt most. Evidence show that many other cancers such as vaginal, anal, oropharyngeal, penile are because of persistent infection with HPV especially, high-risk types. AIM We mapped evidence on the incidence, prevalence, mortality, and the trends of human papillomavirus-related cancers in SSA. METHODS A comprehensive literature search was conducted from several databases including PubMed, Google scholar, Science Direct, and CINAHL and MEDLINE via EBSCOhost as well as World Health Organization website for grey literature. Studies reporting HPV-related cancers in SSA outcomes including prevalence, incidence, mortality, and trends were included in this study. The risk of bias of the included studies were assessed using the mixed methods appraisal tool version 2011. We employed PRISMA (preferred reporting items for systematic reviews and meta-analyses) to report the search results. Thematic analysis used to reveal the emerging themes from the included studies. RESULTS Seventy-four (74) studies were retrieved at full article screening, eight of them (six reviews, and two quantitative study) were eligible for data extraction. The degree of agreement between the two independent reviewers following full article screening, was 86.49% agreement versus 64.57% likely by chance which constituted moderate to significant agreement (Kappa statistic = 0.62, p-value< 0.05). Of the eight included studies, four (50%) studies generalized about SSA with no country of interest; two (25%) studies were conducted in Nigeria; one (12.5%) reported about Uganda, Zambia, Guinea, Malawi Tanzania, Mali, Mozambique, Zimbabwe; and one (12.5%) reported about Ethiopia, Senegal, Zimbabwe and Uganda. These eight included studies reported evidence on more than one outcome of interest. Four studies reported about the prevalence of HPV-related cancers, seven studies reported about the incidence, four studies reported about mortality, and four studies reported about the trends of HPV-related cancers. CONCLUSION This study observation highlighted a gap of knowledge regarding the epidemiological data on the recent HPV prevalence in SSA, which will have a potential impact in determining the distribution of HPV on different body sites (cervix, penis, vagina, vulva, anus and oropharynx). Ongoing research projects are recommended in SSA to enhance the value of HPV, and HPV-associated cancers epidemiological data to inform strategies or/and policies on prevention, diagnosis, and treatment of HPV-related conditions.
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Affiliation(s)
- Kabelo M. B. Lekoane
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, 2nd Floor George Campbell Building, Howard College Campus, Durban, 4001 South Africa
| | - Desmond Kuupiel
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, 2nd Floor George Campbell Building, Howard College Campus, Durban, 4001 South Africa
- Research for Sustainable Development, Sunyani, Ghana
| | - Tivani P. Mashamba-Thompson
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, 2nd Floor George Campbell Building, Howard College Campus, Durban, 4001 South Africa
| | - Themba G. Ginindza
- Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Natal, 2nd Floor George Campbell Building, Howard College Campus, Durban, 4001 South Africa
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Schiffman M, de Sanjose S. False positive cervical HPV screening test results. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2019; 7:184-187. [PMID: 31029852 PMCID: PMC6514435 DOI: 10.1016/j.pvr.2019.04.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/13/2019] [Accepted: 04/24/2019] [Indexed: 11/22/2022]
Abstract
In cervical cancer screening, HPV testing is best at reassuring women when they are negative, but proper management of HPV positives is still evolving. Most HPV infections are benign, and over-reacting clinically to HPV positivity can cause psychological and possible iatrogenic physical (e.g., obstetrical) harm. We describe the built-in false positives in current tests, and the real harm that can result when the meaning of such false positive HPV tests is misunderstood. We suggest steps that could reduce harm being done by flawed tests and excessive clinical responses to positive HPV testing. We focus the discussion by presenting an illustrative case.
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Affiliation(s)
- Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, US National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Silvia de Sanjose
- Sexual and Reproductive Health Program, PATH, Seattle, 98121, USA; Ciber Epidemiologia y Salud Publica, Barcelona, Spain.
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Reder H, Wagner S, Gamerdinger U, Sandmann S, Wuerdemann N, Braeuninger A, Dugas M, Gattenloehner S, Klussmann JP, Wittekindt C. Genetic alterations in human papillomavirus-associated oropharyngeal squamous cell carcinoma of patients with treatment failure. Oral Oncol 2019; 93:59-65. [PMID: 31109697 DOI: 10.1016/j.oraloncology.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/15/2019] [Accepted: 04/22/2019] [Indexed: 01/15/2023]
Abstract
OBJECTIVES Despite improved survival rates of patients with HPV-associated OPSCC, a subset has distant metastasis or develops local recurrence during follow-up. To investigate potential underlying genetic alterations, we analyzed patients with HPV-driven OPSCC who suffered from recurrence in comparison to matching pairs with successful tumor control. MATERIALS AND METHODS We performed chromosomal copy number analyses and targeted next generation sequencing using a custom panel comprising genes that are frequently mutated in HPV-associated OPSCC. RESULTS Specific differences regarding chromosomal aberrations were not observed between both groups. In HPV-driven OPSCC from patients with recurrence we found higher mutation rates compared to patients with successful tumor control. Especially mutation rates of HRAS (p ≤ 0.05) PIK3R1, STK11 and TP63 (p ≤ 0.1 each) were statistically significant or trending towards significance. The respective genes can be linked to transcription factors and signaling pathways involved in cell cycle regulation, proliferation and survival. Additionally, combinations of alterations were observed on chromosomes 16 and 19, which might also influence outcome. CONCLUSION Patients with HPV-driven OPSCC who develop recurrence or have metastasis may be defined by genetic alterations that might be responsible for poor outcome after standard therapy. This might be of importance for stratification in future de-escalation and targeted therapy.
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Affiliation(s)
- Henrike Reder
- Department of Otorhinolaryngology, Head and Neck Surgery, Justus-Liebig University Giessen, 35392 Giessen, Germany.
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Ulrike Gamerdinger
- Department of Pathology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, Westphalian Wilhelms University Muenster, 48149 Muenster, Germany
| | - Nora Wuerdemann
- Department of Otorhinolaryngology, Head and Neck Surgery, Justus-Liebig University Giessen, 35392 Giessen, Germany; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, 50931 Cologne, Germany
| | - Andreas Braeuninger
- Department of Pathology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Martin Dugas
- Institute of Medical Informatics, Westphalian Wilhelms University Muenster, 48149 Muenster, Germany
| | - Stefan Gattenloehner
- Department of Pathology, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Justus-Liebig University Giessen, 35392 Giessen, Germany; Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, 50931 Cologne, Germany
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, Justus-Liebig University Giessen, 35392 Giessen, Germany
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Harlé A, Guillet J, Thomas J, Demange J, Dolivet G, Peiffert D, Leroux A, Sastre-Garau X. HPV insertional pattern as a personalized tumor marker for the optimized tumor diagnosis and follow-up of patients with HPV-associated carcinomas: a case report. BMC Cancer 2019; 19:277. [PMID: 30922253 PMCID: PMC6437879 DOI: 10.1186/s12885-019-5447-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 03/07/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND In clinical oncology, only a few applications have been developed using HPV as a personalized tumor marker, a lack most probably related to the limited information obtained by the classical Polymerase Chain Reaction (PCR) approach. To overcome this limitation, we have recently developed the capture-based Next-Generation Sequencing (NGS) "CaptHPV" assay, designed to provide an extensive and comprehensive molecular characterization of HPV DNA sequences associated with neoplasias, ie the sequence of the viral genome (245 genotypes), its physical state, viral load, integration site and genomic alterations at integration locus. These data correspond to highly specific tumor markers that can be used to improve diagnosis and patient's follow-up. CASE PRESENTATION We report here a case that is a straightforward and practical illustration of the power of the CaptHPV method. A patient developed successively a carcinoma of the anal canal and of the tongue. The two tumors were squamous cell carcinoma, found associated with HPV16 using PCR. In order to document a possible metastasis to the tongue from the anal cancer, we performed CaptHPV analysis on the two tumors. The analysis of the anal carcinoma found 55 viral/human hybrid reads allowing the identification of the HPV16 DNA integration in the 4q25 chromosomal band locus with a 178,808 bp deletion in the cell genome. Molecular analysis of the tongue tumor disclosed 6110 reads of HPV16, with a viral pattern strictly identical to that of the anal tumor. A total of 131 hybrid reads between HPV16 and the cell genome were found, corresponding exactly to the same locus of integration of viral DNA at the 4q25 site. The 178,808 bp genomic deletion was also found in the lingual tumor. The exact identity of HPV insertional signatures in the two tumors, demonstrates unambiguously that the tongue tumor derived from the anal cancer whereas neither histological immunophenotyping nor classical viral analysis using PCR could allow a definitive diagnosis. CONCLUSION Our observation indicates that the establishment of a detailed cartography of HPV DNA sequences in a tumor specimen provides crucial information for the design of specific biomarkers that can be used for diagnostic, prognostic or predictive purposes.
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Affiliation(s)
- Alexandre Harlé
- Université de Lorraine, Nancy, France
- CNRS, UMR, 7039 CRAN, Nancy, France
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Julie Guillet
- Université de Lorraine, Nancy, France
- CNRS, UMR, 7039 CRAN, Nancy, France
- Département de chirurgie oncologique, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jacques Thomas
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Jessica Demange
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Gilles Dolivet
- CNRS, UMR, 7039 CRAN, Nancy, France
- Département de chirurgie oncologique, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Didier Peiffert
- Université de Lorraine, Nancy, France
- Département de radiothérapie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Agnès Leroux
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Xavier Sastre-Garau
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-lès-Nancy, France
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Abstract
The inactivation of critical cell cycle checkpoints by the human papillomavirus (HPV) oncoprotein E7 results in replication stress (RS) that leads to genomic instability in premalignant lesions. Intriguingly, RS tolerance is achieved through several mechanisms, enabling HPV to exploit the cellular RS response for viral replication and to facilitate viral persistence in the presence of DNA damage. As such, inhibitors of the RS response pathway may provide a novel approach to target HPV-associated lesions and cancers.
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77
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Gorphe P, Chekkoury Idrissi Y, Tao Y, Moya-Plana A, Casiraghi O, Janot F, Blanchard P, Mirghani H, Temam S. Smoking and papillomavirus DNA in patients with p16-positive N3 oropharyngeal squamous cell carcinoma. Head Neck 2018; 41:1039-1045. [PMID: 30552841 DOI: 10.1002/hed.25523] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 08/20/2018] [Accepted: 10/05/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND We investigated the survival of patients with a p16-positive N3 oropharyngeal squamous cell carcinoma (OPSCC) and the prognostic significance of patient, tumor, and treatment characteristics. METHODS We retrospectively reviewed the data of patients treated at our Cancer Center for a p16-positive N3 OPSCC between 2003 and 2016. End points were overall survival (OS) and progression-free survival (PFS). RESULTS A total of 29 patients were included. The 5-year OS and PFS were 67.5% and 59.1%, respectively. Smoking history above 10 pack-years and the absence of human papillomavirus DNA were associated with worse OS (P = .02 and P = .03, respectively) and PFS (P = .02 and P = .02, respectively). Induction chemotherapy or radical neck dissection were not associated with different treatment outcomes. CONCLUSION Patients with an N3 p16-positive oropharyngeal cancer in our series had a 5-year OS rate of 67.5%. Smoking history and viral DNA were prognostic factors associated with survival.
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Affiliation(s)
- Philippe Gorphe
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Younes Chekkoury Idrissi
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Yungan Tao
- Department of Radiotherapy, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Antoine Moya-Plana
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Odile Casiraghi
- Department of Pathology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - François Janot
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Pierre Blanchard
- Department of Radiotherapy, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Haïtham Mirghani
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Stéphane Temam
- Department of Head and Neck Oncology, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
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Guerrero Flórez M, Guerrero Gómez OA, Mena Huertas J, Yépez Chamorro MC. Mapping of microRNAs related to cervical cancer in Latin American human genomic variants. F1000Res 2018; 6:946. [PMID: 37766816 PMCID: PMC10521080 DOI: 10.12688/f1000research.10138.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 09/29/2023] Open
Abstract
Background: MicroRNAs are related to human cancers, including cervical cancer (CC) caused by HPV. In 2018, approximately 56.075 cases and 28.252 deaths from this cancer were registered in Latin America and the Caribbean according to GLOBOCAN reports. The main molecular mechanism of HPV in CC is related to integration of viral DNA into the hosts' genome. However, the different variants in the human genome can result in different integration mechanisms, specifically involving microRNAs (miRNAs). Methods: The miRNAs associated with CC were obtained from literature, the miRNA sequences and four human genome variants (HGV) from Latin American populations were obtained from miRBase and 1000 Genomes Browser, respectively. HPV integration sites near cell cycle regulatory genes were identified. miRNAs were mapped on HGV. miRSNPs were identified in the miRNA sequences located at HPV integration sites on the Latin American HGV. Results: Two hundred seventy-two miRNAs associated with CC were identified in 139 reports from different geographic locations. By mapping with Blast-Like Alignment Tool (BLAT), 2028 binding sites were identified from these miRNAs on the human genome (version GRCh38/hg38); 42 miRNAs were located on unique integration sites; and miR-5095, miR-548c-5p and miR-548d-5p were involved with multiple genes related to the cell cycle. Thirty-seven miRNAs were mapped on the Latin American HGV (PUR, MXL, CLM and PEL), but only miR-11-3p, miR-31-3p, miR-107, miR-133a-3p, miR-133a-5p, miR-133b, miR-215-5p, miR-491-3p, miR-548d-5p and miR-944 were conserved. Conclusions: Ten miRNAs were conserved in the four HGV. In the remaining 27 miRNAs, substitutions, deletions or insertions were observed. These variation patterns can imply differentiated mechanisms towards each genomic variant in human populations because of specific genomic patterns and geographic features. These findings may help in determining susceptibility for CC development. Further identification of cellular genes and signalling pathways involved in CC progression could lead new therapeutic strategies based on miRNAs.
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Affiliation(s)
- Milena Guerrero Flórez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Olivia Alexandra Guerrero Gómez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Jaqueline Mena Huertas
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - María Clara Yépez Chamorro
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
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79
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Jeannot E, Harlé A, Holmes A, Sastre-Garau X. Nuclear factor I X is a recurrent target for HPV16 insertions in anal carcinomas. Genes Chromosomes Cancer 2018; 57:638-644. [PMID: 30264502 DOI: 10.1002/gcc.22675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/25/2022] Open
Abstract
Anal carcinomas (AC) are associated with human papillomavirus (HPV) DNA sequences, but little is known about the physical state of the viral genome in carcinoma cells. To define the integration status and gene(s) targeted by viral insertions in AC, tumor DNAs extracted from 35 tumor specimen samples in patients with HPV16-associated invasive carcinoma were analyzed using the detection of integrated papillomavirus sequences-PCR approach. The genomic status at integration sites was assessed using comparative genomic hybridization-array assay and gene expression using reverse transcription quantitative PCR (RT-qPCR). HPV16 DNA was found integrated in 25/35 (71%) cases and the integration locus could be determined at the molecular level in 19 cases (29 total integration loci). HPV DNA was inserted on different chromosomes, but 5 cases harbored viral sequences at 19p13.2, within the nuclear factor I X (NFIX) locus. Viral DNA mapped between the most distal and the two proximal alternatively expressed exons of this gene in three cases (CA21, CA04, and CA35) and upstream of this gene (663 kb and 2.3 Mb) in the others. CGH arrays showed genomic gains/amplifications at the NFIX region, associated with HPV within the gene and RT-qPCR, revealed NFIX mRNA overexpression. Other genes targeted by integration were IL20RB, RPS6KA2, MSRA1, PIP5K1B, SLX4IP, CECR1, BCAR3, ATF6, CSNK1G1, APBA2, AGK, ILF3, PVT1, TRMT1, RAD51B, FASN, CCDC57, DSG3, and ZNF563. We identified recurrent targeting of NFIX by HPV16 insertion in anal carcinomas, supporting a role for this gene in oncogenesis, as reported for non-HPV tumors.
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Affiliation(s)
- Emmanuelle Jeannot
- Department of Theranostic and Diagnostic Medicine, Institut Curie, PSL Research University, Paris, Saint-Cloud, France
| | - Alexandre Harlé
- Université de Lorraine, Nancy, France.,CNRS UMR 7039 CRAN, Vandoeuvre-Lès-Nancy, France.,Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
| | - Allyson Holmes
- Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Institut Curie, PSL Research University, Paris, France
| | - Xavier Sastre-Garau
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Vandoeuvre-Lès-Nancy, France
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80
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Carrillo D, Muñoz JP, Huerta H, Leal G, Corvalán A, León O, Calaf GM, Urzúa U, Boccardo E, Tapia JC, Aguayo F. Upregulation of PIR gene expression induced by human papillomavirus E6 and E7 in epithelial oral and cervical cells. Open Biol 2018; 7:rsob.170111. [PMID: 29118270 PMCID: PMC5717337 DOI: 10.1098/rsob.170111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/05/2017] [Indexed: 12/18/2022] Open
Abstract
The hallmark of high-risk human papillomavirus (HR-HPV)-related carcinogenesis is E6 and E7 oncogene overexpression. The aim of this work was to characterize epithelial oral and cervical cancer cells that express HR-HPV E6 and E7 oncoproteins. Transcriptomic assay using DNA microarrays revealed that PIR gene expression was detected in oral cells in an HR-HPV E6/E7-dependent manner. In addition, PIR was overexpressed in HPV-positive SiHa and Ca Ski cells, whereas it was undetectable in HPV-negative C33A cells. The PIR expression was dependent on functional HR-HPV E6 and E7 oncoproteins even though the E7 oncoprotein had higher activity to induce PIR overexpression in comparison with E6. In addition, using an siRNA for PIR silencing in oral cells ectopically expressing HR-HPV E6/E7, there was a significant increase in E-cadherin transcripts and a decrease in Vimentin, Slug, Zeb and Snail transcripts, suggesting that HR-HPV-induced PIR overexpression is involved in epithelial–mesenchymal transition. Furthermore, migration of PIR-silenced cells was significantly decreased. Finally, using inhibitors of some specific pathways, it was found that EGFR/ERK and PI3 K/AKT signalling pathways are important for E7-mediated PIR overexpression. It can be concluded that PIR gene expression is highly dependent on the expression of HR-HPV oncoproteins and is important for EMT regulation.
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Affiliation(s)
- Diego Carrillo
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Juan P Muñoz
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Hernán Huerta
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Gabriel Leal
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Alejandro Corvalán
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile.,UC-Center for Investigational Oncology (CITO), Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Oscar León
- Virology Program, Instituto de Ciencias Biomédicas (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Gloria M Calaf
- Center for Advanced Research, Tarapaca University, Arica, Chile.,Center for Radiological Research, Columbia University Medical Center, New York, NY, USA
| | - Ulises Urzúa
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Enrique Boccardo
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Julio C Tapia
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile
| | - Francisco Aguayo
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Independencia 1027, PO 8389100, Santiago, Chile .,Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile, Santiago, Chile
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81
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Characteristic of HPV Integration in the Genome and Transcriptome of Cervical Cancer Tissues. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6242173. [PMID: 30018982 PMCID: PMC6029443 DOI: 10.1155/2018/6242173] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/29/2018] [Accepted: 05/09/2018] [Indexed: 01/22/2023]
Abstract
High-risk HPV is clearly associated with cervical cancer. HPV integration has been confirmed to promote carcinogenesis in the previous studies. In our study, a total of 285 DNA breakpoints and 287 RNA breakpoints were collected. We analyzed the characteristic of HPV integration in the DNA and RNA samples. The results revealed that the patterns of HPV integration in RNA and DNA samples differ significantly. FHIT, KLF5, and LINC00392 were the hotspot genes integrated by HPV in the DNA samples. RAD51B, CASC8, CASC21, ERBB2, TP63, TEX41, RAP2B, and MYC were the hotspot genes integrated by HPV in RNA samples. Breakpoints of DNA samples were significantly prone to the region of INTRON (P < 0.01, Chi-squared test), whereas in the RNA samples, the breakpoints were prone to EXON. Pathway analysis had revealed that the breakpoints of RNA samples were enriched in the pathways of transcriptional misregulation in cancer, cancer pathway, and pathway of adherens junction. Breakpoints of DNA samples were enriched in the pathway of cholinergic synapse. In summary, our data helped to gain insights into the HPV integration sites in DNA and RNA samples of cervical cancer. It had provided theoretical basis for understanding the mechanism of tumorigenesis from the perspective of HPV integration in the HPV-associated cervical cancers.
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82
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Tang KW, Larsson E. Tumour virology in the era of high-throughput genomics. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0265. [PMID: 28893932 PMCID: PMC5597732 DOI: 10.1098/rstb.2016.0265] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
With the advent of massively parallel sequencing, oncogenic viruses in tumours can now be detected in an unbiased and comprehensive manner. Additionally, new viruses or strains can be discovered based on sequence similarity with known viruses. Using this approach, the causative agent for Merkel cell carcinoma was identified. Subsequent studies using data from large collections of tumours have confirmed models built during decades of hypothesis-driven and low-throughput research, and a more detailed and comprehensive description of virus-tumour associations have emerged. Notably, large cohorts and high sequencing depth, in combination with newly developed bioinformatical techniques, have made it possible to rule out several suggested virus-tumour associations with a high degree of confidence. In this review we discuss possibilities, limitations and insights gained from using massively parallel sequencing to characterize tumours with viral content, with emphasis on detection of viral sequences and genomic integration events.This article is part of the themed issue 'Human oncogenic viruses'.
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Affiliation(s)
- Ka-Wei Tang
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
| | - Erik Larsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9A, 405 30 Gothenburg, Sweden
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83
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Groves IJ, Coleman N. Human papillomavirus genome integration in squamous carcinogenesis: what have next-generation sequencing studies taught us? J Pathol 2018; 245:9-18. [PMID: 29443391 DOI: 10.1002/path.5058] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 02/01/2018] [Accepted: 02/06/2018] [Indexed: 12/31/2022]
Abstract
Human papillomavirus (HPV) infection is associated with ∼5% of all human cancers, including a range of squamous cell carcinomas. Persistent infection by high-risk HPVs (HRHPVs) is associated with the integration of virus genomes (which are usually stably maintained as extrachromosomal episomes) into host chromosomes. Although HRHPV integration rates differ across human sites of infection, this process appears to be an important event in HPV-associated neoplastic progression, leading to deregulation of virus oncogene expression, host gene expression modulation, and further genomic instability. However, the mechanisms by which HRHPV integration occur and by which the subsequent gene expression changes take place are incompletely understood. The advent of next-generation sequencing (NGS) of both RNA and DNA has allowed powerful interrogation of the association of HRHPVs with human disease, including precise determination of the sites of integration and the genomic rearrangements at integration loci. In turn, these data have indicated that integration occurs through two main mechanisms: looping integration and direct insertion. Improved understanding of integration sites is allowing further investigation of the factors that provide a competitive advantage to some integrants during disease progression. Furthermore, advanced approaches to the generation of genome-wide samples have given novel insights into the three-dimensional interactions within the nucleus, which could act as another layer of epigenetic control of both virus and host transcription. It is hoped that further advances in NGS techniques and analysis will not only allow the examination of further unanswered questions regarding HPV infection, but also direct new approaches to treating HPV-associated human disease. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Ian J Groves
- Department of Pathology, University of Cambridge, Cambridge, UK
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84
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Karbalaie Niya MH, Keyvani H, Safarnezhad Tameshkel F, Salehi-Vaziri M, Teaghinezhad-S S, Bokharaei Salim F, Monavari SHR, Javanmard D. Human Papillomavirus Type 16 Integration Analysis by Real-time PCR Assay in Associated Cancers. Transl Oncol 2018; 11:593-598. [PMID: 29547758 PMCID: PMC5854915 DOI: 10.1016/j.tranon.2018.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
Human papillomavirus (HPV) is a common viral infection worldwide associated with a variety of cancers. The integration of the HPV genome in these patients causes chromosomal instability and triggers carcinogenesis. The aim of this study was to investigate the HPV-16 genome physical status in four major cancers related to HPV infection. Formalin-fixed paraffin-embedded blocks from our previous projects on head and neck, colorectal, penile, and cervical cancers were collected, and HPV-16–positive specimens were used for further analysis. The DNA extraction copy number of E2 and E7 genes was calculated by qualitative real-time PCR method. Serially diluted standards that were cloned in PUC57 plasmid were used. Standard curve and melting curve analysis was used for quantification. Of the 672 specimens studied, 76 (11.3%) were HPV-16 positive. We found that 35.6% (16/45) were integrated. Statistical analysis showed that there were significant correlations between integration of HPV-16 and cervical cancer end-stage carcinogenesis (P < .0001), episomal form, and ASCUS lesions (P = .045). Significant correlation in penile cancer patients was seen between the episomal form and high-grade cancer stage (P = .037). Integration is a major factor in the carcinogenesis mechanism of HPV and has different prevalence in various cancers with a higher rate in progression except in penile cancer.
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Affiliation(s)
| | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran; Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | | | - Mostafa Salehi-Vaziri
- Research Centre for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran; Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran
| | - Sedigheh Teaghinezhad-S
- Department of Microbiology, Faculty of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Farah Bokharaei Salim
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran; HIV Laboratory of National Center, Deputy of Health, Iran University of Medical Sciences, Tehran, Iran
| | | | - Davod Javanmard
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
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85
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Mirabello L, Clarke MA, Nelson CW, Dean M, Wentzensen N, Yeager M, Cullen M, Boland JF, Schiffman M, Burk RD. The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis. Viruses 2018; 10:v10020080. [PMID: 29438321 PMCID: PMC5850387 DOI: 10.3390/v10020080] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/24/2018] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Of the ~60 human papillomavirus (HPV) genotypes that infect the cervicovaginal epithelium, only 12–13 “high-risk” types are well-established as causing cervical cancer, with HPV16 accounting for over half of all cases worldwide. While HPV16 is the most important carcinogenic type, variants of HPV16 can differ in their carcinogenicity by 10-fold or more in epidemiologic studies. Strong genotype-phenotype associations embedded in the small 8-kb HPV16 genome motivate molecular studies to understand the underlying molecular mechanisms. Understanding the mechanisms of HPV genomic findings is complicated by the linkage of HPV genome variants. A panel of experts in various disciplines gathered on 21 November 2016 to discuss the interdisciplinary science of HPV oncogenesis. Here, we summarize the discussion of the complexity of the viral–host interaction and highlight important next steps for selected applied basic laboratory studies guided by epidemiological genomic findings.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Correspondence: (L.M.); (R.D.B.)
| | - Megan A. Clarke
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Chase W. Nelson
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: (L.M.); (R.D.B.)
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86
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Warburton A, Redmond CJ, Dooley KE, Fu H, Gillison ML, Akagi K, Symer DE, Aladjem MI, McBride AA. HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression. PLoS Genet 2018; 14:e1007179. [PMID: 29364907 PMCID: PMC5798845 DOI: 10.1371/journal.pgen.1007179] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 02/05/2018] [Accepted: 01/01/2018] [Indexed: 12/12/2022] Open
Abstract
Integration of human papillomavirus (HPV) genomes into cellular chromatin is common in HPV-associated cancers. Integration is random, and each site is unique depending on how and where the virus integrates. We recently showed that tandemly integrated HPV16 could result in the formation of a super-enhancer-like element that drives transcription of the viral oncogenes. Here, we characterize the chromatin landscape and genomic architecture of this integration locus to elucidate the mechanisms that promoted de novo super-enhancer formation. Using next-generation sequencing and molecular combing/fiber-FISH, we show that ~26 copies of HPV16 are integrated into an intergenic region of chromosome 2p23.2, interspersed with 25 kb of amplified, flanking cellular DNA. This interspersed, co-amplified viral-host pattern is frequent in HPV-associated cancers and here we designate it as Type III integration. An abundant viral-cellular fusion transcript encoding the viral E6/E7 oncogenes is expressed from the integration locus and the chromatin encompassing both the viral enhancer and a region in the adjacent amplified cellular sequences is strongly enriched in the super-enhancer markers H3K27ac and Brd4. Notably, the peak in the amplified cellular sequence corresponds to an epithelial-cell-type specific enhancer. Thus, HPV16 integration generated a super-enhancer-like element composed of tandem interspersed copies of the viral upstream regulatory region and a cellular enhancer, to drive high levels of oncogene expression.
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Affiliation(s)
- Alix Warburton
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Catherine J. Redmond
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katharine E. Dooley
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Haiqing Fu
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Maura L. Gillison
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Keiko Akagi
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - David E. Symer
- Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
- Human Cancer Genetics Program, Department of Cancer Biology and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
- Department of Biomedical Informatics (adjunct), The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, United States of America
| | - Mirit I. Aladjem
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Racial/ethnic differences in HPV 16/18 genotypes and integration status among women with a history of cytological abnormalities. Gynecol Oncol 2017; 148:357-362. [PMID: 29276057 DOI: 10.1016/j.ygyno.2017.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVE HPV genotype distribution varies by race/ethnicity, but is unclear whether there are racial/ethnic variations in HPV 16/18 integration in the host genome. We describe HPV16/18 infection and integration status in a racially/ethnically diverse sample of women with a recent abnormal Pap test. METHODS Patients (n=640) represent a subset of women participating in a clinical trial. Cervical swabs were tested for HPV16/18 DNA using type-specific polymerase chain reaction assays. Viral integration status was assessed using type-specific integration assays and categorized as fully integrated, fully non-integrated, or mixed. Unconditional logistic regression was used to generate unadjusted (OR) and adjusted odds ratios (aOR) to assess the association between self-reported race/ethnicity and risk of these outcomes. RESULTS Hispanic and non-Hispanic black women had half the odds of prevalent HPV16 compared to non-Hispanic white women (aORs: 0.43 and 0.45, respectively). The prevalence odds of HPV18 was less than half among Hispanic women (aOR: 0.48), but not significantly different between black and white women (aOR: 0.72). Among women with prevalent HPV16, the odds of fully integrated viral DNA were significantly higher among black women (aORs: 2.78) and marginally higher among Hispanic women (aOR: 1.93). No racial/ethnic differences were observed for HPV18 DNA integration. CONCLUSIONS While HPV16 and 18 infections were less prevalent among Hispanic and black women compared to whites, their HPV16 DNA was more likely to be present in a fully integrated state. This could potentially contribute to the higher rates of abnormal cytology and cervical dysplasia observed among Hispanic and black women.
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88
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Pinatti LM, Walline HM, Carey TE. Human Papillomavirus Genome Integration and Head and Neck Cancer. J Dent Res 2017; 97:691-700. [PMID: 29227715 DOI: 10.1177/0022034517744213] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We conducted a critical review of human papillomavirus (HPV) integration into the host genome in oral/oropharyngeal cancer, reviewed the literature for HPV-induced cancers, and obtained current data for HPV-related oral and oropharyngeal cancers. In addition, we performed studies to identify HPV integration sites and the relationship of integration to viral-host fusion transcripts and whether integration is required for HPV-associated oncogenesis. Viral integration of HPV into the host genome is not required for the viral life cycle and might not be necessary for cellular transformation, yet HPV integration is frequently reported in cervical and head and neck cancer specimens. Studies of large numbers of early cervical lesions revealed frequent viral integration into gene-poor regions of the host genome with comparatively rare integration into cellular genes, suggesting that integration is a stochastic event and that site of integration may be largely a function of chance. However, more recent studies of head and neck squamous cell carcinomas (HNSCCs) suggest that integration may represent an additional oncogenic mechanism through direct effects on cancer-related gene expression and generation of hybrid viral-host fusion transcripts. In HNSCC cell lines as well as primary tumors, integration into cancer-related genes leading to gene disruption has been reported. The studies have shown that integration-induced altered gene expression may be associated with tumor recurrence. Evidence from several studies indicates that viral integration into genic regions is accompanied by local amplification, increased expression in some cases, interruption of gene expression, and likely additional oncogenic effects. Similarly, reported examples of viral integration near microRNAs suggest that altered expression of these regulatory molecules may also contribute to oncogenesis. Future work is indicated to identify the mechanisms of these events on cancer cell behavior.
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Affiliation(s)
- L M Pinatti
- 1 Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, MI, USA.,2 Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - H M Walline
- 2 Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - T E Carey
- 2 Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
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89
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Moody C. Mechanisms by which HPV Induces a Replication Competent Environment in Differentiating Keratinocytes. Viruses 2017; 9:v9090261. [PMID: 28925973 PMCID: PMC5618027 DOI: 10.3390/v9090261] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Human papillomaviruses (HPV) are the causative agents of cervical cancer and are also associated with other genital malignancies, as well as an increasing number of head and neck cancers. HPVs have evolved their life cycle to contend with the different cell states found in the stratified epithelium. Initial infection and viral genome maintenance occurs in the proliferating basal cells of the stratified epithelium, where cellular replication machinery is abundant. However, the productive phase of the viral life cycle, including productive replication, late gene expression and virion production, occurs upon epithelial differentiation, in cells that normally exit the cell cycle. This review outlines how HPV interfaces with specific cellular signaling pathways and factors to provide a replication-competent environment in differentiating cells.
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Affiliation(s)
- Cary Moody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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90
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Playing with fire: consequences of human papillomavirus DNA replication adjacent to genetically unstable regions of host chromatin. Curr Opin Virol 2017; 26:63-68. [PMID: 28779692 DOI: 10.1016/j.coviro.2017.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/21/2017] [Accepted: 07/18/2017] [Indexed: 12/20/2022]
Abstract
Papillomaviruses are small DNA viruses that replicate persistently in the stratified epithelial surfaces of the host. They have minimal coding capacity and must hijack many cellular processes to complete their life cycle. For example, viral genomes are tethered to host chromatin to ensure that they are effectively partitioned in dividing cells, and the host DNA damage and repair pathways are usurped to replicate viral DNA in differentiated cells. These processes result in the close juxtaposition of viral DNA with host DNA that is undergoing replication stress. This could explain the propensity of oncogenic human papillomaviruses (HPVs) to accidently integrate into common fragile sites in host DNA.
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91
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Litwin TR, Clarke MA, Dean M, Wentzensen N. Somatic Host Cell Alterations in HPV Carcinogenesis. Viruses 2017; 9:v9080206. [PMID: 28771191 PMCID: PMC5580463 DOI: 10.3390/v9080206] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
High-risk human papilloma virus (HPV) infections cause cancers in different organ sites, most commonly cervical and head and neck cancers. While carcinogenesis is initiated by two viral oncoproteins, E6 and E7, increasing evidence shows the importance of specific somatic events in host cells for malignant transformation. HPV-driven cancers share characteristic somatic changes, including apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC)-driven mutations and genomic instability leading to copy number variations and large chromosomal rearrangements. HPV-associated cancers have recurrent somatic mutations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and phosphatase and tensin homolog (PTEN), human leukocyte antigen A and B (HLA-A and HLA-B)-A/B, and the transforming growth factor beta (TGFβ) pathway, and rarely have mutations in the tumor protein p53 (TP53) and RB transcriptional corepressor 1 (RB1) tumor suppressor genes. There are some variations by tumor site, such as NOTCH1 mutations which are primarily found in head and neck cancers. Understanding the somatic events following HPV infection and persistence can aid the development of early detection biomarkers, particularly when mutations in precancers are characterized. Somatic mutations may also influence prognosis and treatment decisions.
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Affiliation(s)
- Tamara R Litwin
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
| | - Megan A Clarke
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA.
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD 20850, USA.
| | - Nicolas Wentzensen
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA.
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92
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Affiliation(s)
- Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alix Warburton
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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93
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Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
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Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
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94
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Zhao JW, Fang F, Guo Y, Zhu TL, Yu YY, Kong FF, Han LF, Chen DS, Li F. HPV16 integration probably contributes to cervical oncogenesis through interrupting tumor suppressor genes and inducing chromosome instability. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:180. [PMID: 27884161 PMCID: PMC5123399 DOI: 10.1186/s13046-016-0454-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022]
Abstract
Background The integration of human papilloma virus (HPV) into host genome is one of the critical steps that lead to the progression of precancerous lesion into cancer. However, the mechanisms and consequences of such integration events are poorly understood. This study aims to explore those questions by studying high risk HPV16 integration in women with cervical intraepithelial neoplasia (CIN) and cervical squamous cell carcinoma (SCC). Methods Specifically, HPV integration status of 13 HPV16-infected patients were investigated by ligation-mediated PCR (DIPS-PCR) followed by DNA sequencing. Results In total, 8 HPV16 integration sites were identified inside or around genes associated with cancer development. In particular, the well-studied tumor suppressor genes SCAI was found to be integrated by HPV16, which would likely disrupt its expression and therefore facilitate the migration of tumor. On top of that, we observed several cases of chromosome translocation events coincide with HPV integration, which suggests the existence of chromosome instability. Additionally, short overlapping sequences were observed between viral derived and host derived fragments in viral-cellular junctions, indicating that integration was mediated by micro homology-mediated DNA repair pathway. Conclusions Overall, our study suggests a model in which HPV16 might contribute to oncogenesis not only by disrupting tumor suppressor genes, but also by inducing chromosome instability. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0454-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Wei Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Fang Fang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Yi Guo
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Tai-Lin Zhu
- Abbey College Cambridge, Homerton Gardens, Cambridge, CB2 8EB, UK
| | - Yun-Yun Yu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Fan-Fei Kong
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Ling-Fei Han
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Dong-Sheng Chen
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK. .,Fitzwilliam College, University of Cambridge, Storey's Way, Cambridge, CB3 0DG, UK.
| | - Fang Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 200040, China.
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Gender and age-specific seroprevalence of human papillomavirus 16 and 18 in general population in Tehran, Iran. Med Microbiol Immunol 2016; 206:105-110. [PMID: 27858157 DOI: 10.1007/s00430-016-0487-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/10/2016] [Indexed: 12/13/2022]
Abstract
The assessment of the gender and age-specific seroprevalence of human papillomavirus (HPV) is essential for planning of HPV vaccine implementation into the preventive programs. In this study, we aimed to determine the age-specific seroprevalence of HPV-16 and 18 in both males and females in Tehran, Iran. Three hundred and seventy-eight women (10-35 years) and 162 men (10-25 years) from Tehran, Iran, were enrolled. Anti-HPV IgG antibodies against HPV-16 and HPV-18 were detected by ELISA using papillomavirus type 16 and 18 L1-capsids as antigen. HPV-16 antibody was detected in 15.6 and 13.6% of women and men, respectively. Antibody against HPV-18 was found positive in 12.7 and 8% of women and men, respectively. The highest seroprevalence of HPV-16 and 18 were seen in women aged 26-30 years (22.2 and 19.4%, respectively), and the lowest HPV-16 and 18 seropositivity rates were seen in males and females aged 10-15 years (9.3 and 1.9%, respectively). In our cohort of study, in males, both anti-HPV-16 and 18 increased after age 15 years, peaking in men aged 21-25 years. In women, both HPV-16 and 18 seropositivity increased after 15 years, declined at 21-25 years, peaked in women aged 26-30 years and again decreased after 30 years. Our data showed increasing exposure rate to high-risk HPV vaccine types in our studied population over 15 years of age. In order to prevent the HPV-related cancers, implementation of HPV vaccine into the national immunization program in Iran and vaccination of females and males less than 15 years of age are suggested.
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