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Catalán-Castorena O, Garibay-Cerdenares OL, Illades-Aguiar B, Rodríguez-Ruiz HA, Zubillaga-Guerrero MI, Leyva-Vázquez MA, Encarnación-Guevara S, Alarcón-Romero LDC. The role of HR-HPV integration in the progression of premalignant lesions into different cancer types. Heliyon 2024; 10:e34999. [PMID: 39170128 PMCID: PMC11336306 DOI: 10.1016/j.heliyon.2024.e34999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 08/23/2024] Open
Abstract
High-risk human papillomavirus (HR-HPV) is associated with the development of different types of cancer, such as cervical, head and neck (including oral, laryngeal, and oropharyngeal), vulvar, vaginal, penile, and anal cancers. The progression of premalignant lesions to cancer depends on factors associated with the host cell and the different epithelia infected by HPV, such as basal cells of the flat epithelium and the cells of the squamocolumnar transformation zone (STZ) found in the uterine cervix and the anal canal, which is rich in heparan sulfate proteoglycans and integrin-like receptors. On the other hand, factors associated with the viral genotype, infection with multiple viruses, viral load, viral persistence, and type of integration determine the viral breakage pattern and the sites at which the virus integrates into the host cell genome (introns, exons, intergenic regions), inducing the loss of function of tumor suppressor genes and increasing oncogene expression. This review describes the role of viral integration and the molecular mechanisms induced by HR-HPV in different types of tissues. The purpose of this review is to identify the common factors associated with the role of integration events in the progression of premalignant lesions in different types of cancer.
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Affiliation(s)
- Oscar Catalán-Castorena
- Research in Cytopathology and Histochemical Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | - Olga Lilia Garibay-Cerdenares
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
- CONAHCyT-Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | - Berenice Illades-Aguiar
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | - Hugo Alberto Rodríguez-Ruiz
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | - Ma. Isabel Zubillaga-Guerrero
- Research in Cytopathology and Histochemical Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | - Marco Antonio Leyva-Vázquez
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
| | | | - Luz del Carmen Alarcón-Romero
- Research in Cytopathology and Histochemical Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo, Guerrero, 39089, Mexico
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2
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Demers I, Balaji H, Feitsma H, Stelloo E, Swennenhuis J, Sergeeva I, Wuerdemann N, van den Hout MFCM, Wagner S, Kremer B, Klussmann JP, Huebbers CU, Speel EJM. Proximity ligation-based sequencing for the identification of human papillomavirus genomic integration sites in formalin-fixed paraffin embedded oropharyngeal squamous cell carcinomas. J Med Virol 2024; 96:e29837. [PMID: 39105417 DOI: 10.1002/jmv.29837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 07/15/2024] [Accepted: 07/21/2024] [Indexed: 08/07/2024]
Abstract
Human papillomavirus (HPV) infections are an increasing cause of oropharyngeal squamous cell carcinomas (OPSCC). Integration of the viral genome into the host genome is suggested to affect carcinogenesis, however, the correlation with OPSCC patient prognosis is still unclear. Research on HPV integration is hampered by current integration detection technologies and their unsuitability for formalin-fixed paraffin-embedded (FFPE) tissues. This study aims to develop and validate a novel targeted proximity-ligation based sequencing method (targeted locus amplification/capture [TLA/TLC]) for HPV integration detection in cell lines and FFPE OPSCCs. For the identification of HPV integrations, TLA/TLC was applied to 7 cell lines and 27 FFPE OPSCCs. Following preprocessing steps, a polymerase chain reaction (PCR)-based HPV enrichment was performed on the cell lines and a capture-based HPV enrichment was performed on the FFPE tissues before paired-end sequencing. TLA was able to sequence up to hundreds of kb around the target, detecting exact HPV integration loci, structural variants, and chromosomal rearrangements. In all cell lines, one or more integration sites were identified, in accordance with detection of integrated papillomavirus sequences PCR data and the literature. TLC detected integrated HPV in 15/27 FFPE OPSCCs and identified simple and complex integration patterns. In general, TLA/TLC confirmed PCR data and detected additional integration sites. In conclusion TLA/TLC reliably and robustly detects HPV integration in cell lines and FFPE OPSCCs, enabling large, population-based studies on the clinical relevance of HPV integration. Furthermore, this approach might be valuable for clonality assessment of HPV-related tumors in clinical diagnostics.
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Affiliation(s)
- Imke Demers
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Harini Balaji
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany
| | | | | | | | | | - Nora Wuerdemann
- Department of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Mari F C M van den Hout
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Giessen, Giessen, Germany
| | - Bernd Kremer
- Department of Otorhinolaryngology and Head and Neck Surgery, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jens P Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Christian U Huebbers
- Jean-Uhrmacher-Institute for Otorhinolaryngological Research, University of Cologne, Cologne, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University of Cologne, Cologne, Germany
| | - Ernst-Jan M Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
- Department of Pathology and Clinical Bioinformatics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
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3
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Sanchez DF, Oliveira P. Pathology of Squamous Cell Carcinoma of the Penis: Back to Square One. Urol Clin North Am 2024; 51:313-325. [PMID: 38925734 DOI: 10.1016/j.ucl.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The landscape of squamous cell carcinoma of the penis (SCC-P) has undergone a significant transformation since the new World Health Organization classification of genitourinary cancers and recent European Association of Urology/American Association of Clinical Oncology guidelines. These changes emphasize the necessity to categorize SCC-P into 2 groups based on its association with human papillomavirus (HPV) infection. This shift has major implications, considering that prior knowledge was derived from a mix of both groups. Given the distinct prognosis, treatment options, and staging systems observed for HPV-associated tumors in other body areas, the question now arises: will similar patterns emerge for SCC-P?
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Affiliation(s)
- Diego F Sanchez
- Translational Oncogenomics Group, Manchester Cancer Research Centre & CRUK-MI, Wilmslow Road, Manchester M20 4GJ, UK.
| | - Pedro Oliveira
- Department of Pathology, Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
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4
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Sivars L, Jylhä C, Crona Guterstam Y, Zupancic M, Lindqvist B, Nordenskjöld M, Tham E, Hellman K. Cell-Free Human Papillomavirus DNA Is a Sensitive Biomarker for Prognosis and for Early Detection of Relapse in Locally Advanced Cervical Cancer. Clin Cancer Res 2024; 30:2764-2771. [PMID: 38669077 DOI: 10.1158/1078-0432.ccr-23-3941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/23/2024] [Accepted: 04/24/2024] [Indexed: 07/02/2024]
Abstract
PURPOSE Human papillomavirus (HPV) is the cause of the majority of cervical cancer cases and has been showed to be released as cell-free tumor DNA (ctHPV DNA) into the circulation. Here, we analyze if ctHPV DNA could be used as a prognostic biomarker and/or to detect relapse earlier than traditional methods in locally advanced cervical cancer (LACC). EXPERIMENTAL DESIGN A total of 74 patients with LACC were included; 66of 74 were positive for 13 high-risk HPV types on a bead-based assay of tumor biopsy samples. HPV-type-specific droplet digital PCR assays were developed. Longitudinal plasma samples were then analyzed for the biopsy-verified HPV type for each patient. In total, 418 plasma samples were analyzed. Patients were followed for a median of 37 months. Results were correlated to tumor and clinical characteristics. RESULTS Of the pretreatment plasma samples, 92.4% were positive for ctHPV DNA. Persistent ctHPV DNA in end-of-treatment, early follow-up (1-2 months after end-of-treatment), or tumor evaluation (3-4 months after end-of-treatment) plasma was correlated with worse progression-free survival (P < 0.001) compared with if ctHPV DNA was not found. The positive predictive value of ctHPV status at early follow-up for predicting disease progression was 87.5%, and the negative predictive value was 89.3%. ctHPV DNA was found in plasma before relapse was diagnosed using radiology in all patients (n = 10) who experienced relapse after complete clinical response to treatment with a median 315 days lead time. CONCLUSIONS ctHPV DNA in follow-up plasma is a promising prognostic biomarker in patients with LACC, useful for analysis of response to therapy and for early detection of relapse.
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Affiliation(s)
- Lars Sivars
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Cecilia Jylhä
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Ylva Crona Guterstam
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Gynaecology and Reproductive Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Mark Zupancic
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Medical Unit Head, Neck, Lung, and Skin Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Britta Lindqvist
- Department of Gynaecologic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Hellman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Gynaecologic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
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5
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Shen-Gunther J, Easley A. HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis. Viruses 2024; 16:975. [PMID: 38932267 PMCID: PMC11209625 DOI: 10.3390/v16060975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis, leveraging customized viral databases in CLC Microbial Genomics. By analyzing sequenced data from virally infected cancer cell lines (including SiHa, HeLa, CaSki, C-33A, DoTc2, 2A3, SCC154 for HPV; 3B2, SNU-182 for HBV; and ACH-2 for HIV-1), we precisely pinpointed viral integration sites. The workflow also highlighted disrupted and neighboring human genes that may play a crucial role in tumor development. Our results included informative virus-host read mappings, genomic breakpoints, and integration circular plots. These visual representations enhance our understanding of the integration process. In conclusion, our seamless end-to-end workflow bridges the gap in understanding viral contributions to cancer development, paving the way for improved diagnostics and treatment strategies.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA
| | - Acarizia Easley
- Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
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6
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Catalán-Castorena O, Garibay-Cerdenares OL, Illades-Aguiar B, Castillo-Sánchez R, Zubillaga-Guerrero MI, Leyva-Vazquez MA, Encarnacion-Guevara S, Flores-Alfaro E, Ramirez-Ruano M, del Carmen Alarcón-Romero L. Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma. Cancers (Basel) 2024; 16:2225. [PMID: 38927930 PMCID: PMC11202195 DOI: 10.3390/cancers16122225] [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: 03/28/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
HPV 16 integration is crucial for the onset and progression of premalignant lesions to invasive squamous cell carcinoma (ISCC) because it promotes the amplification of proto-oncogenes and the silencing of tumor suppressor genes; some of these are proteins with PDZ domains involved in homeostasis and cell polarity. Through a bioinformatics approach based on interaction networks, a group of proteins associated with HPV 16 infection, PDZ domains, and direct physical interaction with E6 and related to different hallmarks of cancer were identified. MAGI-1 was selected to evaluate the expression profile and subcellular localization changes in premalignant lesions and ISCC with HPV 16 in an integrated state in cervical cytology; the profile expression of MAGI-1 diminished according to lesion grade. Surprisingly, in cell lines CaSki and SiHa, the protein localization was cytoplasmic and nuclear. In contrast, in histological samples, a change in subcellular localization from the cytoplasm in low-grade squamous intraepithelial lesions (LSIL) to the nucleus in the high-grade squamous intraepithelial lesion (HSIL) was observed; in in situ carcinomas and ISCC, MAGI-1 expression was absent. In conclusion, MAGI-1 expression could be a potential biomarker for distinguishing those cells with normal morphology but with HPV 16 integrated from those showing morphology-related uterine cervical lesions associated with tumor progression.
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Affiliation(s)
- Oscar Catalán-Castorena
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
| | - Olga Lilia Garibay-Cerdenares
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
- CONAHCyT-Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico
| | - Berenice Illades-Aguiar
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
| | - Rocio Castillo-Sánchez
- Cell Biology Department, CINVESTAV-IPN Research Institute, Ciudad de México 07360, Mexico;
| | - Ma. Isabel Zubillaga-Guerrero
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
| | - Marco Antonio Leyva-Vazquez
- Molecular Biomedicine Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (B.I.-A.); (M.A.L.-V.)
| | - Sergio Encarnacion-Guevara
- Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca 62210, Morelos, Mexico;
| | - Eugenia Flores-Alfaro
- Clinical and Molecular Epidemiology Research Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico;
| | - Mónica Ramirez-Ruano
- Functional Genomics and Proteomics Laboratory, Faculty of Chemical-Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico;
| | - Luz del Carmen Alarcón-Romero
- Cytopathology and Histochemistry Research Laboratory, Faculty of Chemical and Biological Sciences, Autonomous University of Guerrero, Chilpancingo 39070, Guerrero, Mexico; (O.C.-C.); (M.I.Z.-G.)
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7
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Zhao Q, Yang S, Hao S, Chen Z, Tang L, Wu Z, Wu J, Xu M, Ma Z, Zhou L, Xu J, Qin Q. Identification of transcriptionally-active human papillomavirus integrants through nanopore sequencing reveals viable targets for gene therapy against cervical cancer. J Med Virol 2024; 96:e29769. [PMID: 38932482 DOI: 10.1002/jmv.29769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.
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Affiliation(s)
- Qianqian Zhao
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Shuaibing Yang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Shijia Hao
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zejia Chen
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Lihua Tang
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhaoting Wu
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jiaxin Wu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Mingqian Xu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Zebiao Ma
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jianzhen Xu
- Computational Systems Biology Laboratory, Department of Bioinformatics, Shantou University Medical College, Shantou, China
| | - Qingsong Qin
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
- International Science and Technology Collaboration Center for Emerging Infectious Diseases, Shantou University Medical College, Shantou, China
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8
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Singh AK, Walavalkar K, Tavernari D, Ciriello G, Notani D, Sabarinathan R. Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers. Mol Oncol 2024; 18:1189-1208. [PMID: 38013620 PMCID: PMC11076994 DOI: 10.1002/1878-0261.13559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Abstract
Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated HPV DNA on host chromatin structure and gene regulation remains less understood. We investigated genome-wide patterns of HPV integrations and associated host gene expression changes in the context of host chromatin states and topologically associating domains (TADs). HPV integrations were significantly enriched in active chromatin regions and depleted in inactive ones. Interestingly, regardless of chromatin state, genomic regions flanking HPV integrations showed transcriptional upregulation. Nevertheless, upregulation (both local and long-range) was mostly confined to TADs with integration, but not affecting adjacent TADs. Few TADs showed recurrent integrations associated with overexpression of oncogenes within them (e.g. MYC, PVT1, TP63 and ERBB2) regardless of proximity. Hi-C and 4C-seq analyses in cervical cancer cell line (HeLa) demonstrated chromatin looping interactions between integrated HPV and MYC/PVT1 regions (~ 500 kb apart), leading to allele-specific overexpression. Based on these, we propose HPV integrations can trigger multimodal oncogenic activation to promote cancer progression.
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Affiliation(s)
- Anurag Kumar Singh
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Kaivalya Walavalkar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
| | - Daniele Tavernari
- Department of Computational BiologyUniversity of Lausanne (UNIL)Switzerland
- Swiss Cancer Center LemanLausanneSwitzerland
- Swiss Institute for Experimental Cancer Research (ISREC), EPFLLausanneSwitzerland
| | - Giovanni Ciriello
- Department of Computational BiologyUniversity of Lausanne (UNIL)Switzerland
- Swiss Cancer Center LemanLausanneSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Dimple Notani
- National Centre for Biological SciencesTata Institute of Fundamental ResearchBengaluruIndia
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9
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Chatterjee S, Starrett GJ. Microhomology-mediated repair machinery and its relationship with HPV-mediated oncogenesis. J Med Virol 2024; 96:e29674. [PMID: 38757834 DOI: 10.1002/jmv.29674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Human Papillomaviruses (HPV) are a diverse family of non-enveloped dsDNA viruses that infect the skin and mucosal epithelia. Persistent HPV infections can lead to cancer frequently involving integration of the virus into the host genome, leading to sustained oncogene expression and loss of capsid and genome maintenance proteins. Microhomology-mediated double-strand break repair, a DNA double-stranded breaks repair pathway present in many organisms, was initially thought to be a backup but it's now seen as vital, especially in homologous recombination-deficient contexts. Increasing evidence has identified microhomology (MH) near HPV integration junctions, suggesting MH-mediated repair pathways drive integration. In this comprehensive review, we present a detailed summary of both the mechanisms underlying MH-mediated repair and the evidence for its involvement in HPV integration in cancer. Lastly, we highlight the involvement of these processes in the integration of other DNA viruses and the broader implications on virus lifecycles and host innate immune response.
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Affiliation(s)
- Subhajit Chatterjee
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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10
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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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11
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Mallick S, Choi Y, Taylor AM, Cosper PF. Human Papillomavirus-Induced Chromosomal Instability and Aneuploidy in Squamous Cell Cancers. Viruses 2024; 16:501. [PMID: 38675844 PMCID: PMC11053578 DOI: 10.3390/v16040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN) and aneuploidy are hallmarks of cancer. CIN is defined as a continuous rate of chromosome missegregation events over the course of multiple cell divisions. CIN causes aneuploidy, a state of abnormal chromosome content differing from a multiple of the haploid. Human papillomavirus (HPV) is a well-known cause of squamous cancers of the oropharynx, cervix, and anus. The HPV E6 and E7 oncogenes have well-known roles in carcinogenesis, but additional genomic events, such as CIN and aneuploidy, are often required for tumor formation. HPV+ squamous cancers have an increased frequency of specific types of CIN, including polar chromosomes. CIN leads to chromosome gains and losses (aneuploidies) specific to HPV+ cancers, which are distinct from HPV- cancers. HPV-specific CIN and aneuploidy may have implications for prognosis and therapeutic response and may provide insight into novel therapeutic vulnerabilities. Here, we review HPV-specific types of CIN and patterns of aneuploidy in squamous cancers, as well as how this impacts patient prognosis and treatment.
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Affiliation(s)
- Samyukta Mallick
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA
| | - Yeseo Choi
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Alison M. Taylor
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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12
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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13
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Bi Y, Hu J, Zeng L, Chen G, Cai H, Cao H, Ma Q, Wu X. Characteristics of HPV integration in cervical adenocarcinoma and squamous carcinoma. J Cancer Res Clin Oncol 2023; 149:17973-17986. [PMID: 37966613 PMCID: PMC10725361 DOI: 10.1007/s00432-023-05494-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023]
Abstract
PURPOSE HPV integration usually occurs in HPV-related cancer, and is the main cause of cancer. But the carcinogenic mechanism of HPV integration is unclear. The study aims to provide a theoretical basis for understanding the pathogenesis of cervical adenocarcinoma (AC) and cervical squamous carcinoma (SCC). METHODS We used HPV capture sequencing to obtain HPV integration sites in AC and SCC, and analyzed cytobands, distribution of genetic and genomic elements, identified integration hotspot genes, clinicopathological parameters, breakpoints of HPV16 and performed pathway analysis. Then we conducted immunohistochemical (IHC) assay to preliminarily verify the expression of most frequently integrated genes in AC, STARD3 and ERBB2. RESULTS The results revealed that the most frequently observed integrated cytoband was 17q12 in AC and 21p11.2 in SCC, respectively. The breakpoints in both AC and SCC were more tended to occur within gene regions, compared to intergenetic regions. Compared to SCC samples, AC samples had a higher prevalence of genomic elements. In AC, HPV integration has no significantly difference with clinicopathological parameters, but in SCC integration correlated with differentiation (P < 0.05). Breakpoints of HPV in SCC located in LCR more frequently compared to AC, which destroyed the activation of promoter p97. Hotspot genes of HPV integration were STARD3 and ERBB2 in AC, and RNA45S rDNA and MIR3648-1 in SCC, respectively. Meanwhile, we preliminarily proved that the expression of STARD3 and ERBB2, the most frequently integrated genes, would increase after integration. CONCLUSION These results suggested that HPV may utilize the powerful hosts' promoters to express viral oncogenes and overexpression of viral oncogenes plays a significant role in the carcinogenesis of SCC. In AC, HPV integration may affect hosts' oncogenes, and the dysregulation of oncogenes may primarily contribute to progression of AC.
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Affiliation(s)
- Yuxin Bi
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Junbo Hu
- Department of Pathology, Maternal and Child Health Hospital of Hubei Province, Wuhan, China
| | - Ling Zeng
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongning Cai
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Huang Cao
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
- Hubei Provincial Center for Medical Genetics, Wuhan, China
| | - Quanfu Ma
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China
| | - Xufeng Wu
- Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Clinical Medical Research Center for Gynecologic Malignancy, Wuhan, China.
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14
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Ambrosio MR, Niccolai E, Petrelli F, Di Gloria L, Bertacca G, Giusti A, Baldi S, Cavazzana A, Palmeri M, Perotti B, Ramazzotti M, Arganini M, Amedei A. Immune landscape and oncobiota in HPV-Associated Colorectal Cancer: an explorative study. Clin Exp Med 2023; 23:5101-5112. [PMID: 37612430 PMCID: PMC10725376 DOI: 10.1007/s10238-023-01165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023]
Abstract
Worldwide more than 550,000 new patients suffering from malignant tumors are associated with human papillomaviruses (HPV) infection. However, only a small portion of patients infected progress to cancer, suggesting that other factors other than HPV may play a role. Some studies have investigated HPV infection in colorectal cancer (CRC) with discordant results; moreover, the role of HPV in CRC development is still unknown. We investigated HPV infection in 50 CRC from different regions, excluding the anal one, by immunohistochemistry (IHC), real-time PCR and RNA-seq. For each patient, we studied the tumor microenvironment in neoplastic and matched non-neoplastic samples, and we compared the tumor-infiltrating immune cell phenotypes among HPV-positive and negative samples. Finally, we compared the CRC-associated microbiota in HPV-positive and negative neoplastic samples by 16S rRNA sequencing. HPV infection was identified in 20% of CRC from the right side (caecum, ascending and transverse colon) and in 40% from the left side (descending colon and rectum). In all HPV-positive CRCs we found no expression of p53 and RB, thus suggesting HPV involvement in tumorigenesis. As far as the tumor microenvironment is concerned, in HPV-related cancers we observed a neoplastic environment with a reduced immune surveillance but an enhanced cytotoxic response by lymphocytes. HPV-positive and -negative CRC showed a different microbiota with lack of species normally found in CRC in the HPV-positive ones. Our results support the carcinogenic significance of HPV in CRC, suggesting a role of HPV in modulating the tumor immune microenvironment.
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Affiliation(s)
| | - Elena Niccolai
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | | | - Leandro Di Gloria
- Department of Biomedical, Experimental and Clinical Sciences, "Mario Serio" University of Florence, Florence, Italy
| | - Gloria Bertacca
- Clinical Chemical Analysis and Immuno Allergology Department, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Andrea Giusti
- Pathology Unit, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Simone Baldi
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | | | - Matteo Palmeri
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Bruno Perotti
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Matteo Ramazzotti
- Department of Biomedical, Experimental and Clinical Sciences, "Mario Serio" University of Florence, Florence, Italy
| | - Marco Arganini
- Surgery Unit, Ospedale Unico Versilia, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Largo Brambilla 3, 50134, Florence, Italy.
- Internal Interdisciplinary Medicine Unit, Careggi University Hospital, 50134, Florence, Italy.
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15
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Abstract
High-risk human papillomaviruses (HPVs) are associated with several human cancers. HPVs are small, DNA viruses that rely on host cell machinery for viral replication. The HPV life cycle takes place in the stratified epithelium, which is composed of different cell states, including terminally differentiating cells that are no longer active in the cell cycle. HPVs have evolved mechanisms to persist and replicate in the stratified epithelium by hijacking and modulating cellular pathways, including the DNA damage response (DDR). HPVs activate and exploit DDR pathways to promote viral replication, which in turn increases the susceptibility of the host cell to genomic instability and carcinogenesis. Here, we review recent advances in our understanding of the regulation of the host cell DDR by high-risk HPVs during the viral life cycle and discuss the potential cellular consequences of modulating DDR pathways.
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Affiliation(s)
- Caleb J Studstill
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;
| | - Cary A Moody
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA;
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16
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Clarke MA. HPV Testing and its Role in Cervical Cancer Screening. Clin Obstet Gynecol 2023; 66:448-469. [PMID: 37650662 DOI: 10.1097/grf.0000000000000793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The recognition that persistent infection with carcinogenic human papillomavirus (HPV) is a necessary cause of cervical precancer and cancer has led to the introduction of HPV testing into cervical cancer screening, either as a primary screening test or in conjunction with cervical cytology (i.e., co-testing). HPV testing has much higher sensitivity for detection of cervical precancer and provides greater long-term reassurance if negative compared to cytology. However, most HPV infections are transient, and do not progress to invasive cancer, thus triage tests are required to identify individuals who should be referred to colposcopy for diagnostic evaluation. This chapter begins with a description of the biology, natural history, and epidemiology of HPV as a foundation for understanding the role of HPV in cervical carcinogenesis. This section is followed by a detailed discussion regarding the introduction of HPV-based testing and triage into cervical cancer screening and management. Summarized triage tests include cervical cytology, HPV genotyping, p16/Ki-67 dual stain, and HPV and cellular methylation markers. The final section of this chapter includes an important discussion on cervical cancer disparities, particularly within the United States, followed by concluding remarks.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, Maryland
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17
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Rodriguez I, Rossi NM, Keskus A, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley K, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.21.23294276. [PMID: 37662332 PMCID: PMC10473792 DOI: 10.1101/2023.08.21.23294276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and this is one of the first analyses of these events using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes and only one BFB breakpoint showed chromothripsis. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Indeed, YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that cervical cancer patients with YAP1/BIRC2/BIRC3-amplification, especially those of African American ancestry, might benefit from targeted therapy. In summary, we uncovered new insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F. Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Tim O’Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Laksh Malik
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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18
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Modic Z, Cemazar M, Markelc B, Cör A, Sersa G, Kranjc Brezar S, Jesenko T. HPV-positive murine oral squamous cell carcinoma: development and characterization of a new mouse tumor model for immunological studies. J Transl Med 2023; 21:376. [PMID: 37296466 PMCID: PMC10257320 DOI: 10.1186/s12967-023-04221-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Infection with high-risk human papillomavirus (HPV) strains is one of the risk factors for the development of oral squamous cell carcinoma (OSCC). Some patients with HPV-positive OSCC have a better prognosis and respond better to various treatment modalities, including radiotherapy or immunotherapy. However, since HPV can only infect human cells, there are only a few immunocompetent mouse models available that enable immunological studies. Therefore, the aim of our study was to develop a transplantable immunocompetent mouse model of HPV-positive OSCC and characterize it in vitro and in vivo. METHODS Two monoclonal HPV-positive OSCC mouse cell lines were established by inducing the expression of HPV-16 oncogenes E6 and E7 in the MOC1 OSCC cell line using retroviral transduction. After confirming stable expression of HPV-16 E6 and E7 with quantitative real-time PCR and immunofluorescence staining, the cell lines were further characterized in vitro using proliferation assay, wound healing assay, clonogenic assay and RNA sequencing. In addition, tumor models were characterized in vivo in C57Bl/6NCrl mice in terms of their histological properties, tumor growth kinetics, and radiosensitivity. Furthermore, immunofluorescence staining of blood vessels, hypoxic areas, proliferating cells and immune cells was performed to characterize the tumor microenvironment of all three tumor models. RESULTS Characterization of the resulting MOC1-HPV cell lines and tumor models confirmed stable expression of HPV-16 oncogenes and differences in cell morphology, in vitro migration capacity, and tumor microenvironment characteristics. Although the cell lines did not differ in their intrinsic radiosensitivity, one of the HPV-positive tumor models, MOC1-HPV K1, showed a significantly longer growth delay after irradiation with a single dose of 15 Gy compared to parental MOC1 tumors. Consistent with this, MOC1-HPV K1 tumors had a lower percentage of hypoxic tumor area and a higher percentage of proliferating cells. Characteristics of the newly developed HPV-positive OSCC tumor models correlate with the transcriptomic profile of MOC1-HPV cell lines. CONCLUSIONS In conclusion, we developed and characterized a novel immunocompetent mouse model of HPV-positive OSCC that exhibits increased radiosensitivity and enables studies of immune-based treatment approaches in HPV-positive OSCC.
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Affiliation(s)
- Ziva Modic
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia.
- Faculty of Health Sciences, University of Primorska, Polje 42, Izola, Slovenia.
| | - Bostjan Markelc
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia
| | - Andrej Cör
- Department of Research, Valdoltra Orthopedic Hospital, Jadranska cesta 31, Ankaran, Slovenia
- Faculty of Education, University of Primorska, Cankarjeva pot 5, Koper, Slovenia
| | - Gregor Sersa
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia
| | - Simona Kranjc Brezar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia
| | - Tanja Jesenko
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia.
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia.
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19
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Rossi NM, Dai J, Xie Y, Wangsa D, Heselmeyer-Haddad K, Lou H, Boland JF, Yeager M, Orozco R, Freites EA, Mirabello L, Gharzouzi E, Dean M. Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis. Cancer Res 2023; 83:1768-1781. [PMID: 36971511 PMCID: PMC10239328 DOI: 10.1158/0008-5472.can-22-3030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
SIGNIFICANCE Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.
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Affiliation(s)
- Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jieqiong Dai
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Darawalee Wangsa
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Heselmeyer-Haddad
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Lou
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F. Boland
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Enrique Alvirez Freites
- Hospital Central Universitario “Dr. Antonio M Pineda,” Barquisimeto, Lara State, Venezuela, and Universidad Andino de Cusco, Cusco, Perú
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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20
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Zhao J, Zheng W, Wang L, Jiang H, Wang X, Hou J, Xu A, Cong J. Human papillomavirus (HPV) integration signature in cervical lesions: identification of MACROD2 gene as HPV hot spot integration site. Arch Gynecol Obstet 2023; 307:1115-1123. [PMID: 36008642 DOI: 10.1007/s00404-022-06748-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND High-risk HPV is clearly associated with cervical cancer. Integration of HPV DNA into the host genome is considered a key event in driving cervical carcinogenesis. However, the mechanism on how HR-HPV integration influences the host genome structure has remained enigmatic. METHODS In our study, 25 DNA samples including 11 from fresh-frozen cervical carcinomas and 14 from fresh-frozen high-grade squamous intraepithelial lesion (HSILs) were detected using the method of HPV capture combined with next generation sequencing. RESULTS We calculated the frequency in each viral gene or region and found that breakpoints were prone to occur in L1 and L2 instead of E2 in the cervical cancer (P = 0.0004 and P = 5.15 × 10-40) and HSIL group (P = 2.1 × 10-32 and P = 7.06 × 10-13). The results revealed that HPV16 showed a strong tendency toward intronic region (P = 5.02 × 10-64) but a subtle tendency toward intergenic region (P = 0.04). The most frequent integration site was in the MACROD2 gene (introns 2, 4, 5, 6, 8 and 9), which in MACROD2 functional domain. CONCLUSION Our results revealed that MACROD2 is HPV hot spot integration site in cervical lesions, and its deficiency alter DNA repair and sensitivity to DNA damage thought impaired PARP1 activity resulting in chromosome instability.
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Affiliation(s)
- Junwei Zhao
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Wei Zheng
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Liqian Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Haiyang Jiang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Xiuli Wang
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Jianqing Hou
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China
| | - Anli Xu
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
| | - Jianglin Cong
- Department of Gynecology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20, East Yuhuangding Road, Zhifu District, Yantai, 264000, Shandong, China.
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21
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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22
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Hurel C, Carsuzaa F, Salleron J, Gorphe P, Righini C, Rogé M, de Mones E, Morinière S, Vergez S, Thariat J, Dufour X. Impact of HPV status in T1-2 oropharyngeal squamous cell carcinoma with bulky N3 nodes: a multicenter GETTEC study. Eur Arch Otorhinolaryngol 2023; 280:847-853. [PMID: 36068323 DOI: 10.1007/s00405-022-07637-8] [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: 06/13/2022] [Accepted: 08/30/2022] [Indexed: 01/21/2023]
Abstract
PURPOSE The purpose of our study was to investigate the impact of HPV status in oncologic outcomes in patients with T1-2 oropharyngeal SCC associated with bulky N3 nodes, and to determine progression prognosis factors aiming to define the best therapeutic strategies for these patients. METHODS This multicenter retrospective study included patients with T1-2 oropharyngeal SCC with N3 nodes treated between 2010 and 2015 in 8 French comprehensive cancer centers. HPV status was determined with P16 hyperexpression in immunohistochemistry. HPV-positive patients were separated into 2 groups according to the associated smoking history (HPV + T +) or not (HPV + T-). We compared the oncological outcomes of patients according to HPV-status and smoking history. RESULTS Of 67 patients with T1-2 N3 oropharyngeal SCC, 36 patients (53.7%) were HPV negative and 31 patients (46.3%) HPV positive. 2-year PFS was significantly better in HPV + T- group (p = 0.036). The risk of death or progression was significantly reduced in HPV + T- comparatively to HPV- (HR 0.25 95%CI [0.07; 0.89]). 2-year OS was significantly better in HPV + T- group than in the other two groups (p = 0.017). CONCLUSION In patients with T1-2 oropharyngeal SCC associated with bulky N3 nodes, HPV positive patients without smoking history had better OS and PFS than HPV positive patients with smoking history and HPV negative patients. Thus, HPV status is a significant prognostic factor for survival but this benefit is altered when smoking history is associated. N3 HPV positive patients with smoking history have to be classified as high-risk.
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Affiliation(s)
- Charles Hurel
- Head and Neck Surgery, Service ORL, chirurgie cervico-maxillo-faciale et audiophonologie, Centre Hospitalier Universitaire de Poitiers, 2 rue de la Milétrie, 86021, Poitiers Cedex, France
| | - Florent Carsuzaa
- Head and Neck Surgery, Service ORL, chirurgie cervico-maxillo-faciale et audiophonologie, Centre Hospitalier Universitaire de Poitiers, 2 rue de la Milétrie, 86021, Poitiers Cedex, France.
| | - Julia Salleron
- Cellule Data Biostatistique, Institut de Cancérologie de Lorraine, Université de Lorraine, 54519, Vandœuvre-lès-Nancy, France
| | - Philippe Gorphe
- Department of Head and Neck Oncology, Gustave Roussy, University Paris-Saclay, Villejuif, France
| | - Christian Righini
- Head and Neck Surgery, University Hospital of Grenoble, La Tronche, France
| | | | - Erwan de Mones
- Head and Neck Surgery, University Hospital of Tours, Tours, France
| | - Sylvain Morinière
- Head and Neck Surgery, University Hospital of Bordeaux, Bordeaux cedex, France
| | - Sébastien Vergez
- Institut Universitaire du Cancer de Toulouse Oncopole-CHU de Toulouse, Toulouse, France
| | | | - Xavier Dufour
- Head and Neck Surgery, Service ORL, chirurgie cervico-maxillo-faciale et audiophonologie, Centre Hospitalier Universitaire de Poitiers, 2 rue de la Milétrie, 86021, Poitiers Cedex, France
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23
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Fan J, Fu Y, Peng W, Li X, Shen Y, Guo E, Lu F, Zhou S, Liu S, Yang B, Qin X, Hu D, Xiao R, Li X, Yang S, Yuan C, Shu Y, Huang H, Wan T, Pi Y, Wang S, Chen W, Wang H, Zhong L, Yuan L, Wen B, Kong B, Mills GB, Zou D, Xia B, Song K, Chen G, Ma D, Sun C. Multi-omics characterization of silent and productive HPV integration in cervical cancer. CELL GENOMICS 2023; 3:100211. [PMID: 36777180 PMCID: PMC9903858 DOI: 10.1016/j.xgen.2022.100211] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/21/2022] [Accepted: 10/12/2022] [Indexed: 01/13/2023]
Abstract
Cervical cancer (CC) that is caused by high-risk human papillomavirus (HPV) remains a significant public health problem worldwide. HPV integration sites can be silent or actively transcribed, leading to the production of viral-host fusion transcripts. Herein, we demonstrate that only productive HPV integration sites were nonrandomly distributed across both viral and host genomes, suggesting that productive integration sites are under selection and likely to contribute to CC pathophysiology. Furthermore, using large-scale, multi-omics (clinical, genomic, transcriptional, proteomic, phosphoproteomic, and single-cell) data, we demonstrate that tumors with productive HPV integration are associated with higher E6/E7 proteins and enhanced tumor aggressiveness and immunoevasion. Importantly, productive HPV integration increases from carcinoma in situ to advanced disease. This study improves our understanding of the functional consequences of HPV fusion transcripts on the biology and pathophysiology of HPV-driven CCs, suggesting that productive HPV integration should be evaluated as an indicator of high risk for progression to aggressive cancers.
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Affiliation(s)
- Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Wenju Peng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Xiong Li
- Department of Gynecology & Obstetrics, Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yuanming Shen
- Department of Gynecologic Oncology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610000, China
| | - Si Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Xu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Siqi Yang
- Department of Gynecologic Oncology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250000, China,Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan 250000, China,Division of Gynecology Oncology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - Yao Shu
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250000, China,Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan 250000, China,Division of Gynecology Oncology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - He Huang
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China
| | - Ting Wan
- Department of Gynecologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou 510000, China
| | - Yanan Pi
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Shuxiang Wang
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Wenjuan Chen
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China
| | - Haixia Wang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China
| | - Lin Zhong
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China
| | - Li Yuan
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China
| | - Baogang Wen
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250000, China,Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan 250000, China,Division of Gynecology Oncology, Qilu Hospital of Shandong University, Jinan 250000, China
| | - Gordon B. Mills
- Department of Cell, Developmental, and Cancer Biology, Oregon Health and Sciences University, Portland, OR 97201, USA,Knight Cancer Institute, Portland, OR 97201, USA
| | - Dongling Zou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 404100, China,Corresponding author
| | - Bairong Xia
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China,Corresponding author
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250000, China,Gynecology Oncology Key Laboratory, Qilu Hospital of Shandong University, Jinan 250000, China,Division of Gynecology Oncology, Qilu Hospital of Shandong University, Jinan 250000, China,Corresponding author
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China,Corresponding author
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China,Corresponding author
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China,Corresponding author
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24
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Zhi W, Wei Y, Lazare C, Meng Y, Wu P, Gao P, Lin S, Peng T, Chu T, Liu B, Ding W, Cao C, Wu P. HPV-CCDC106 integration promotes cervical cancer progression by facilitating the high expression of CCDC106 after HPV E6 splicing. J Med Virol 2023; 95:e28009. [PMID: 35854676 PMCID: PMC9796641 DOI: 10.1002/jmv.28009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/11/2023]
Abstract
Human papillomavirus (HPV) integration and high expression of HPV oncogenes (E6 and E7) are important mechanisms for HPV carcinogenesis in cervical cancer. However, the relationship between HPV integration and HPV E6 spliced transcripts, as well as the underlying mechanisms of HPV integration in carcinogenesis after HPV E6 splicing remains unclear. We analyzed HPV-coiled-coil domain containing 106 (CCDC106) integration samples to characterize the roles of HPV integration, E6 spliceosome I (E6*I), and high CCDC106 expression in cervical carcinogenesis. We found that E6 was alternatively spliced into the E6*I transcript in HPV-CCDC016 integration samples with low p53 expression, in contrast to the role of E6*I in preventing p53 degradation in cervical cancer cells. In addition, CCDC106 was highly expressed after HPV-CCDC106 integration, and interacted with p53, resulting in p53 degradation and cervical cancer cell progression in vitro and in vivo. Importantly, when E6*I was highly expressed in cervical cancer cells, overexpression of CCDC106 independently degraded p53 and promoted cervical cancer cell progression. In this study, we explored the underlying mechanisms of HPV-CCDC106 integration in HPV carcinogenesis after HPV E6 splicing, which should provide insight into host genome dysregulation in cervical carcinogenesis.
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Affiliation(s)
- Wenhua Zhi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Ye Wei
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cordelle Lazare
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yifan Meng
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Ping Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Peipei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Shitong Lin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Ting Peng
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Tian Chu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Binghan Liu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wencheng Ding
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Canhui Cao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Shenzhen HospitalShenzhen Peking University‐The Hong Kong University of Science and Technology Medical CenterGuangdongChina
| | - Peng Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina,Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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25
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Silva JM, Qi W, Pinho AJ, Pratas D. AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. Gigascience 2022; 12:giad101. [PMID: 38091509 PMCID: PMC10716826 DOI: 10.1093/gigascience/giad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC-biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the model's ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances-namely, local, medium, or distant associations. FINDINGS This article addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference and alignment free, providing additional methodologies for testing, including a highly flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar. CONCLUSIONS The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multithreading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.
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Affiliation(s)
- Jorge M Silva
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse, 190, 8057, Zurich, Switzerland
- SIB, Swiss Institute of Bioinformatics, 1202, Geneva, Switzerland
| | - Armando J Pinho
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Diogo Pratas
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
- Department of Virology, University of Helsinki, Haartmaninkatu, 3, 00014 Helsinki, Finland
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26
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Friedman MJ, Lee H, Kwon YC, Oh S. Dynamics of Viral and Host 3D Genome Structure upon Infection. J Microbiol Biotechnol 2022; 32:1515-1526. [PMID: 36398441 PMCID: PMC9843816 DOI: 10.4014/jmb.2208.08020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022]
Abstract
Eukaryotic chromatin is highly organized in the 3D nuclear space and dynamically regulated in response to environmental stimuli. This genomic organization is arranged in a hierarchical fashion to support various cellular functions, including transcriptional regulation of gene expression. Like other host cellular mechanisms, viral pathogens utilize and modulate host chromatin architecture and its regulatory machinery to control features of their life cycle, such as lytic versus latent status. Combined with previous research focusing on individual loci, recent global genomic studies employing conformational assays coupled with high-throughput sequencing technology have informed models for host and, in some cases, viral 3D chromosomal structure re-organization during infection and the contribution of these alterations to virus-mediated diseases. Here, we review recent discoveries and progress in host and viral chromatin structural dynamics during infection, focusing on a subset of DNA (human herpesviruses and HPV) as well as RNA (HIV, influenza virus and SARS-CoV-2) viruses. An understanding of how host and viral genomic structure affect gene expression in both contexts and ultimately viral pathogenesis can facilitate the development of novel therapeutic strategies.
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Affiliation(s)
- Meyer J. Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Haram Lee
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Young-Chan Kwon
- Center for Convergent Research of Emerging Virus Infections, Korean Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Soohwan Oh
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
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27
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High-Risk Human Papillomavirus Infection in Lung Cancer: Mechanisms and Perspectives. BIOLOGY 2022; 11:biology11121691. [PMID: 36552201 PMCID: PMC9775033 DOI: 10.3390/biology11121691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Lung cancer is a very prevalent and heterogeneous group of malignancies, and most of them are etiologically associated with tobacco smoking. However, viral infections have been detected in lung carcinomas, with high-risk human papillomaviruses (HR-HPVs) being among them. The role of HR-HPVs in lung cancer has been considered to be controversial. This issue is due to the highly variable presence of this virus in lung carcinomas worldwide, and the low viral load frequently that is detected. In this review, we address the epidemiological and mechanistic findings regarding the role of HR-HPVs in lung cancer. Some mechanisms of HR-HPV-mediated lung carcinogenesis have been proposed, including (i) HPV works as an independent carcinogen in non-smoker subjects; (ii) HPV cooperates with carcinogenic compounds present in tobacco smoke; (iii) HPV promotes initial alterations being after cleared by the immune system through a "hit and run" mechanism. Additional research is warranted to clarify the role of HPV in lung cancer.
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28
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Yangyanqiu W, Shuwen H. Bacterial DNA involvement in carcinogenesis. Front Cell Infect Microbiol 2022; 12:996778. [PMID: 36310856 PMCID: PMC9600336 DOI: 10.3389/fcimb.2022.996778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/27/2022] [Indexed: 10/29/2023] Open
Abstract
The incidence of cancer is high worldwide, and biological factors such as viruses and bacteria play an important role in the occurrence of cancer. Helicobacter pylori, human papillomavirus, hepatitis B viruses and other organisms have been identified as carcinogens. Cancer is a disease driven by the accumulation of genome changes. Viruses can directly cause cancer by changing the genetic composition of the human body, such as cervical cancer caused by human papillomavirus DNA integration and liver cancer caused by hepatitis B virus DNA integration. Recently, bacterial DNA has been found around cancers such as pancreatic cancer, breast cancer and colorectal cancer, and the idea that bacterial genes can also be integrated into the human genome has become a hot topic. In the present paper, we reviewed the latest phenomenon and specific integration mechanism of bacterial DNA into the human genome. Based on these findings, we also suggest three sources of bacterial DNA in cancers: bacterial DNA around human tissues, free bacterial DNA in bacteremia or sepsis, and endogenous bacterial DNA in the human genome. Clarifying the theory that bacterial DNA integrates into the human genome can provide a new perspective for cancer prevention and treatment.
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Affiliation(s)
- Wang Yangyanqiu
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
| | - Han Shuwen
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
- Graduate School of Medical college of Zhejiang University, Hangzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer, Huzhou, China
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29
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The Drivers, Mechanisms, and Consequences of Genome Instability in HPV-Driven Cancers. Cancers (Basel) 2022; 14:cancers14194623. [PMID: 36230545 PMCID: PMC9564061 DOI: 10.3390/cancers14194623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Cells infected with high-risk human papillomaviruses (HPV) can accumulate DNA damage and eventually transform into HPV-driven cancers. Genome instability, or the progressive accumulation of DNA alterations (e.g., mutations), in HPV-infected cells is directly induced by the HPV genes and indirectly promoted by HPV infection through the consequences of chronic infection maintenance, increased cell growth, and accumulation of damaging mutations in genes that themselves affect genome instability. While the HPV genome typically exists as a separate entity within cells, genome instability increases the chances of HPV integrating within the host (human) genome, which is common in HPV-induced cancers. The DNA regions surrounding HPV integrations are unstable and can undergo complex alterations that affect both human and HPV genes. This review discusses HPV-dependent and -independent drivers and mechanisms of genome instability in HPV-driven cancers, both globally and around sites of HPV integration, and describes the changes induced in the tumour genome. Abstract Human papillomavirus (HPV) is the causative driver of cervical cancer and a contributing risk factor of head and neck cancer and several anogenital cancers. HPV’s ability to induce genome instability contributes to its oncogenicity. HPV genes can induce genome instability in several ways, including modulating the cell cycle to favour proliferation, interacting with DNA damage repair pathways to bring high-fidelity repair pathways to viral episomes and away from the host genome, inducing DNA-damaging oxidative stress, and altering the length of telomeres. In addition, the presence of a chronic viral infection can lead to immune responses that also cause genome instability of the infected tissue. The HPV genome can become integrated into the host genome during HPV-induced tumorigenesis. Viral integration requires double-stranded breaks on the DNA; therefore, regions around the integration event are prone to structural alterations and themselves are targets of genome instability. In this review, we present the mechanisms by which HPV-dependent and -independent genome instability is initiated and maintained in HPV-driven cancers, both across the genome and at regions of HPV integration.
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30
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Løvestad AH, Repesa A, Costanzi JM, Lagström S, Christiansen IK, Rounge TB, Ambur OH. Differences in integration frequencies and APOBEC3 profiles of five high-risk HPV types adheres to phylogeny. Tumour Virus Res 2022; 14:200247. [PMID: 36100161 PMCID: PMC9485212 DOI: 10.1016/j.tvr.2022.200247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 02/06/2023] Open
Abstract
Persistent infection with Human Papillomavirus (HPV) is responsible for almost all cases of cervical cancers, and HPV16 and HPV18 associated with the majority of these. These types differ in the proportion of viral minor nucleotide variants (MNVs) caused by APOBEC3 mutagenesis as well as integration frequencies. Whether these traits extend to other types remains uncertain. This study aimed to investigate and compare genomic variability and chromosomal integration in the two phylogenetically distinct Alpha-7 and Alpha-9 clades of carcinogenic HPV types. The TaME-seq protocol was employed to sequence cervical cell samples positive for HPV31, HPV33 or HPV45 and combine these with data from a previous study on HPV16 and HPV18. APOBEC3 mutation signatures were found in Alpha-9 (HPV16/31/33) but not in Alpha-7 (HPV18/45). HPV45 had significantly more MNVs compared to the other types. Alpha-7 had higher integration frequency compared to Alpha-9. An increase in integration frequency with increased diagnostic severity was found for Alpha-7. The results highlight important differences and broaden our understanding of the molecular mechanisms behind cervical cancer induced by high-risk HPV types from the Alpha-7 and Alpha-9 clades.
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Affiliation(s)
- Alexander Hesselberg Løvestad
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Adina Repesa
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Jean-Marc Costanzi
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - 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
| | - 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
| | - Trine B. Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway,Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway,Corresponding author. Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Ole Herman Ambur
- Department of Life Sciences and Health, Faculty of Health Sciences, OsloMet - Oslo Metropolitan University, Oslo, Norway,Corresponding authors.
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31
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Labarge B, Hennessy M, Zhang L, Goldrich D, Chartrand S, Purnell C, Wright S, Goldenberg D, Broach JR. Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer. Mol Cancer Res 2022; 20:1420-1428. [PMID: 35657601 PMCID: PMC9437566 DOI: 10.1158/1541-7786.mcr-21-0831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Human papillomavirus (HPV)-positive head and neck cancers, predominantly oropharyngeal squamous cell carcinoma (OPSCC), exhibit epidemiologic, clinical, and molecular characteristics distinct from those OPSCCs lacking HPV. We applied a combination of whole-genome sequencing and optical genome mapping to interrogate the genome structure of HPV-positive OPSCCs. We found that the virus had integrated in the host genome in two thirds of the tumors examined but resided solely extrachromosomally in the other third. Integration of the virus occurred at essentially random sites within the genome. Focal amplification of the virus and the genomic sequences surrounding it often occurred subsequent to integration, with the number of tandem repeats in the chromosome accounting for the increased copy number of the genome sequences flanking the site of integration. In all cases, viral integration correlated with pervasive genome-wide somatic alterations at sites distinct from that of viral integration and comprised multiple insertions, deletions, translocations, inversions, and point mutations. Few or no somatic mutations were present in tumors with only episomal HPV. Our data could be interpreted by positing that episomal HPV is captured in the host genome following an episode of global genome instability during tumor development. Viral integration correlated with higher grade tumors, which may be explained by the associated extensive mutation of the genome and suggests that HPV integration status may inform prognosis. IMPLICATIONS Our results indicate that HPV integration in head and neck cancer correlates with extensive pangenomic structural variation, which may have prognostic implications.
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Affiliation(s)
- Brandon Labarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Max Hennessy
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Lijun Zhang
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldrich
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Carson Purnell
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Sage Wright
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldenberg
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania
| | - James R. Broach
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania.,Corresponding Author: James R. Broach, Department of Biochemistry, Penn State College of Medicine, Hershey, PA 17033. Phone: 717-531-8586; E-mail:
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32
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da Silva J, da Costa CC, de Farias Ramos I, Laus AC, Sussuchi L, Reis RM, Khayat AS, Cavalli LR, Pereira SR. Upregulated miRNAs on the TP53 and RB1 Binding Seedless Regions in High-Risk HPV-Associated Penile Cancer. Front Genet 2022; 13:875939. [PMID: 35812732 PMCID: PMC9263206 DOI: 10.3389/fgene.2022.875939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/26/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer development by the human papillomavirus (HPV) infection can occur through the canonical HPV/p53/RB1 pathway mediated by the E2/E6/E7 viral oncoproteins. During the transformation process, HPV inserts its genetic material into host Integration Sites (IS), affecting coding genes and miRNAs. In penile cancer (PeCa) there is limited data on the miRNAs that regulate mRNA targets associated with HPV, such as the TP53 and RB1 genes. Considering the high frequency of HPV infection in PeCa patients in Northeast Brazil, global miRNA expression profiling was performed in high-risk HPV-associated PeCa that presented with TP53 and RB1 mRNA downregulated expression. The miRNA expression profile of 22 PeCa tissue samples and five non-tumor penile tissues showed 507 differentially expressed miRNAs: 494 downregulated and 13 upregulated (let-7a-5p, miR-130a-3p, miR-142-3p, miR-15b-5p miR-16-5p, miR-200c-3p, miR-205-5p, miR-21-5p, miR-223-3p, miR-22-3p, miR-25-3p, miR-31-5p and miR-93-5p), of which 11 were identified to be in HPV16-IS and targeting TP53 and RB1 genes. One hundred and thirty-one and 490 miRNA binding sites were observed for TP53 and RB1, respectively, most of which were in seedless regions. These findings suggest that up-regulation of miRNA expression can directly repress TP53 and RB1 expression by their binding sites in the non-canonical seedless regions.
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Affiliation(s)
- Jenilson da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Brazil
| | - Carla Cutrim da Costa
- Degree in Biological Sciences, Department of Biology, Federal University of Maranhão, São Luís, Brazil
| | - Ingryd de Farias Ramos
- Postgraduate Program in Oncology and Medical Sciences, Federal University of Pará, Belém, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Luciane Sussuchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Brazil
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
- *Correspondence: Silma Regina Pereira,
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33
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Cereceda K, Bravo N, Jorquera R, González-Stegmaier R, Villarroel-Espíndola F. Simultaneous and Spatially-Resolved Analysis of T-Lymphocytes, Macrophages and PD-L1 Immune Checkpoint in Rare Cancers. Cancers (Basel) 2022; 14:2815. [PMID: 35681797 PMCID: PMC9179863 DOI: 10.3390/cancers14112815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Penile, vulvar and anal neoplasms show an incidence lower than 0.5% of the population per year and therefore can be considered as rare cancers but with a dramatic impact on quality of life and survival. This work describes the experience of a Chilean cancer center using multiplexed immunofluorescence to study a case series of four penile cancers, two anal cancers and one vulvar cancer and simultaneous detection of CD8, CD68, PD-L1, Cytokeratin and Ki-67 in FFPE samples. Fluorescent image analyses were performed using open sources for automated tissue segmentation and cell phenotyping. Our results showed an objective and reliable counting of objects with a single or combined labeling or within a specific tissue compartment. The variability was below 10%, and the correlation between analytical events was 0.92-0.97. Critical cell phenotypes, such as TILs, PD-L1+ or proliferative tumor cells were detected in a supervised and unsupervised manner with a limit of detection of less than 1% of relative abundance. Finally, the observed diversity and abundance of the different cell phenotypes within the tumor microenvironment for the three studied tumor types confirmed that our methodology is useful and robust to be applicable for many other solid tumors.
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Affiliation(s)
- Karina Cereceda
- Translational Medicine Laboratory, Department of Cancer Research, Instituto Oncologico Fundacion Arturo Lopez Perez, Santiago 8320000, Chile; (K.C.); (R.J.); (R.G.-S.)
| | - Nicolas Bravo
- Medical Informatics Unit, Department of Cancer Research, Instituto Oncologico Fundacion Arturo Lopez Perez, Santiago 8320000, Chile;
| | - Roddy Jorquera
- Translational Medicine Laboratory, Department of Cancer Research, Instituto Oncologico Fundacion Arturo Lopez Perez, Santiago 8320000, Chile; (K.C.); (R.J.); (R.G.-S.)
| | - Roxana González-Stegmaier
- Translational Medicine Laboratory, Department of Cancer Research, Instituto Oncologico Fundacion Arturo Lopez Perez, Santiago 8320000, Chile; (K.C.); (R.J.); (R.G.-S.)
| | - Franz Villarroel-Espíndola
- Translational Medicine Laboratory, Department of Cancer Research, Instituto Oncologico Fundacion Arturo Lopez Perez, Santiago 8320000, Chile; (K.C.); (R.J.); (R.G.-S.)
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34
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Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer. Nat Commun 2022; 13:2563. [PMID: 35538075 PMCID: PMC9091225 DOI: 10.1038/s41467-022-30190-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
Integration of human papillomavirus (HPV) DNA into the human genome is considered as a key event in cervical carcinogenesis. Here, we perform comprehensive characterization of large-range virus-human integration events in 16 HPV16-positive cervical tumors using the Nanopore long-read sequencing technology. Four distinct integration types characterized by the integrated HPV DNA segments are identified with Type B being particularly notable as lacking E6/E7 genes. We further demonstrate that multiple clonal integration events are involved in the use of shared breakpoints, the induction of inter-chromosomal translocations and the formation of extrachromosomal circular virus-human hybrid structures. Combined with the corresponding RNA-seq data, we highlight LINC00290, LINC02500 and LENG9 as potential driver genes in cervical cancer. Finally, we reveal the spatial relationship of HPV integration and its various structural variations as well as their functional consequences in cervical cancer. These findings provide insight into HPV integration and its oncogenic progression in cervical cancer. The molecular mechanisms underlying cervical carcinogenesis following integration of HPV DNA into the human genome remain elusive. Here, the authors perform long-read sequencing in 16 HPV16-positive cervical tumors and identify distinct integration types, structural variations and potential driver genes.
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35
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Symer DE, Akagi K, Geiger HM, Song Y, Li G, Emde AK, Xiao W, Jiang B, Corvelo A, Toussaint NC, Li J, Agrawal A, Ozer E, El-Naggar AK, Du Z, Shewale JB, Stache-Crain B, Zucker M, Robine N, Coombes KR, Gillison ML. Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers. Genome Res 2021; 32:55-70. [PMID: 34903527 PMCID: PMC8744672 DOI: 10.1101/gr.275911.121] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022]
Abstract
Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes. The HPV oncoproteins E6 and E7 are necessary but insufficient for cancer formation, indicating that additional secondary genetic events are required. Here, we investigate potential oncogenic impacts of virus integration. Analysis of 105 HPV-positive oropharyngeal cancers by whole-genome sequencing detects virus integration in 77%, revealing five statistically significant sites of recurrent integration near genes that regulate epithelial stem cell maintenance (i.e., SOX2, TP63, FGFR, MYC) and immune evasion (i.e., CD274). Genomic copy number hyperamplification is enriched 16-fold near HPV integrants, and the extent of focal host genomic instability increases with their local density. The frequency of genes expressed at extreme outlier levels is increased 86-fold within ±150 kb of integrants. Across 95% of tumors with integration, host gene transcription is disrupted via intragenic integrants, chimeric transcription, outlier expression, gene breaking, and/or de novo expression of noncoding or imprinted genes. We conclude that virus integration can contribute to carcinogenesis in a large majority of HPV-positive oropharyngeal cancers by inducing extensive disruption of host genome structure and gene expression.
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Affiliation(s)
- David E Symer
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Keiko Akagi
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Yang Song
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gaiyun Li
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Weihong Xiao
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Bo Jiang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - André Corvelo
- New York Genome Center, New York, New York 10013, USA
| | | | - Jingfeng Li
- Division of Medical Oncology, Department of Internal Medicine, Ohio State University, Columbus, Ohio 43210, USA
| | - Amit Agrawal
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Enver Ozer
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Adel K El-Naggar
- Division of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zoe Du
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jitesh B Shewale
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | | | - Mark Zucker
- Department of Biomedical Informatics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | | | - Kevin R Coombes
- Department of Biomedical Informatics, Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Maura L Gillison
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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36
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Genome-Wide Profiling Reveals HPV Integration Pattern and Activated Carcinogenic Pathways in Penile Squamous Cell Carcinoma. Cancers (Basel) 2021; 13:cancers13236104. [PMID: 34885212 PMCID: PMC8657281 DOI: 10.3390/cancers13236104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Penile squamous cell carcinoma (PSCC) has been regarded as an HPV-related cancer for a long time. However, the integration pattern and carcinogenic pathways of HPV in PSCC remain unclear. The results of this study provide insights into the HPV-related carcinogenic mechanism in PSCC, which may be less prone to involvement in the traditional E6/E7 carcinogenic process, and are characterized by effects on the host genome, which result in the inactivation of tumor suppressors (CADM2, etc.) and the activation of oncogenes (KLF5, etc.), thus activating oncogenic signaling pathways (MAPK, JAK/STAT, etc.). This study could enhance our understanding of HPV integration and pave the way for subsequent HPV studies in PSCC. Abstract Human papillomavirus (HPV) is a significant etiologic driver of penile squamous cell carcinoma (PSCC). The integration pattern of HPV and its carcinogenic mechanism in PSCC remain largely unclear. We retrospectively reviewed 108 PSCC cases who received surgery between 2008 and 2017. Using high-throughput viral integration detection, we identified 35 HPV-integrated PSCCs. Unlike cervical cancer, the HPV E2 oncogene was not prone to involvement in integration. Eleven of the 35 (31.4%) HPV-integrated PSCCs harbored intact HPV E2; these tumors had lower HPV E6 and E7 expression and higher expression of p53 and pRb proteins than those with disrupted E2 did (p < 0.001 and p = 0.024). Integration breakpoints are preferentially distributed in or near host genes, including previously reported hotspots (KLF5, etc.) and newly identified hotspots (CADM2, etc.), which are mainly involved in oncogenic signaling pathways (MAPK, JAK/STAT, etc.). Regarding the phosphorylation levels of JNK, p38 was higher in HPV-positive tumors with MAPK-associated integration than those in HPV-positive tumors with other integration and those in HPV-negative tumors. In vitro, KLF5 knockdown inhibited proliferation and invasion of PSCC cells, while silencing CADM2 promoted migration and invasion. In conclusion, this study enhances our understanding of HPV-induced carcinogenesis in PSCC, which may not only rely on the E6/E7 oncogenes, but mat also affect the expression of critical genes and thus activate oncogenic pathways.
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37
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Virus against virus: strategies for using adenovirus vectors in the treatment of HPV-induced cervical cancer. Acta Pharmacol Sin 2021; 42:1981-1990. [PMID: 33633364 PMCID: PMC8633276 DOI: 10.1038/s41401-021-00616-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/17/2021] [Indexed: 01/31/2023] Open
Abstract
Although most human papillomavirus (HPV) infections are harmless, persistent infection with high-risk types of HPV is known to be the leading cause of cervical cancer. Following the infection of the epithelium and integration into the host genome, the oncogenic proteins E6 and E7 disrupt cell cycle control by inducing p53 and retinoblastoma (Rb) degradation. Despite the FDA approval of prophylactic vaccines, there are still issues with cervical cancer treatment; thus, many therapeutic approaches have been developed to date. Due to strong immunogenicity, a high capacity for packaging foreign DNA, safety, and the ability to infect a myriad of cells, adenoviruses have drawn attention of researchers. Adenovirus vectors have been used for different purposes, including as oncolytic agents to kill cancer cells, carrier for RNA interference to block oncoproteins expression, vaccines for eliciting immune responses, especially in cytotoxic T lymphocytes (CTLs), and gene therapy vehicles for restoring p53 and Rb function.
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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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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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Jak HPV wysokiego ryzyka indukuje optymalne środowisko dla własnej replikacji w różnicującym się nabłonku. POSTEP HIG MED DOSW 2021. [DOI: 10.2478/ahem-2021-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstrakt
Wirusy brodawczaka ludzkiego (HPV) są często czynnikami wywołującymi niegroźne dla człowieka infekcje, ale przetrwałe zakażenie niektórymi typami HPV jest poważnym zagrożeniem dla zdrowia, ponieważ jest związane z wieloma nowotworami, w tym z rakiem szyjki macicy oraz rosnącą liczbą nowotworów głowy i szyi. Cykl replikacyjny HPV jest ściśle zależny od różnicowania komórek wielowarstwowego nabłonka, co oznacza, że genom wirusa musi być replikowany za pomocą różnych mechanizmów na różnych etapach różnicowania komórek. Ustanowienie infekcji i utrzymywanie genomu wirusa zachodzi w proliferujących komórkach nabłonka, gdzie dostępność czynników replikacji jest optymalna dla wirusa. Jednak produktywna faza cyklu rozwojowego wirusa, w tym produktywna replikacja, późna ekspresja genów i wytwarzanie wirionów, zachodzi w wyniku różnicowania się nabłonka w komórkach, które prawidłowo opuszczają cykl komórkowy. Wirus wykorzystuje wiele szlaków sygnalizacyjnych komórki, w tym odpowiedź na uszkodzenia DNA (DDR, DNA damage response) do realizacji produktywnej replikacji własnego genomu. Zrozumienie mechanizmów związanych z cyklem replikacyjnym HPV jest potrzebne do ustalenia właściwego podejścia terapeutycznego do zwalczania chorób powodowanych przez HPV.
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HPV and Recurrent Respiratory Papillomatosis: A Brief Review. Life (Basel) 2021; 11:life11111279. [PMID: 34833157 PMCID: PMC8618609 DOI: 10.3390/life11111279] [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: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent Respiratory Papillomatosis (RRP) is a rare but severe manifestation of human papillomavirus (HPV). As our knowledge about HPV infections has expanded, it has become possible to understand the course of RRP disease and unravel plausible efficient methods to manage the disease. However, the surge in reports on HPV has not been accompanied by a similar increase in research about RRP specifically. In this paper, we review the clinical manifestation and typical presentation of the illness. In addition, the pathogenesis and progression of the disease are described. On the other hand, we discuss the types of treatments currently available and future treatment strategies. The role of vaccination in both the prevention and treatment of RRP will also be reviewed. We believe this review is essential to update the general knowledge on RRP with the latest information available to date to enhance our understanding of RRP and its management.
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Multi-omics mapping of human papillomavirus integration sites illuminates novel cervical cancer target genes. Br J Cancer 2021; 125:1408-1419. [PMID: 34526665 PMCID: PMC8575955 DOI: 10.1038/s41416-021-01545-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/04/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Integration of human papillomavirus (HPV) into the host genome is a dominant feature of invasive cervical cancer (ICC), yet the tumorigenicity of cis genomic changes at integration sites remains largely understudied. METHODS Combining multi-omics data from The Cancer Genome Atlas with patient-matched long-read sequencing of HPV integration sites, we developed a strategy for using HPV integration events to identify and prioritise novel candidate ICC target genes (integration-detected genes (IDGs)). Four IDGs were then chosen for in vitro functional studies employing small interfering RNA-mediated knockdown in cell migration, proliferation and colony formation assays. RESULTS PacBio data revealed 267 unique human-HPV breakpoints comprising 87 total integration events in eight tumours. Candidate IDGs were filtered based on the following criteria: (1) proximity to integration site, (2) clonal representation of integration event, (3) tumour-specific expression (Z-score) and (4) association with ICC survival. Four candidates prioritised based on their unknown function in ICC (BNC1, RSBN1, USP36 and TAOK3) exhibited oncogenic properties in cervical cancer cell lines. Further, annotation of integration events provided clues regarding potential mechanisms underlying altered IDG expression in both integrated and non-integrated ICC tumours. CONCLUSIONS HPV integration events can guide the identification of novel IDGs for further study in cervical carcinogenesis and as putative therapeutic targets.
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Bardhan A, Banerjee A, Basu K, Pal DK, Ghosh A. PRNCR1: a long non-coding RNA with a pivotal oncogenic role in cancer. Hum Genet 2021; 141:15-29. [PMID: 34727260 PMCID: PMC8561087 DOI: 10.1007/s00439-021-02396-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been gaining importance in the field of cancer research in recent years. PRNCR1 (prostate cancer-associated non-coding RNA1) is a 12.7 kb, intron-less lncRNA found to play an oncogenic role in malignancy of diverse organs including prostate, breast, lung, oral cavity, colon and rectum. Single-nucleotide polymorphisms (SNPs) of PRNCR1 locus have been found to be associated with cancer susceptibility in different populations. In this review, an attempt has been made for the first time to summarize all sorts of available data on PRNCR1 to date from relevant databases (GeneCard, LncExpDB, Ensembl genome browser, and PubMed). As functional roles of PRNCR1, miRNA (microRNA) sponging was mostly highlighted in the pathogenesis of different cancer; in addition, an association of the lncRNA with chromatin-modifying complex to enhance androgen receptor-mediated gene transcription was reported in prostate cancer. Diagnostic and prognostic importance of PRNCR1 was found in some malignancies suggesting potency of the lncRNA to serve as a clinical biomarker. For PRNCR1 SNPs, although cancer susceptibility of the risk alleles/genotypes was reported in different populations, majorities of the findings were not replicated and underlying molecular mechanisms remained unexplored. Therapeutic implication of PRNCR1 was not studied well and future research may come up in this direction for intervening novel strategies to fight against cancer.
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Affiliation(s)
- Abhishek Bardhan
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Anwesha Banerjee
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India
| | - Keya Basu
- Department of Pathology, IPGME&R, Kolkata, West Bengal, India
| | | | - Amlan Ghosh
- Genetics of Non-Communicable Diseases, Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, West Bengal, 700073, India.
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Sastre-Garau X, Diop M, Martin F, Dolivet G, Marchal F, Charra-Brunaud C, Peiffert D, Leufflen L, Dembélé B, Demange J, Tosti P, Thomas J, Leroux A, Merlin JL, Diop-Ndiaye H, Costa JM, Salleron J, Harlé A. A NGS-based Blood Test For the Diagnosis of Invasive HPV-associated Carcinomas with Extensive Viral Genomic Characterization. Clin Cancer Res 2021; 27:5307-5316. [PMID: 34108183 PMCID: PMC9401522 DOI: 10.1158/1078-0432.ccr-21-0293] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Use of circulating tumor DNA (ctDNA) for diagnosis is limited regarding the low number of target molecules in early-stage tumors. Human papillomavirus (HPV)-associated carcinomas represent a privileged model using circulating viral DNA (ctHPV DNA) as a tumor marker. However, the plurality of HPV genotypes represents a challenge. The next-generation sequencing (NGS)-based CaptHPV approach is able to characterize any HPV DNA sequence. To assess the ability of this method to establish the diagnosis of HPV-associated cancer via a blood sample, we analyzed ctHPV DNA in HPV-positive or HPV-negative carcinomas. EXPERIMENTAL DESIGN Patients (135) from France and Senegal with carcinoma developed in the uterine cervix (74), oropharynx (25), oral cavity (19), anus (12), and vulva (5) were prospectively registered. Matched tumor tissue and blood samples (10 mL) were taken before treatment and independently analyzed using the CaptHPV method. RESULTS HPV prevalence in tumors was 60.0% (81/135; 15 different genotypes). Viral analysis of plasmas compared with tumors was available for 134 patients. In the group of 80 patients with HPV-positive tumors, 77 were also positive in plasma (sensitivity 95.0%); in the group of 54 patients with HPV-negative tumors, one was positive in plasma (specificity 98.1%). In most cases, the complete HPV pattern observed in tumors could be established from the analysis of ctHPV DNA. CONCLUSIONS In patients with carcinoma associated with any HPV genotype, a complete viral genome characterization can be obtained via the analysis of a standard blood sample. This should favor the development of noninvasive diagnostic tests providing the identification of personalized tumor markers. See related commentary by Rostami et al., p. 5158.
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Affiliation(s)
- Xavier Sastre-Garau
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France.,Service de Pathologie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Mamadou Diop
- Institut du Cancer Joliot Curie, CHU Aristide Le Dantec, Dakar, Sénégal
| | | | - Gilles Dolivet
- CNRS CRAN UMR 7039, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Département de Chirurgie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Frédéric Marchal
- CNRS CRAN UMR 7039, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Département de Chirurgie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Claire Charra-Brunaud
- Département de Radiothérapie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Didier Peiffert
- CNRS CRAN UMR 7039, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Département de Radiothérapie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Léa Leufflen
- Département de Chirurgie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Birama Dembélé
- Institut du Cancer Joliot Curie, CHU Aristide Le Dantec, Dakar, Sénégal
| | - Jessica Demange
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Priscillia Tosti
- Unité de Recherche Clinique, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Jacques Thomas
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Agnès Leroux
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France.,CNRS CRAN UMR 7039, Université de Lorraine, Vandœuvre-lès-Nancy, France
| | | | | | - Julia Salleron
- Unité de Biostatistiques, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre-Lès-Nancy, France.,CNRS CRAN UMR 7039, Université de Lorraine, Vandœuvre-lès-Nancy, France.,Corresponding Author: Alexandre Harlé, Service de Biopathologie, Institut de Cancérologie de Lorraine, 6 Avenue de Bourgogne, 54519 Vandoeuvre-lès-Nancy, France. Phone: 3 83–65 6–119; E-mail:
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Human papillomavirus and ovarian cancer (review of literature and meta-analysis). INFECTION GENETICS AND EVOLUTION 2021; 95:105086. [PMID: 34536579 DOI: 10.1016/j.meegid.2021.105086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 01/05/2023]
Abstract
Many factors are involved in carcinogenesis of the ovary, such human genetic and physiological characteristics as lifestyle, existing diseases of the reproductive system, and, as suggested, the human papillomavirus (HPV). It is well known that the human papillomavirus virus of high carcinogenic risk (HCR) plays a crucial role in the onset and development of cervical cancer, as well as cases of HPV positive breast cancer and endometrial cancer. The data on the presence of HPV in ovarian cancer are ambiguous: the researchers claim that there is no complete effect of the virus on the development of this type of cancer, and the detection of HPV in 60-80% of tumors. In this regard, there is a need to systematize the currently available research results on this controversial issue and conduct a meta-analysis of the association of HPV infection with the risk of ovarian cancer.
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Warburton A, Della Fera AN, McBride AA. Dangerous Liaisons: Long-Term Replication with an Extrachromosomal HPV Genome. Viruses 2021; 13:1846. [PMID: 34578427 PMCID: PMC8472234 DOI: 10.3390/v13091846] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 01/17/2023] Open
Abstract
Papillomaviruses cause persistent, and usually self-limiting, infections in the mucosal and cutaneous surfaces of the host epithelium. However, in some cases, infection with an oncogenic HPV can lead to cancer. The viral genome is a small, double-stranded circular DNA molecule that is assembled into nucleosomes at all stages of infection. The viral minichromosome replicates at a low copy number in the nucleus of persistently infected cells using the cellular replication machinery. When the infected cells differentiate, the virus hijacks the host DNA damage and repair pathways to replicate viral DNA to a high copy number to generate progeny virions. This strategy is highly effective and requires a close association between viral and host chromatin, as well as cellular processes associated with DNA replication, repair, and transcription. However, this association can lead to accidental integration of the viral genome into host DNA, and under certain circumstances integration can promote oncogenesis. Here we describe the fate of viral DNA at each stage of the viral life cycle and how this might facilitate accidental integration and subsequent carcinogenesis.
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Affiliation(s)
| | | | - Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; (A.W.); (A.N.D.F.)
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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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48
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Detection of Human Papillomavirus Integration in Brain Metastases from Oropharyngeal Tumors by Targeted Sequencing. Viruses 2021; 13:v13081536. [PMID: 34452401 PMCID: PMC8402651 DOI: 10.3390/v13081536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/11/2022] Open
Abstract
Human papillomavirus (HPV) positive and negative head and neck squamous cell carcinoma (HNSCC) are known to have differential phenotypes, including the incidence and location of metastases. HPV positive (HPV+) HNSCC are more likely to metastasize to distant sites, such as the lung, brain, and skin. Among these locations, metastasis to the brain is a rare event, and little is known about specific risk factors for this phenotype. In this report, we describe two patients who developed brain metastases from HNSCC. Both patient tumors had p16INK4a overexpression, suggesting these tumors were HPV+. This was confirmed after PCR, in situ hybridization, and mass spectrometry detected the presence of HPV type 16 (HPV16) DNA, RNA and protein. To further characterize the presence of HPV16, we used a target enrichment strategy on tumor DNA and RNA to isolate the viral sequences from the brain metastases. Analysis by targeted next generation sequencing revealed that both tumors had the HPV genome integrated into the host genome at known hotspots, 8q24.21 and 14q24.1. Applying a similar target enrichment strategy to a larger cohort of HPV+ HNSCC brain metastases could help to identify biomarkers that can predict metastasis and/or identify novel therapeutic options.
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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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Gorur A, Patiño M, Takahashi H, Corrales G, Pickering CR, Gleber-Netto FO, Myers JN, Cata JP. Mu-opioid receptor activation promotes in vitro and in vivo tumor growth in head and neck squamous cell carcinoma. Life Sci 2021; 278:119541. [PMID: 33930368 DOI: 10.1016/j.lfs.2021.119541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/13/2021] [Accepted: 04/18/2021] [Indexed: 11/29/2022]
Abstract
AIMS In vitro and in vivo studies suggest that the mu-opioid receptor (MOR) is involved in tumorigenesis, and metastasis in cancer. In humans, the use of MOR agonists (opioids) is associated with head and neck squamous cell carcinoma (HNSCC) progression. In the present study, we aimed to examine the role of MOR activation in MOR (+) HNSCC. MAIN METHODS FaDu, MDA686Tu and UMSCC47 cell lines were used in in vitro and in vivo experiments. Cells and animals were treated with a highly selective MOR agonist DAMGO, [D-Ala (2), Me Phe (4), Glycol (5)]-enkephalin] or saline 0.9%. KEY FINDINGS MOR activation significantly increased the proliferation, colony formation, invasion, and migration of FaDu and MDA6868Tu cells and promoted tumor growth in vivo. SIGNIFICANCE These findings suggest that MOR is implicated in tumorigenesis of HNSCC. Overall, our findings identify that MOR could be used as a potential therapeutic target in patients with MOR (+) HNSCC.
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Affiliation(s)
- Aysegul Gorur
- Department of Anesthesiology and Perioperative Medicine, the University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA; Anesthesiology and Surgical Oncology Research Group, Houston, TX 77030, USA
| | - Miguel Patiño
- Anesthesiology and Surgical Oncology Research Group, Houston, TX 77030, USA; Department of Anesthesiology, Massachusetts General Hospital, Harvard University, Boston, MA 02114, USA
| | - Hideaki Takahashi
- Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - German Corrales
- Department of Anesthesiology and Perioperative Medicine, the University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA; Anesthesiology and Surgical Oncology Research Group, Houston, TX 77030, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Frederico O Gleber-Netto
- Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey N Myers
- Anesthesiology and Surgical Oncology Research Group, Houston, TX 77030, USA; Department of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juan P Cata
- Department of Anesthesiology and Perioperative Medicine, the University of Texas MD, Anderson Cancer Center, Houston, TX 77030, USA; Anesthesiology and Surgical Oncology Research Group, Houston, TX 77030, USA.
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