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Sastre-Garau X, Estrada-Virrueta L, Radvanyi F. HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas. Cancers (Basel) 2024; 16:1584. [PMID: 38672666 PMCID: PMC11048798 DOI: 10.3390/cancers16081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
In HPV-associated carcinomas, some examples of cancer-related genes altered by viral insertion and corresponding to potential therapeutic targets have been described, but no quantitative assessment of these events, including poorly recurrent targets, has been reported to date. To document these occurrences, we built and analyzed a database comprised of 1455 cases, including HPV genotypes and tumor localizations. Host DNA sequences targeted by viral integration were classified as "non-recurrent" (one single reported case; 838 loci), "weakly recurrent" (two reported cases; 82 loci), and highly recurrent (≥3 cases; 43 loci). Whereas the overall rate of cancer-related target genes was 3.3% in the Gencode database, this rate increased to 6.5% in "non-recurrent", 11.4% in "weakly recurrent", and 40.1% in "highly recurrent" genes targeted by integration (p = 4.9 × 10-4). This rate was also significantly higher in tumors associated with high-risk HPV16/18/45 than other genotypes. Among the genes targeted by HPV insertion, 30.2% corresponded to direct or indirect druggable targets, a rate rising to 50% in "highly recurrent" targets. Using data from the literature and the DepMap 23Q4 release database, we found that genes targeted by viral insertion could be new candidates potentially involved in HPV-associated oncogenesis. A more systematic characterization of HPV/host fusion DNA sequences in HPV-associated cancers should provide a better knowledge of HPV-driven carcinogenesis and favor the development of personalize patient treatments.
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Affiliation(s)
- Xavier Sastre-Garau
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, 94010 Créteil, France
| | - Lilia Estrada-Virrueta
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
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2
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Rosendo-Chalma P, Antonio-Véjar V, Ortiz Tejedor JG, Ortiz Segarra J, Vega Crespo B, Bigoni-Ordóñez GD. The Hallmarks of Cervical Cancer: Molecular Mechanisms Induced by Human Papillomavirus. BIOLOGY 2024; 13:77. [PMID: 38392296 PMCID: PMC10886769 DOI: 10.3390/biology13020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Human papillomaviruses (HPVs) and, specifically, high-risk HPVs (HR-HPVs) are identified as necessary factors in the development of cancer of the lower genital tract, with CaCU standing out as the most prevalent tumor. This review summarizes ten mechanisms activated by HR-HPVs during cervical carcinogenesis, which are broadly associated with at least seven of the fourteen distinctive physiological capacities of cancer in the newly established model by Hanahan in 2022. These mechanisms involve infection by human papillomavirus, cellular tropism, genetic predisposition to uterine cervical cancer (CaCU), viral load, viral physical state, regulation of epigenetic mechanisms, loss of function of the E2 protein, deregulated expression of E6/E7 oncogenes, regulation of host cell protein function, and acquisition of the mesenchymal phenotype.
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Affiliation(s)
- Pedro Rosendo-Chalma
- Laboratorio de Virus y Cáncer, Unidad de Investigación Biomédica en Cáncer of Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (IIB-UNAM), Mexico City 14080, Mexico
- Unidad Académica de Posgrado, Universidad Católica de Cuenca, Cuenca 010101, Ecuador
| | - Verónica Antonio-Véjar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo 39090, Guerrero, Mexico
| | - Jonnathan Gerardo Ortiz Tejedor
- Unidad Académica de Posgrado, Universidad Católica de Cuenca, Cuenca 010101, Ecuador
- Carrera de Bioquímica y Farmacia, Universidad Católica de Cuenca, Cuenca 010101, Ecuador
| | - Jose Ortiz Segarra
- Carrera de Medicina, Facultad de Ciencias Médicas, Universidad de Cuenca, Cuenca 010107, Ecuador
| | - Bernardo Vega Crespo
- Carrera de Medicina, Facultad de Ciencias Médicas, Universidad de Cuenca, Cuenca 010107, Ecuador
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3
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Wang Y, Li T, Yin J, Liu Y, Li Z, Liu Y, Chen T, Chen S, Dai Y, Cui J, Liu B, Feng X, Zhang S, Chen W. Concordance between the BD Onclarity and Roche cobas assays for detection of HPV DNA in a Chinese population. J Med Virol 2022; 94:6037-6046. [PMID: 35978268 DOI: 10.1002/jmv.28072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/09/2022] [Accepted: 08/16/2022] [Indexed: 01/06/2023]
Abstract
As cervical cancer screening shifts from cytology to human papillomavirus (HPV) testing, a major issue involves validating more HPV tests. In recent years, some HPV tests are used for clinical performance verification in China. The purpose of this study was to explore whether the BD Onclarity (Becton, Dickinson and Company)HPV assay differs from the Roche cobas (Roche Molecular Systems)HPV assay, as determined using 944 cervical samples, including 588 with sequencing results. In the nucleic acid assay accuracy verification, the assays showed excellent concordance for detection of HPV16 (κ = 0.93, 95% confidence interval [CI]: 0.89-0.97) and HPV18 (κ = 0.90, 95% CI: 0.83-0.97), and very good concordance for the 12 other high-risk types (HPV31/33/35/39/45/51/52/56/58/59/66/68, κ = 0.79, 95% CI: 0.75-0.83). The overall agreement for HPV DNA detection between Onclarity and cobas was very good (κ = 0.7755). No difference for ≥CIN2 sensitivity was observed between Onclarity and cobas (both 96.5%), whereas the ≥CIN2 specificity for detection of Onclarity (16.6%, 95% CI: 13.7-19.9) was higher than that of cobas (11.5%, 95% CI: 9.1-14.5). Onclarity exhibited comparable screening performance and triage efficiency compared to cobas in the detection of cervical disease in Chinese women.
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Affiliation(s)
- Yakun Wang
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tingyuan Li
- Center for Cancer Prevention Research, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jian Yin
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yin Liu
- Henan Cancer Hospital Department of Cancer Epidemiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhifang Li
- Department of Public Health and Preventive Medicine, Changzhi Medical College, Changzhi, Shanxi, China
| | - Yujing Liu
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tingting Chen
- Department of Epidemiology and Biostatistics, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Simiao Chen
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Dai
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianfeng Cui
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Liu
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangxian Feng
- Department of Public Health and Preventive Medicine, Changzhi Medical College, Changzhi, Shanxi, China
| | - Shaokai Zhang
- Henan Cancer Hospital Department of Cancer Epidemiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Wen Chen
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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4
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Andralojc KM, Elmelik D, Rasing M, Pater B, Siebers AG, Bekkers R, Huynen MA, Bulten J, Loopik D, Melchers WJG, Leenders WPJ. Targeted RNA next generation sequencing analysis of cervical smears can predict the presence of hrHPV-induced cervical lesions. BMC Med 2022; 20:206. [PMID: 35676700 PMCID: PMC9178797 DOI: 10.1186/s12916-022-02386-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Because most cervical cancers are caused by high-risk human papillomaviruses (hrHPVs), cervical cancer prevention programs increasingly employ hrHPV testing as a primary test. The high sensitivity of HPV tests is accompanied by low specificity, resulting in high rates of overdiagnosis and overtreatment. Targeted circular probe-based RNA next generation sequencing (ciRNAseq) allows for the quantitative detection of RNAs of interest with high sequencing depth. Here, we examined the potential of ciRNAseq-testing on cervical scrapes to identify hrHPV-positive women at risk of having or developing high-grade cervical intraepithelial neoplasia (CIN). METHODS We performed ciRNAseq on 610 cervical scrapes from the Dutch cervical cancer screening program to detect gene expression from 15 hrHPV genotypes and from 429 human genes. Differentially expressed hrHPV- and host genes in scrapes from women with outcome "no CIN" or "CIN2+" were identified and a model was built to distinguish these groups. RESULTS Apart from increasing percentages of hrHPV oncogene expression from "no CIN" to high-grade cytology/histology, we identified genes involved in cell cycle regulation, tyrosine kinase signaling pathways, immune suppression, and DNA repair being expressed at significantly higher levels in scrapes with high-grade cytology and histology. Machine learning using random forest on all the expression data resulted in a model that detected 'no CIN' versus CIN2+ in an independent data set with sensitivity and specificity of respectively 85 ± 8% and 72 ± 13%. CONCLUSIONS CiRNAseq on exfoliated cells in cervical scrapes measures hrHPV-(onco)gene expression and host gene expression in one single assay and in the process identifies HPV genotype. By combining these data and applying machine learning protocols, the risk of CIN can be calculated. Because ciRNAseq can be performed in high-throughput, making it cost-effective, it can be a promising screening technology to stratify women at risk of CIN2+. Further increasing specificity by model improvement in larger cohorts is warranted.
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Affiliation(s)
- Karolina M Andralojc
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands.,Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands
| | - Menno Rasing
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Bernard Pater
- Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands
| | - Albert G Siebers
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.,PALGA, De Bouw 123, Houten, 3991 SZ, The Netherlands
| | - Ruud Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital Eindhoven, Michelangelolaan 2, Eindhoven, 5623 EJ, The Netherlands.,GROW, School for Oncology and Reproductive Biology, Maastricht University, Maastricht, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute of Molecular Life Sciences, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Johan Bulten
- Department of Pathology, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Gynecology and Obstetrics, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboudumc, PO Box 9101, Nijmegen, 6500 HB, The Netherlands
| | - William P J Leenders
- Department of Biochemistry, Radboudumc, Radboud Institute of Molecular Life Sciences, Geert Grooteplein 26, Nijmegen, 6525 GA, The Netherlands. .,Predica Diagnostics, Toernooiveld 1, Nijmegen, 6525 ED, The Netherlands.
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5
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Lagström S, Løvestad AH, Umu SU, Ambur OH, Nygård M, Rounge TB, Christiansen IK. HPV16 and HPV18 type-specific APOBEC3 and integration profiles in different diagnostic categories of cervical samples. Tumour Virus Res 2021; 12:200221. [PMID: 34175494 PMCID: PMC8287217 DOI: 10.1016/j.tvr.2021.200221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
Human papillomavirus (HPV) 16 and 18 are the most predominant types in cervical cancer. Only a small fraction of HPV infections progress to cancer, indicating that additional factors and genomic events contribute to the carcinogenesis, such as minor nucleotide variation caused by APOBEC3 and chromosomal integration. We analysed intra-host minor nucleotide variants (MNVs) and integration in HPV16 and HPV18 positive cervical samples with different morphology. Samples were sequenced using an HPV whole genome sequencing protocol TaME-seq. A total of 80 HPV16 and 51 HPV18 positive samples passed the sequencing depth criteria of 300× reads, showing the following distribution: non-progressive disease (HPV16 n = 21, HPV18 n = 12); cervical intraepithelial neoplasia (CIN) grade 2 (HPV16 n = 27, HPV18 n = 9); CIN3/adenocarcinoma in situ (AIS) (HPV16 n = 27, HPV18 n = 30); cervical cancer (HPV16 n = 5). Similar numbers of MNVs in HPV16 and HPV18 samples were observed for most viral genes, with the exception of HPV18 E4 with higher numbers across clinical categories. APOBEC3 signatures were observed in HPV16 lesions, while similar mutation patterns were not detected for HPV18. The proportion of samples with integration was 13% for HPV16 and 59% for HPV18 positive samples, with a noticeable portion located within or close to cancer-related genes.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Research, Cancer Registry of Norway, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet, Oslo Metropolitan University, Oslo, Norway
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway.
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway.
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6
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Warburton A, Markowitz TE, Katz JP, Pipas JM, McBride AA. Recurrent integration of human papillomavirus genomes at transcriptional regulatory hubs. NPJ Genom Med 2021; 6:101. [PMID: 34848725 PMCID: PMC8632991 DOI: 10.1038/s41525-021-00264-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers, and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites but often only one “driver” site that expressed viral RNA. As common fragile sites and active enhancer elements are cell-type-specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration “hotspots” that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters and accidental integration could promote viral oncogene expression and carcinogenesis.
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Affiliation(s)
- Alix Warburton
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, MSC3209, Bethesda, MD, 20892, USA
| | - Tovah E Markowitz
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua P Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison A McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 33 North Drive, MSC3209, Bethesda, MD, 20892, USA.
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Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art. Cancers (Basel) 2021; 13:cancers13164089. [PMID: 34439243 PMCID: PMC8394665 DOI: 10.3390/cancers13164089] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/29/2022] Open
Abstract
A constantly increasing incidence in high-risk Human Papillomaviruses (HPV)s driven head and neck squamous cell carcinomas (HNSCC)s, especially of oropharyngeal origin, is being observed. During persistent infections, viral DNA integration into the host genome may occur. Studies are examining if the physical status of the virus (episomal vs. integration) affects carcinogenesis and eventually has further-reaching consequences on disease progression and outcome. Here, we review the literature of the most recent five years focusing on the impact of HPV integration in HNSCCs, covering aspects of detection techniques used (from PCR up to NGS approaches), integration loci identified, and associations with genomic and clinical data. The consequences of HPV integration in the human genome, including the methylation status and deregulation of genes involved in cell signaling pathways, immune evasion, and response to therapy, are also summarized.
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Groves IJ, Drane ELA, Michalski M, Monahan JM, Scarpini CG, Smith SP, Bussotti G, Várnai C, Schoenfelder S, Fraser P, Enright AJ, Coleman N. Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis. PLoS Pathog 2021; 17:e1009875. [PMID: 34432858 PMCID: PMC8439666 DOI: 10.1371/journal.ppat.1009875] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 09/14/2021] [Accepted: 08/07/2021] [Indexed: 12/26/2022] Open
Abstract
Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art 'HPV integrated site capture' (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a 'looping' mechanism by which flanking host regions become amplified. Furthermore, using our 'HPV16-specific Region Capture Hi-C' technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a 'cancer-causing gene' is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.
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Affiliation(s)
- Ian J. Groves
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Emma L. A. Drane
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Marco Michalski
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jack M. Monahan
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Cinzia G. Scarpini
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen P. Smith
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Giovanni Bussotti
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, United Kingdom
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - Anton J. Enright
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Evaluation of Integrated HPV DNA as Individualized Biomarkers for the Detection of Recurrent CIN2/3 during Post-Treatment Surveillance. Cancers (Basel) 2021; 13:cancers13133309. [PMID: 34282754 PMCID: PMC8269020 DOI: 10.3390/cancers13133309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/11/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary HPV-DNA integration into the host genome is a frequent step in cervical carcinogenesis and is considered to be a tumor-driving event. Viral integration sites are unique for each patient and could thus serve as highly specific molecular markers for the detection of recurrent disease. Unexpectedly, our study showed that integration sites as individualized biomarkers could not detect all recurrent pre-cancers (CIN2/3). Nevertheless, this is the first study which has identified and validated integration sites in a large number of CIN3 (n = 445) and as such has unraveled several novel findings: The integration frequency observed in CIN3 was much lower than anticipated (10.8% in CIN3 vs. 80% in cervical cancer). Moreover, in contrast to the monoclonal situation in cervical carcinoma, integrated HPV-DNA in CIN3 is most likely confined to clonally expanding subpopulations. Abstract Purpose: Post-treatment follow-up in women with cervical pre-cancers (CIN3) is mandatory due to relapse in up to 10% of patients. Standard follow-up based on hrHPV-DNA/cytology co-testing has high sensitivity but limited specificity. The aim of our prospective, multicenter, observational study was to test the hypothesis that an individualized viral-cellular-junction test (vcj-PCR) combined with cytology has a lower false positive rate for the prediction of recurrence compared to standard co-testing. Methods: Pre-surgical cervical swabs served for the identification of HPV16/18 DNA integration sites by next-generation-sequencing (NGS). Samples taken at 6, 12 and 24 months post-surgery were evaluated by cytology, hrHPV-DNA and the patients’ individual HPV-integration sites (vcj-PCR on the basis of NGS). Results: Integration sites were detected in 48 of 445 patients (10.8%), 39 of them had valid follow-up data. The false positive rate was 18.2% (95% CI 8.6–34.4%) for standard hrHPV/cytology at six months compared to 12.1% (95% CI 4.8–27.3%) for vcj-PCR/cytology, respectively (McNemar p = 0.50). Six patients developed recurrences (1 CIN2, 5 CIN3) during follow-up. Standard co-testing detected all, whereas vcj-PCR/cytology detected only five patients with recurrences. Data of 269 patients without evidence of HPV16/18 integration were subject to post-hoc analyses. Standard co-testing revealed a false positive rate of 15.7% (95% CI 11.7–20.7%) and predicted ten of fourteen recurrences at six months. Conclusions: Although highly specific on its own vcj-PCR could not detect all recurrent CIN2/3. Possible reasons for this unexpected result may be multifocal lesions, intratumoral heterogeneity with respect to HPV integration and/or incident CIN.
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10
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Pisarska J, Baldy-Chudzik K. MicroRNA-Based Fingerprinting of Cervical Lesions and Cancer. J Clin Med 2020; 9:jcm9113668. [PMID: 33203149 PMCID: PMC7698009 DOI: 10.3390/jcm9113668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
The regulatory functions of microRNA (miRNA) are involved in all processes contributing to carcinogenesis and response to viral infections. Cervical cancer in most cases is caused by the persistence of high-risk human papillomavirus (HR-HPV) infection. While oncogenic human papillomaviruses induce aberrant expression of many cellular miRNAs, this dysregulation could be harnessed as a marker in early diagnosis of HR-HPV infection, cervical squamous intraepithelial lesions, and cancer. In recent years, growing data indicate that miRNAs show specific patterns at various stages of cervical pathology. The aim of this review is to systematize current reports on miRNA capacity that can be utilized in personalized diagnostics of cervical precancerous and cancerous lesions. The analysis of the resources available in online databases (National Center for Biotechnology Information—NCBI, PubMed, ScienceDirect, Scopus) was performed. To date, no standardized diagnostic algorithm using the miRNA pattern in cervical pathology has been defined. However, the high sensitivity and specificity of the reported assays gives hope for the development of non-invasive diagnostic tests that take into account the heterogeneity of tumor-related changes. Due to this variability resulting in difficult to predict clinical outcomes, precise molecular tools are needed to improve the diagnostic and therapeutic process.
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11
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Diefenbach D, Greten HJ, Efferth T. Genomic landscape analyses in cervical carcinoma and consequences for treatment. Curr Opin Pharmacol 2020; 54:142-157. [PMID: 33166910 DOI: 10.1016/j.coph.2020.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 11/28/2022]
Abstract
Where we are on the road to 'tailor-made' precision medicine for drug-resistant cervical carcinoma? We explored studies about analyses of viral and human genomes, epigenomes and transcriptomes, DNA mutation analyses, their importance in detecting HPV sequences, mechanisms of drug resistance to established and targeted therapies with small molecule or therapeutic antibodies, to radiosensitivity and to chemoradiotherapy. The value of repurposing of old drugs initially approved for other disease indications and now considered for cervix cancer therapy is also discussed. The microbiome influences drug response and survival too. HPV genomic integration sites were less significant. Nomograms (Lee et al., 2013) even outperformed FIGO staging regarding prediction of five-year overall survival times. We conclude that there are still many loose threads to be followed up, before coherent conclusions for individualized therapy of drug-resistant cervical carcinoma can be drawn.
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Affiliation(s)
- Dominik Diefenbach
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany.
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12
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Molina MA, Carosi Diatricch L, Castany Quintana M, Melchers WJ, Andralojc KM. Cervical cancer risk profiling: molecular biomarkers predicting the outcome of hrHPV infection. Expert Rev Mol Diagn 2020; 20:1099-1120. [PMID: 33044104 DOI: 10.1080/14737159.2020.1835472] [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] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Cervical cancer affects half a million women worldwide annually. Given the association between high-risk human papillomavirus (hrHPV) infection and carcinogenesis, hrHPV DNA testing became an essential diagnostic tool. However, hrHPV alone does not cause the disease, and, most importantly, many cervical lesions regress to normal in a year because of the host immune system. Hence, the low specificity of hrHPV DNA tests and their inability to predict the outcome of infections have triggered a further search for biomarkers. AREAS COVERED We evaluated the latest viral and cellular biomarkers validated for clinical use as primary screening or triage for cervical cancer and assessed their promise for prevention as well as potential use in the future. The literature search focused on effective biomarkers for different stages of the disease, aiming to determine their significance in predicting the outcome of hrHPV infections. EXPERT OPINION Biomarkers such as p16/Ki-67, hrHPV genotyping, hrHPV transcriptional status, and methylation patterns have demonstrated promising results. Their eventual implementation in the screening programs may support the prompt diagnosis of hrHPV infection and its progression to cancer. These biomarkers will help in making clinical management decisions on time, thus, saving the lives of hrHPV-infected women, particularly in developing countries.
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Affiliation(s)
- Mariano A Molina
- Department of Microbiology, Faculty of Science, Radboud University , Nijmegen, The Netherlands.,Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | | | - Marina Castany Quintana
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Willem Jg Melchers
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands
| | - Karolina M Andralojc
- Department of Medical Microbiology, Radboud university medical center , Nijmegen, The Netherlands.,Department of Biochemistry, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands
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13
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Liu JJ, Ho JY, Lee JE, Hur SY, Yoo J, Kim KR, Ryu D, Kim TM, Choi YJ. Genomic, transcriptomic, and viral integration profiles associated with recurrent/metastatic progression in high-risk human papillomavirus cervical carcinomas. Cancer Med 2020; 9:8243-8257. [PMID: 33017516 PMCID: PMC7643681 DOI: 10.1002/cam4.3426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/16/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Acquisition of recurrent/metastatic potential by a tumor cell defines a critical step in malignant progression. However, understanding of metastatic progression at the molecular level is scarce for cervical carcinomas (CES). In this study, we performed genomic, transcriptomic, and viral profiling of five pairs of primary (CES‐P) and matched recurrent/metastatic tumors (CES‐R/M) with high risk human papillomavirus. Whole exome sequencing revealed mutation features of CES‐R/M including elevated mutation burdens and prevalent copy number alterations compared to their matched CES‐P. A relative deficit of APOBEC‐related mutation signatures accompanying the transcriptional downregulation of APOBEC3A was observed for CES‐R/M. Mutations in genes encoding epigenetic regulators were commonly observed as CES‐R/M‐specific alterations. Immunoprofiling and gene set analysis revealed CES‐Ps were enriched with transcripts representing activated anticancer immunity such as interferon‐gamma pathway, while CES‐R/M exhibited upregulation of genes involved in epithelial‐mesenchymal transition and angiogenesis. Viral capture sequencing revealed that integration sites remained enriched in viral E1 protein domain during malignant progression. Moreover, we found transcriptional upregulation of POSTN and downregulation of APOBEC3A were associated with unfavorable clinical outcomes in CES. Comprehensive genomic and transcriptomic profiling of a rare cohort including CES‐R/M identified metastases‐specific features to advance the molecular understanding into CES metastatic progression with potential clinical implications.
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Affiliation(s)
- Jing Jing Liu
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Obstetrics and Gynecology, Yantai Affiliated Hospital of Bin Zhou Medical University, College of Medicine, Bin Zhou Medical University, Yantai, China.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Yoon Ho
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Eum Lee
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Soo Young Hur
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jinseon Yoo
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyu Ryung Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Daeun Ryu
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tae Min Kim
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Youn Jin Choi
- Department of Obstetrics and Gynecology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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14
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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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15
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Karbalaie Niya MH, Mobini Kesheh M, Keshtmand G, Basi A, Rezvani H, Imanzade F, Panahi M, Rakhshani N. Integration rates of human papilloma virus genome in a molecular survey on cervical specimens among Iranian patients. Eur J Cancer Prev 2020; 28:537-543. [PMID: 30444753 DOI: 10.1097/cej.0000000000000498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The human papilloma virus (HPV) as a major causative agent of different cancers is under investigation globally. In this study, we aim to investigate HPV infection in different cytological and pathological stages by different molecular methods, and then the viral genome integration of HPV-16 and -18 is determined by a specific real-time PCR method. The study included women who underwent liquid-based cytology. HPV PCR was conducted by MY09/11 universal primers, HPV genotyping was performed by INNO-LiPA HPV genotyping assay, and the viral genome status was defined by two real-time PCR assays. The statistics were calculated by SPSS v.22 software. In 1668 women included in the study with mean age±std. deviation of 35.6±0.7, HPV was detected in 632 (38%) participants. Following genotyping analyses, 16 HPV types and 713 strains were detected. HPV-16 and HPV-18 from high-risk types and HPV-6 and HPV-11 from low-risk types were the dominant types. We found HPV-16 strains in mixed form (58.8%), and of the HPV-18 strains, the episomal form was prevalent (92.9%). The statistics revealed significant presence of HPV-6 and within normal limits cases; HPV-16 and atypical squamous cells of undetermined significance; HPV-33 as well as HPV-39 and low-grade squamous intraepithelial lesion; HPV-6 and atypical squamous cells of undetermined significance; and HPV-35 as well as HPV-56 and squamous cell carcinoma. Our study showed high prevalence of HPV in low-grade cervical lesions, although it is associated with higher grades. The HPV molecular testing extra to cytology is recommended. HPV-16 and HPV-18 have different programs in genome integration in infected cells.
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Affiliation(s)
| | | | | | - Ali Basi
- Department of Hematology and Oncology, Iran University of Medical Sciences
| | | | - Farid Imanzade
- Pediatrics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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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: 19] [Impact Index Per Article: 4.8] [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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17
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Van Arsdale A, Patterson NE, Maggi EC, Agoni L, Van Doorslaer K, Harmon B, Nevadunsky N, Kuo DY, Einstein MH, Lenz J, Montagna C. Insertional oncogenesis by HPV70 revealed by multiple genomic analyses in a clinically HPV-negative cervical cancer. Genes Chromosomes Cancer 2020; 59:84-95. [PMID: 31407403 PMCID: PMC6916423 DOI: 10.1002/gcc.22799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cervical carcinogenesis, the second leading cause of cancer death in women worldwide, is caused by multiple types of human papillomaviruses (HPVs). To investigate a possible role for HPV in a cervical carcinoma that was HPV-negative by PCR testing, we performed HPV DNA hybridization capture plus massively parallel sequencing. This detected a subgenomic, URR-E6-E7-E1 segment of HPV70 DNA, a type not generally associated with cervical cancer, inserted in an intron of the B-cell lymphoma/leukemia 11B (BCL11B) gene in the human genome. Long range DNA sequencing confirmed the virus and flanking BCL11B DNA structures including both insertion junctions. Global transcriptomic analysis detected multiple, alternatively spliced, HPV70-BCL11B, fusion transcripts with fused open reading frames. The insertion and fusion transcripts were present in an intraepithelial precursor phase of tumorigenesis. These results suggest oncogenicity of HPV70, identify novel BCL11B variants with potential oncogenic implications, and underscore the advantages of thorough genomic analyses to elucidate insights into HPV-associated tumorigenesis.
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Affiliation(s)
- Anne Van Arsdale
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Nicole E. Patterson
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Elaine C. Maggi
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Lorenzo Agoni
- Department of Women's and Children's HealthObstetrics & Gynecology Unit, Fondazione Poliambulanza Istituto OspedalieroBresciaItaly
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical SciencesCollege of Agriculture and Life Sciences BIO5 Institute University of ArizonaTusconArizonaUSA
| | - Bryan Harmon
- Department of PathologyAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Nicole Nevadunsky
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Dennis Y.S. Kuo
- Department of Obstetrics & Gynecology and Women's HealthAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Mark H. Einstein
- Department of Obstetrics, Gynecology, and Women's HealthRutgers New Jersey Medical SchoolNewarkNew Jersey
| | - Jack Lenz
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
| | - Cristina Montagna
- Department of GeneticsAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
- Department of PathologyAlbert Einstein College of Medicine, Yeshiva UniversityBronxNew York
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18
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Tian R, Cui Z, He D, Tian X, Gao Q, Ma X, Yang JR, Wu J, Das BC, Severinov K, Hitzeroth II, Debata PR, Xu W, Zhong H, Fan W, Chen Y, Jin Z, Cao C, Yu M, Xie W, Huang Z, Bao Y, Xie H, Yao S, Hu Z. Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles. Carcinogenesis 2019; 40:1220-1228. [PMID: 31102403 DOI: 10.1093/carcin/bgz094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 05/05/2019] [Accepted: 05/16/2019] [Indexed: 12/24/2022] Open
Abstract
Abstract
From initial human papillomavirus (HPV) infection and precursor stages, the development of cervical cancer takes decades. High-sensitivity HPV DNA testing is currently recommended as primary screening method for cervical cancer, whereas better triage methodologies are encouraged to provide accurate risk management for HPV-positive women. Given that virus-driven genomic variation accumulates during cervical carcinogenesis, we designed a 39 Mb custom capture panel targeting 17 HPV types and 522 mutant genes related to cervical cancer. Using capture-based next-generation sequencing, HPV integration status, somatic mutation and copy number variation were analyzed on 34 paired samples, including 10 cases of HPV infection (HPV+), 10 cases of cervical intraepithelial neoplasia (CIN) grade and 14 cases of CIN2+ (CIN2: n = 1; CIN2-3: n = 3; CIN3: n = 9; squamous cell carcinoma: n = 1). Finally, the machine learning algorithm (Random Forest) was applied to build the risk stratification model for cervical precursor lesions based on CIN2+ enriched biomarkers. Generally, HPV integration events (11 in HPV+, 25 in CIN1 and 56 in CIN2+), non-synonymous mutations (2 in CIN1, 12 in CIN2+) and copy number variations (19.1 in HPV+, 29.4 in CIN1 and 127 in CIN2+) increased from HPV+ to CIN2+. Interestingly, ‘common’ deletion of mitochondrial chromosome was significantly observed in CIN2+ (P = 0.009). Together, CIN2+ enriched biomarkers, classified as HPV information, mutation, amplification, deletion and mitochondrial change, successfully predicted CIN2+ with average accuracy probability score of 0.814, and amplification and deletion ranked as the most important features. Our custom capture sequencing combined with machine learning method effectively stratified the risk of cervical lesions and provided valuable integrated triage strategies.
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Affiliation(s)
- Rui Tian
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Dan He
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qinglei Gao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xin Ma
- Department of Urology, The General Hospital of the People’s Liberation Army, Beijing, China
| | - Jian-rong Yang
- Department of Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jun Wu
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, China
| | - Bhudev C Das
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, India
| | | | - Inga Isabel Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, South Africa
| | | | - Wei Xu
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Haolin Zhong
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Weiwen Fan
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Yili Chen
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Zhuang Jin
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Chen Cao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Miao Yu
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Weiling Xie
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Zhaoyue Huang
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Yuxian Bao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
- Generulor Company Bio-X Lab, Guangzhou, Guangdong, China
| | - Hongxian Xie
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
- Generulor Company Bio-X Lab, Guangzhou, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Precision Medicine Institute, Sun Yat-sen University, Yuexiu, Guangzhou, Guangdong, China
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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19
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Li T, Unger ER, Rajeevan MS. Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection. BMC Genomics 2019; 20:231. [PMID: 30894118 PMCID: PMC6425667 DOI: 10.1186/s12864-019-5598-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/12/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome sequence data. Considering the complex workflow for target-enriched next generation sequencing (NGS), we focused on the reproducibility and limit of detection (LOD) of this new universal HPV typing assay in this study. RESULTS We evaluated the reproducibility and LOD for HPV genotyping based on our recently published method that used RNA-baits targeting whole genomes of 191 HPV types, Agilent SureSelect protocol for target enrichment and Illumina HiSeq 2500 for sequencing (eWGS, enriched whole genome sequencing). Two libraries, prepared from pooled plasmids representing 9 vaccine HPV types at varying input (1-625 copies/reaction), were sequenced twice giving four replicates for evaluating reproducibility and LOD. eWGS showed high correlation in the number of reads mapped to HPV reference genomes between the two flow-cell lanes within (R2 = 1) and between experiments (R2 = 0.99). The number of mapped reads was positively correlated to copy number (β = 13.9, p < 0.0001). The limit of blank (LOB) could be calculated based on mapped reads to HPV types not included in each sample. HPV genotyping was reproducible for all 9 types at 625 copies using multiple cut-off criteria but LOD was 25 copies based on number of reads above LOB even when multiple types were present. eWGS showed no bias for HPV genotyping under single or multiple infection (p = 0.16-0.99). CONCLUSIONS The universal eWGS method for HPV genotyping has sensitivity, competitive with widely used consensus PCR methods with reduced type competition, and with the potential for determination of variant and integration status. The protocol used in this study, using defined samples varying in complexity and copy number, analyzed in replicate and duplicate assays, is applicable to most WGS methods.
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Affiliation(s)
- Tengguo Li
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Mangalathu S Rajeevan
- Division of High-Consequence Pathogens & Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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20
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Genome-wide profiling of human papillomavirus DNA integration in liquid-based cytology specimens from a Gabonese female population using HPV capture technology. Sci Rep 2019; 9:1504. [PMID: 30728408 PMCID: PMC6365579 DOI: 10.1038/s41598-018-37871-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/10/2018] [Indexed: 01/02/2023] Open
Abstract
Human papillomavirus (HPV) is recognised as the cause of precancerous and cancerous cervical lesions. Furthermore, in high-grade lesions, HPV is frequently integrated in the host cell genome and associated with the partial or complete loss of the E1 and E2 genes, which regulate the activity of viral oncoproteins E6 and E7. In this study, using a double-capture system followed by high-throughput sequencing, we determined the HPV integration status present in liquid-based cervical smears in an urban Gabonese population. The main inclusion criteria were based on cytological grade and the detection of the HPV16 genotype using molecular assays. The rate of HPV integration in the host genome varied with cytological grade: 85.7% (6/7), 71.4% (5/7), 66.7% (2/3) 60% (3/5) and 30.8% (4/13) for carcinomas, HSIL, ASCH, LSIL and ASCUS, respectively. For high cytological grades (carcinomas and HSIL), genotypes HPV16 and 18 represented 92.9% of the samples (13/14). The integrated form of HPV16 genotype was mainly found in high-grade lesions in 71.4% of samples regardless of cytological grade. Minority genotypes (HPV33, 51, 58 and 59) were found in LSIL samples, except HPV59, which was identified in one HSIL sample. Among all the HPV genotypes identified after double capture, 10 genotypes (HPV30, 35, 39, 44, 45, 53, 56, 59, 74 and 82) were detected only in episomal form. Our study revealed that the degree of HPV integration varies with cervical cytological grade. The integration event might be a potential clinical prognostic biomarker for the prediction of the progression of neoplastic lesions.
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21
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Lagström S, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Sci Rep 2019; 9:524. [PMID: 30679491 PMCID: PMC6345795 DOI: 10.1038/s41598-018-36669-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/26/2018] [Indexed: 12/11/2022] Open
Abstract
HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
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Affiliation(s)
- Sonja Lagström
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Sinan Uğur Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Maija Lepistö
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Roger Meisal
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.,Clinical Molecular Biology (EpiGen), Medical Division, Akershus University Hospital and Institute of Clinical Medicine, University of, Oslo, Norway
| | - Ole Herman Ambur
- Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway.
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22
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Huang J, Qian Z, Gong Y, Wang Y, Guan Y, Han Y, Yi X, Huang W, Ji L, Xu J, Su M, Yuan Q, Cui S, Zhang J, Bao C, Liu W, Chen X, Zhang M, Gao X, Wu R, Zhang Y, Xu H, Zhu S, Zhu H, Yang L, Xu X, Zhou P, Liang Z. Comprehensive genomic variation profiling of cervical intraepithelial neoplasia and cervical cancer identifies potential targets for cervical cancer early warning. J Med Genet 2018; 56:186-194. [PMID: 30567904 PMCID: PMC6581088 DOI: 10.1136/jmedgenet-2018-105745] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022]
Abstract
Background To better understand the pathogenesis of cervical cancer (CC), we systematically analysed the genomic variation and human papillomavirus (HPV) integration profiles of cervical intraepithelial neoplasia (CIN) and CC. Methods We performed whole-genome sequencing or whole-exome sequencing of 102 tumour-normal pairs and human papillomavirus probe capture sequencing of 45 CCs, 44 CIN samples and 25 normal cervical samples, and constructed strict integrated workflow of genomic analysis. Results Mutational analysis identified eight significantly mutated genes in CC including four genes (FAT1, MLL3, MLL2 and FADD), which have not previously been reported in CC. Targetable alterations were identified in 55.9% of patients. In addition, HPV integration breakpoints occurred in 97.8% of the CC samples, 70.5% of the CIN samples and 42.8% of the normal cervical samples with HPV infection. Integrations of high-risk HPV strains in CCs, including HPV16, 18, 33 and 58, also occurred in the CIN samples. Moreover, gene mutations were detected in 52% of the CIN specimens, and 54.8% of these mutations occurred in genes that also mutated in CCs. Conclusion Our results lay the foundation for a deep understanding of the molecular mechanisms and finding new diagnostic and therapeutic targets of CC.
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Affiliation(s)
- Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at Shanghai, Shanghai, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Yanzhou Wang
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
| | | | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liyan Ji
- Geneplus-Beijing, Beijing, China
| | - Jiajia Xu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Mengyuan Su
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Qing Yuan
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shujian Cui
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at Shanghai, Shanghai, China
| | - Jinling Zhang
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan University, Shenzhen, China
| | - Chaohui Bao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical University, Shenzhen, Guangdong, China
| | - Xi Chen
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ming Zhang
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Xiaohuan Gao
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Renhua Wu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Yinxin Zhang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huicheng Xu
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, China
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Pingyu Zhou
- STD Institute, Shanghai Skin Disease Hospital, Tong Ji University, Shanghai, China
| | - Zhiqing Liang
- Department of Obstetrics and Gynecology, Southwestern Hospital, Third Military Medical University, Chongqing, China
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23
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Zhou QH, Deng CZ, Li ZS, Chen JP, Yao K, Huang KB, Liu TY, Liu ZW, Qin ZK, Zhou FJ, Huang W, Han H, Liu RY. Molecular characterization and integrative genomic analysis of a panel of newly established penile cancer cell lines. Cell Death Dis 2018; 9:684. [PMID: 29880898 PMCID: PMC5992159 DOI: 10.1038/s41419-018-0736-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/06/2018] [Accepted: 05/08/2018] [Indexed: 12/22/2022]
Abstract
Cell line models are essential tools to study the molecular mechanisms underlying tumor initiation and progression. There are limited treatment options for penile squamous cell carcinoma (PSCC), accounting for 1–2% of male tumors in developing countries, and limited progress in preclinical research in PSCC due to lacking available models with identified genomic characteristics. Here, biological and molecular characteristics and whole-genomic alterations were analyzed in a panel of PSCC cell lines newly established in our laboratory. These cell lines were all human papillomavirus (HPV)-negative, epithelial-like, immortalized, and tumorigenic in nude mice, whereas they displayed different proliferation, migration and invasion capacities in vitro, and tumorigenic ability in nude mice. They were all cisplatin sensitive, anti-EGFR therapy resistant, and androgen irresponsive. Whole-genomic sequecing analysis revealed that transition mutations (C:G>T:A and T:A>C:G) were the most common substitution types in these cell lines, whereas ERCC5, TP53, PTH1, CLTCL1, NOTCH2, MAP2K3, CDK11A/B, USP6, ADCH5, BCLAF1, CDKN2A, FANCD2, HRAS, and NOTCH1 were the most frequently altered genes. Amplifications of MYC, PLAG1, NCOA2, RUNX1T1, COX6C, and EGFR and losses of FBXW7, TET2, XPC, and FANCE were frequently observed in cell lines. The exomic variations between cell lines and their corresponding cancer tissues were highly consistent. Genetic variations were mainly involved in the MAPK, Jak-STAT, TGF-beta, Notch, and apoptosis signaling pathways. Conclusively, these panel of PSCC cell lines established in our laboratory harbor some common or specific biological characteristics and genomic variations, and they may serve as optimal models to investigate the molecular mechanisms underlying the progression, metastasis, relapses, and treatment resistance of PSCC and to develop effective treatment strategy.
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Affiliation(s)
- Qiang-Hua Zhou
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Chuang-Zhong Deng
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China
| | - Zai-Shang Li
- Department of Urology, Shenzhen People's Hospital, Jinan University, 518020, Shenzhen, China
| | - Jie-Ping Chen
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China
| | - Kai Yao
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Kang-Bo Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Ting-Yu Liu
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Zhuo-Wei Liu
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Zi-Ke Qin
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Fang-Jian Zhou
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China
| | - Wenlin Huang
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.,Guangdong Provincial Key Laboratory of Tumor Targeted Drugs and Guangzhou Enterprise Key Laboratory of Gene Medicine, Guangzhou Doublle Bioproducts Co. Ltd., 510663, Guangzhou, China
| | - Hui Han
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China. .,Department of Urology, Sun Yat-Sen University Cancer Center, 510060, Guangzhou, China.
| | - Ran-Yi Liu
- Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, 510060, Guangzhou, China.
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24
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Prevalence of human papillomavirus genotypes and relative risk of cervical cancer in China: a systematic review and meta-analysis. Oncotarget 2018; 9:15386-15397. [PMID: 29632652 PMCID: PMC5880612 DOI: 10.18632/oncotarget.24169] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 12/06/2017] [Indexed: 11/25/2022] Open
Abstract
High-risk HPV (hrHPV) is related to cervical carcinogenesis, although clinical data comparing the natural history and carcinogenic potential of type-specific HPV remain limited. Furthermore, the nationwide prevalence rates of overall and type-specific HPV among women with cervical precancerous lesions and cancer have not been reported. Here, a meta-analysis was performed for type-specific HPV distribution among 30,165 HPV-positive women, including 12,094 invasive cervical cancers (ICCs), 10,026 cervical intraepithelial neoplasia grade 2/3 (CIN2/3), 3246 CIN1, and 4799 normal cervices from 45 PCR-based studies. We found that HPV16 was the most common hrHPV type involved in cervical disease. The HPV16 positivity rate varied little across normal (22.7%) and CIN1 individuals (23.6%) but increased through the CIN2 (37.6%) and CIN3 patients (51.9%) to 65.6% in ICC cases. HPV16, 18, 35, 39, 45, and 59 were more frequent in ICC than CIN3, with ICC:CIN3 ratios ranging from 2.3 for HPV18 to 1.1 for HPV35/45. HPV31, 33, 52, and 58 were more frequent in CIN3 compared with normal cervices but less common in ICC compared with CIN3 (ICC:CIN3 ratios ranging from 0.6 for HPV58 and 0.4 for HPV52). The ICC:normal ratios were particularly high for HPV18, 52 and 58 in West China (4.1, 3.9 and 2.9, respectively) and for HPV45 and 59 in North China (1.6 and 1.1, respectively). In summary, this study is the most comprehensive analysis of type-specific HPV distribution in cervical carcinogenesis and could be valuable for HPV-based cervical cancer screening strategies and vaccination policies in China.
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25
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Kalu NN, Mazumdar T, Peng S, Shen L, Sambandam V, Rao X, Xi Y, Li L, Qi Y, Gleber-Netto FO, Patel A, Wang J, Frederick MJ, Myers JN, Pickering CR, Johnson FM. Genomic characterization of human papillomavirus-positive and -negative human squamous cell cancer cell lines. Oncotarget 2017; 8:86369-86383. [PMID: 29156801 PMCID: PMC5689691 DOI: 10.18632/oncotarget.21174] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/21/2017] [Indexed: 12/30/2022] Open
Abstract
Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESC) cell lines separately, we performed genomic, viral gene expression, and viral integration analyses on 74 cell lines that include all readily-available HPV-positive (9 HNSCC, 8 CESC) and CESC (8 HPV-positive, 2 HPV-negative) cell lines and 55 HPV-negative HNSCC cell lines. We used over 700 human tumors for comparison. Mutation patterns in the cell lines were similar to those of human tumors. We confirmed HPV viral protein and mRNA expression in the HPV-positive cell lines. We found HPV types in three CESC cell lines that are distinct from those previously reported. We found that cell lines and tumors had similar patterns of viral gene expression; there were few sites of recurrent HPV integration. As seen in tumors, HPV integration did appear to alter host gene expression in cell lines. The HPV-positive cell lines had higher levels of p16 and lower levels of Rb protein expression than did the HPV-negative lines. Although the number of HPV-positive cell lines is limited, our results suggest that these cell lines represent suitable models for studying HNSCC and CESC, both of which are common and lethal.
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Affiliation(s)
- Nene N Kalu
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Current/Present address: Lonza Viral Therapy, Houston, Texas, USA
| | - Tuhina Mazumdar
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shaohua Peng
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Li Shen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vaishnavi Sambandam
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiayu Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lerong Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ameeta Patel
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | | | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Faye M Johnson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas, USA
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26
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Liu Y, Pan Y, Gao W, Ke Y, Lu Z. Whole-Genome Analysis of Human Papillomavirus Types 16, 18, and 58 Isolated from Cervical Precancer and Cancer Samples in Chinese Women. Sci Rep 2017; 7:263. [PMID: 28325903 PMCID: PMC5428204 DOI: 10.1038/s41598-017-00364-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/21/2017] [Indexed: 11/09/2022] Open
Abstract
Human papillomavirus (HPV) types 16, 18 and 58 are ranked the top three high-risk HPV types for cervical intraepithelial neoplasia (CIN) and invasive carcinoma. We aimed to evaluate the diversity of HPV16, HPV18, and HPV58 genetic variants by HPV capture technology combined with next generation sequencing. 295, 73, and 148 variations were observed in 51 HPV16, 7 HPV18, and 11 HPV58 genomes, respectively. HPV16 isolates were predominantly of the A variant lineage, and sublineage A4 (Asian) was the most common. However, there were no significant differences in the distribution of HPV16 A1-3 and A4 variants between CIN1-, CIN2/3, and cervical cancer groups. The 7 HPV18 genomes were assigned to the A3/A4 and A1 sublineages. Of the 11 HPV58 genomes, the most predominant variant sublineages were A2, followed by A1 and B2. The majority of HPV16/18 samples containing contiguous genomic deletions were found to harbor HPV integration. Some T-cell epitope sequences in HPV16 E6 and E7 showed considerable divergence from the prototype NC_001526, suggesting their importance in immunotherapy of HPV-associated carcinomas. In conclusion, sequence diversity and phylogenies of HPV16, 18, and 58 provide the basis for future studies of discrete viral evolution, epidemiology, pathogenicity, and the differences in response to vaccines.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Laboratory of Genetics, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China
| | - Yaqi Pan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Laboratory of Genetics, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China
| | - Weijiao Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gynecologic Oncology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Laboratory of Genetics, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China.
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Laboratory of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, No. 52 Fucheng Road, Beijing, 100142, China.
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