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Li X, Ren C, Huang A, Zhao Y, Wang L, Shen H, Gao C, Chen B, Zhu T, Xiong J, Zhu D, Huang Y, Ding J, Yuan Z, Ding W, Wang H. PIBF1 regulates multiple gene expression via impeding long-range chromatin interaction to drive the malignant transformation of HPV16 integration epithelial cells. J Adv Res 2024; 57:163-180. [PMID: 37182685 PMCID: PMC10918350 DOI: 10.1016/j.jare.2023.04.015] [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: 12/05/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023] Open
Abstract
INTRODUCTION Human papillomavirus (HPV) integration can induce gene expression dysregulation by destroying higher-order chromatin structure in cervical cancer. OBJECTIVES We established a 13q22 site-specific HPV16 gene knock-in cell model to interrogate the changes in chromatin structure at the initial stages of host cell malignant transformation. METHODS We designed a CRISPR-Cas9 system with sgRNA targeting 13q22 site and constructed the HPV16 gene donor. Cells were cotransfected, screened, and fluorescence sorted. The whole genome sequencing (WGS) was used to confirm the precise HPV16 gene integration site. Western blot and qRT-PCR were used to measure gene expression. In vitro and in vivo analysis were performed to estimate the tumorigenic potential of the HPV16 knock-in cell model. Combined Hi-C, chromatin immunoprecipitation and RNA sequencing analyses revealed correlations between chromatin structure and gene expression. We performed a coimmunoprecipitation assay with anti-PIBF1 antibody to identify endogenous interacting proteins. In vivo analysis was used to determine the role of PIBF1 in the tumor growth of cervical cancer cells. RESULTS We successfully established a 13q22 site-specific HPV16 gene knock-in cell model. We found that HPV integration promoted cell proliferation, invasion and stratified growth in vitro, and monoclonal proliferation in vivo. HPV integration divided the affected topologically associated domain (TAD) into two smaller domains, and the progesterone-induced blocking factor 1 (PIBF1) gene near the integration site was upregulated, although PIBF1 was not enriched at the domain boundary by CUT-Tag signal analysis. Moreover, PIBF1 was found to interact with the cohesin complex off chromatin to reduce contact domain formation by disrupting the cohesin ring-shaped structure, causing dysregulation of tumorigenesis-related genes. Xenograft experiments determined the role of PIBF1 in the proliferation in cervical cancer cells. CONCLUSION We highlight that PIBF1, a potential chromatin structure regulatory protein, is activated by HPV integration, which provides new insights into HPV integration-driven cervical carcinogenesis.
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Affiliation(s)
- Xiaomin Li
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Anesthesiology, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Ci Ren
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Anni Huang
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Zhao
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China
| | - Liming Wang
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hui Shen
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chun Gao
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Bingxin Chen
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tong Zhu
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jinfeng Xiong
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Da Zhu
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yafei Huang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianlin Ding
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zan Yuan
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100176, China.
| | - Wencheng Ding
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Hui Wang
- National Clinical Research Center for Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Nachira D, Congedo MT, D’Argento E, Meacci E, Evangelista J, Sassorossi C, Calabrese G, Nocera A, Kuzmych K, Santangelo R, Rindi G, Margaritora S. The Role of Human Papilloma Virus (HPV) in Primary Lung Cancer Development: State of the Art and Future Perspectives. Life (Basel) 2024; 14:110. [PMID: 38255725 PMCID: PMC10817459 DOI: 10.3390/life14010110] [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: 11/14/2023] [Revised: 12/29/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. Notably, the incidence of lung cancer among never-smokers, predominantly women, has been rising in recent years. Among the various implicated risk factors, human papilloma virus (HPV) may play a role in the development of NSCLC in a certain subset of patients. The prevalence of high-risk HPV-DNA within human neoplastic lung cells varies across the world; however, the carcinogenetic role of HPV in NSCLC has not been completely understood. Bloodstream could be one of the routes of transmission from infected sites to the lungs, along with oral (through unprotected oral sex) and airborne transmission. Previous studies reported an elevated risk of NSCLC in patients with prior HPV-related tumors, such as cervical, laryngeal, or oropharyngeal cancer, with better prognosis for HPV-positive lung cancers compared to negative forms. On the other hand, 16% of NSCLC patients present circulating HPV-DNA in peripheral blood along with miRNAs expression. Typically, these patients have a poorly differentiated NSCLC, often diagnosed at an advanced stage. However, HPV-positive lung cancers seem to have a better response to target therapies (EGFR) and immune checkpoint inhibitors and show an increased sensitivity to platinum-based treatments. This review summarizes the current evidence regarding the role of HPV in NSCLC development, especially among patients with a history of HPV-related cancers. It also examines the diagnostic and prognostic significance of HPV, investigating new future perspectives to enhance cancer screening, diagnostic protocols, and the development of more targeted therapies tailored to specific cohorts of NSCLC patients with confirmed HPV infection.
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Affiliation(s)
- Dania Nachira
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Maria Teresa Congedo
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Ettore D’Argento
- Medical Oncology, Comprehensive Cancer Center, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Elisa Meacci
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Jessica Evangelista
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Carolina Sassorossi
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Giuseppe Calabrese
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Adriana Nocera
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Khrystyna Kuzmych
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
| | - Rosaria Santangelo
- Institute of Microbiology, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Guido Rindi
- Institute of Pathology, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Stefano Margaritora
- Department of General Thoracic Surgery, Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (M.T.C.); (E.M.); (J.E.); (C.S.); (G.C.); (A.N.); (K.K.); (S.M.)
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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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Xiong J, Cheng J, Shen H, Ren C, Wang L, Gao C, Zhu T, Li X, Ding W, Zhu D, Wang H. Detection of HPV and Human Chromosome Sites by Dual-Color Fluorescence In Situ Hybridization Reveals Recurrent HPV Integration Sites and Heterogeneity in Cervical Cancer. Front Oncol 2021; 11:734758. [PMID: 34676167 PMCID: PMC8523950 DOI: 10.3389/fonc.2021.734758] [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: 07/01/2021] [Accepted: 09/08/2021] [Indexed: 01/01/2023] Open
Abstract
Human papillomavirus (HPV) integration in the human genome is suggested to be an important cause of cervical cancer. With the development of sequencing technologies, an increasing number of integration “hotspots” have been identified. However, this HPV integration information was derived from analysis of whole cervical cancer tissue, and we know very little about the integration in different cancer cell subgroups or individual cancer cells. This study optimized the preparation of probes and provided a dual-color fluorescence in situ hybridization (FISH) method to detect HPV integration sites in paraffin-embedded cervical cancer samples. We used both HPV probes and site-specific probes: 3p14 (FHIT), 8q24 (MYC), 13q22 (KLF5/KLF12), 3q28 (TP63), and 5p15 (TERT). We detected HPV signals in 75 of the 96 cases of cervical cancer; 62 cases showed punctate signals, and 13 cases showed diffuse punctate signals. We identified 3p14 as a high-frequency HPV integration site in 4 cervical cancer cases. HPV integration at 8p14 occurred in 2 cases of cervical cancer. In the same cervical cancer tissue of sample No.1321, two distinct subgroups of cells were observed based on the HPV probe but showed no difference in cell and nucleus morphology. Our study provides a new method to investigate the frequent HPV integration sites in cervical cancer and reports the heterogeneity within cervical cancer from the perspective of HPV integration.
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Affiliation(s)
- Jinfeng Xiong
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Cheng
- Department of Obstetrics and Gynecology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hui Shen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ci Ren
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chun Gao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaomin Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wencheng Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Da Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
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Raudenská M, Balvan J, Masařík M. Cell death in head and neck cancer pathogenesis and treatment. Cell Death Dis 2021; 12:192. [PMID: 33602906 PMCID: PMC7893032 DOI: 10.1038/s41419-021-03474-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022]
Abstract
Many cancer therapies aim to trigger apoptosis in cancer cells. Nevertheless, the presence of oncogenic alterations in these cells and distorted composition of tumour microenvironment largely limit the clinical efficacy of this type of therapy. Luckily, scientific consensus describes about 10 different cell death subroutines with different regulatory pathways and cancer cells are probably not able to avoid all of cell death types at once. Therefore, a focused and individualised therapy is needed to address the specific advantages and disadvantages of individual tumours. Although much is known about apoptosis, therapeutic opportunities of other cell death pathways are often neglected. Molecular heterogeneity of head and neck squamous cell carcinomas (HNSCC) causing unpredictability of the clinical response represents a grave challenge for oncologists and seems to be a critical component of treatment response. The large proportion of this clinical heterogeneity probably lies in alterations of cell death pathways. How exactly cells die is very important because the predominant type of cell death can have multiple impacts on the therapeutic response as cell death itself acts as a second messenger. In this review, we discuss the different types of programmed cell death (PCD), their connection with HNSCC pathogenesis and possible therapeutic windows that result from specific sensitivity to some form of PCD in some clinically relevant subgroups of HNSCC.
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Affiliation(s)
- Martina Raudenská
- Department of Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic.,Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Jan Balvan
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic
| | - Michal Masařík
- Department of Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic. .,Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic. .,Department of Pathological Physiology, Faculty of Medicine, Masaryk University / Kamenice 5, CZ-625 00, Brno, Czech Republic. .,BIOCEV, First Faculty of Medicine, Charles University, Prumyslova 595, CZ-252 50, Vestec, Czech Republic.
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Pinatti LM, Sinha HN, Brummel CV, Goudsmit CM, Geddes TJ, Wilson GD, Akervall JA, Brenner CJ, Walline HM, Carey TE. Association of human papillomavirus integration with better patient outcomes in oropharyngeal squamous cell carcinoma. Head Neck 2020; 43:544-557. [PMID: 33073473 DOI: 10.1002/hed.26501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/24/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The molecular drivers of human papillomavirus-related head and neck squamous cell carcinoma (HPV + HNSCC) are not entirely understood. This study evaluated the relationship between HPV integration, expression of E6/E7, and patient outcomes in p16+ HNSCCs. METHODS HPV type was determined by HPV PCR-MassArray, and integration was called using detection of integrated papillomavirus sequences polymerase chain reaction (PCR). We investigated whether fusion transcripts were produced by reverse transcriptase polymerase chain reaction (RT-PCR). E6/E7 expression was assessed by quantitative RT-PCR. We assessed if there was a relationship between integration and E6/E7 expression, clinical variables, or patient outcomes. RESULTS Most samples demonstrated HPV integration, which sometimes resulted in a fusion transcript. HPV integration was positively correlated with age at diagnosis and E6/E7 expression. There was a significant difference in survival between patients with vs without integration. CONCLUSIONS Contrary to previous reports, HPV integration was associated with improved patient survival. Therefore, HPV integration may act as a molecular marker of good prognosis.
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Affiliation(s)
- Lisa M Pinatti
- Cancer Biology Program, Program in the Biomedical Sciences, Rackham Graduate School, University of Michigan, Ann Arbor, Michigan, USA.,Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Hana N Sinha
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Collin V Brummel
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine M Goudsmit
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | | | - George D Wilson
- Beaumont BioBank, Beaumont Hospital, Royal Oak, Michigan, USA.,Department of Radiation Oncology, Beaumont Hospital, Royal Oak, Michigan, USA
| | - Jan A Akervall
- Beaumont BioBank, Beaumont Hospital, Royal Oak, Michigan, USA.,Department of Otolaryngology, Saint Joseph Mercy Hospital, Ypsilanti, Michigan, USA
| | - Chad J Brenner
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Heather M Walline
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Thomas E Carey
- Department of Otolaryngology/Head and Neck Surgery, University of Michigan, Ann Arbor, Michigan, USA
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Guo L, Hua K. Cervical Cancer: Emerging Immune Landscape and Treatment. Onco Targets Ther 2020; 13:8037-8047. [PMID: 32884290 PMCID: PMC7434518 DOI: 10.2147/ott.s264312] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Immune cells are essential for defending the body’s balance and have increasingly been implicated in controlling tumor growth. In cervical cancer (CC), the immune landscape is extensively connected with human papillomavirus (HPV) status. Recent insights from studies have revealed that as a result of infection with HPV, immune cell populations such as lymphocytes or monocytes change during carcinogenesis. Immune therapy, in particular checkpoint inhibitors, those targeting PD-1 or PD-L1, has shown promising efficacy. This article reviews the immune landscape and immunotherapy of CC.
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Affiliation(s)
- Luopei Guo
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, People's Republic of China
| | - Keqin Hua
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai 200011, People's Republic of China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, People's Republic of China
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Yang W, Liu Y, Dong R, Liu J, Lang J, Yang J, Wang W, Li J, Meng B, Tian G. Accurate Detection of HPV Integration Sites in Cervical Cancer Samples Using the Nanopore MinION Sequencer Without Error Correction. Front Genet 2020; 11:660. [PMID: 32714374 PMCID: PMC7344299 DOI: 10.3389/fgene.2020.00660] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
During the carcinogenesis of cervical cancer, the DNA of human papillomavirus (HPV) is frequently integrated into the human genome, which might be a biomarker for the early diagnosis of cervical cancer. Although the detection sensitivity of virus infection status increased significantly through the Illumina sequencing platform, there were still disadvantages remain for further improvement, including the detection accuracy and the complex integrated genome structure identification, etc. Nanopore sequencing has been proven to be a fast yet accurate technique of detecting pathogens in clinical samples with significant longer sequencing length. However, the identification of virus integration sites, especially HPV integration sites was seldom carried out by using nanopore platform. In this study, we evaluated the feasibility of identifying HPV integration sites by nanopore sequencer. Specifically, we re-sequenced the integration sites of a previously published sample by both nanopore and Illumina sequencing. After analyzing the results, three points of conclusions were drawn: first, 13 out of 19 previously published integration sites were found from all three datasets (i.e., nanopore, Illumina, and the published data), indicating a high overlap rate and comparability among the three platforms; second, our pipeline of nanopore and Illumina data identified 66 unique integration sites compared with previous published paper with 13 of them being verified by Sanger sequencing, indicating the higher integration sites detection sensitivity of our results compared with published data; third, we established a pipeline which could be used in HPV integration site detection by nanopore sequencing data without doing error correction analysis. In summary, a new nanopore data analysis method was tested and proved to be reliable in integration sites detection compared with methods of existing Illumina data analysis pipeline with less sequencing data required. It provides a solid evidence and tool to support the potential application of nanopore in virus status identification.
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Affiliation(s)
| | - Ying Liu
- Laboratory of Genetics, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd., Beijing, China
| | | | | | | | - Jingjing Li
- The Precision Medicine Centre of Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Bo Meng
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
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10
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Dong L, Zhang L, Hu SY, Feng RM, Zhao XL, Zhang Q, Pan QJ, Zhang X, Qiao YL, Zhao FH. Risk stratification of HPV 16 DNA methylation combined with E6 oncoprotein in cervical cancer screening: a 10-year prospective cohort study. Clin Epigenetics 2020; 12:62. [PMID: 32381054 PMCID: PMC7204324 DOI: 10.1186/s13148-020-00853-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
Background How to best triage human papillomavirus (HPV) positive women remains controversial in an era of HPV primary screening of cervical cancer. Here, we assessed the long-term risk stratification for triaging HPV 16 positive women by standalone HPV 16 methylation and combined with E6 oncoprotein. Methods A total of 1742 women underwent screening with HPV DNA testing, cytology, and visual inspection with acetic acid (VIA) in 2005 and were followed for 10 years. Seventy-seven women with HPV 16 positivity determined by HPV genotyping test were examined via E6 oncoprotein detection and bisulfite pyrosequencing for quantitative methylation of L1 and LCR genes of HPV 16. Results The 10-year cumulative incidence rate (CIR) of cervical intraepithelial neoplasia grade 3 or severe (CIN3+) for HPV 16 positive women was 25.3% (95% CI 14.7–37.3%), which significantly increased in women with high methylation at six sites (CpG 5602, 6650, 7034, 7461, 31, and 37) and in women with positive E6 oncoprotein. A methylation panel based on the above six sites showed a competitive risk stratification compared to cytology (HR 11.5 vs. 8.1), with a higher 10-year CIR of CIN3+ in panel positives (57.2% vs 36.8%) and comparable low risk in panel negatives (5.7% vs 4.8%).The sensitivity and specificity for accumulative CIN3+ was 85.7% (95%CI 60.1–96.0%) and 78.4% (95%CI 62.8–88.6%) for a methylation panel and 57.1% (95%CI 32.6–78.6%) and 86.5% (95%CI 72.0–94.1%) for E6 oncoprotein. The AUC values of methylation standalone and the co-testing of methylation panel and E6 oncoprotein were around 0.80, comparable to 0.68 for cytology, 0.65 for viral load, and superior to 0.52 for VIA (p < 0.05). Conclusions Our findings indicated the promising use of HPV 16 methylation alone or combined with E6 oncoprotein for triaging HPV 16 positive women based on the long-term risk stratification ability.
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Affiliation(s)
- Li Dong
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China.,Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Li Zhang
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Shang-Ying Hu
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Rui-Mei Feng
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Xue-Lian Zhao
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Qian Zhang
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Qin-Jing Pan
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Xun Zhang
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - You-Lin Qiao
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China
| | - Fang-Hui Zhao
- Department of Cancer Epidemiology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, P.O. Box 2258, Beijing, 100021, China.
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11
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Fertey J, Hagmann J, Ruscheweyh HJ, Munk C, Kjaer S, Huson D, Haedicke-Jarboui J, Stubenrauch F, Iftner T. Methylation of CpG 5962 in L1 of the human papillomavirus 16 genome as a potential predictive marker for viral persistence: A prospective large cohort study using cervical swab samples. Cancer Med 2019; 9:1058-1068. [PMID: 31856411 PMCID: PMC6997067 DOI: 10.1002/cam4.2771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 01/06/2023] Open
Abstract
Several studies have demonstrated that the viral genome can be methylated by the host cell during progression from persistent infection to cervical cancer. The aim of this study was to investigate whether methylation at a specific site could predict the development of viral persistence and whether viral load shows a correlation with specific methylation patterns. HPV16‐positive samples from women aged 20–29 years (n = 99) with a follow‐up time of 13 years, were included from a Danish cohort comprising 11 088 women. Viral load was measured by real‐time PCR and methylation status was determined for 39 CpG sites in the upstream regulatory region (URR), E6/E7, and L1 region of HPV16 by next‐generation sequencing. Participants were divided into two groups according to whether they were persistently (≥ 24 months) or transiently HPV16 infected. The general methylation status was significantly different between women with a persistent and women with a transient infection outcome (P = .025). One site located in L1 (nt. 5962) was statistically significantly (P = .00048) different in the methylation status after correction using the Holm‐Sidak method (alpha = 0.05). Correlation analyses of samples from HPV16 persistently infected women suggest that methylation is higher although viral load is lower. This study indicates that methylation at position 5962 of the HPV16 genome within the L1 gene might be a predictive marker for the development of a persistent HPV16 infection.
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Affiliation(s)
- Jasmin Fertey
- Medical Virology, Institute of Medical Virology, University Hospital of Tuebingen, Tuebingen, Germany
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | | | - Christian Munk
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Susanne Kjaer
- Unit of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Daniel Huson
- Centre for Bioinformatics, Tuebingen University, Tuebingen, Germany
| | - Juliane Haedicke-Jarboui
- Medical Virology, Institute of Medical Virology, University Hospital of Tuebingen, Tuebingen, Germany
| | - Frank Stubenrauch
- Medical Virology, Institute of Medical Virology, University Hospital of Tuebingen, Tuebingen, Germany
| | - Thomas Iftner
- Medical Virology, Institute of Medical Virology, University Hospital of Tuebingen, Tuebingen, Germany
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12
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Influence of pre-pregnancy body mass index (p-BMI) and gestational weight gain (GWG) on DNA methylation and protein expression of obesogenic genes in umbilical vein. PLoS One 2019; 14:e0226010. [PMID: 31794592 PMCID: PMC6890247 DOI: 10.1371/journal.pone.0226010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/17/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the regulatory mechanisms that affect obesogenic genes expression in newborns is essential for early prevention efforts, but they remain unclear. Our study aimed to explore whether the maternal p-BMI and GWG were associated with regulatory single-locus DNA methylation in selected obesogenic genes. For this purpose, DNA methylation was assayed by Methylation-Sensitive High Resolution Melting (MS-HRM) technique and Sanger allele-bisulfite sequencing in fifty samples of umbilical vein to evaluate glucosamine-6-phosphate deaminase 2 (GNPDA2), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α), and leptin receptor (LEPR) genes. Correlations between DNA methylation levels and indicators of maternal nutritional status were carried out. Western blotting was used to evaluate protein expression in extracts of the same samples. Results indicated that GNPDA2 and PGC1α genes have the same level of DNA methylation in all samples; however, a differential DNA methylation of LEPR gene promoter was found, correlating it with GWG and this correlation is unaffected by maternal age or unhealthy habits. Furthermore, leptin receptor (Lep-Rb) was upregulated in samples that showed the lowest levels of DNA methylation. This study highlights the association between poor GWG and adjustments on obesogenic genes expression in newborn tissues with potential consequences for development of obesity in the future.
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13
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Zhao J, Zhu J, Guo J, Zhu T, Zhong J, Liu M, Ruan Y, Liao S, Li F. Genetic variability and functional implication of HPV16 from cervical intraepithelial neoplasia in Shanghai women. J Med Virol 2019; 92:372-381. [PMID: 31670402 DOI: 10.1002/jmv.25618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022]
Abstract
Human papillomavirus (HPV)16 gene mutation is usually associated with persistent HPV infection and cervical intraepithelial neoplasia (CIN). However, the functional implications of HPV16 mutations remain poorly understood.145 LCR/E6/E7 of the HPV16 isolates were amplified and sequenced, and HPV16 integration status was detected. In total, 89 SNPs (68 in the LCR, 13 in E6, 8 in E7) were discovered, 11 of which were nonsynonymous mutations (8 in E6, 3 in E7). The H85Y and E120D variants in E6 were significantly reduced in the high-grade squamous intraepithelial lesion (HSIL) group compared to the <HSIL group (P = .046 and .005), conversely the N29S in E7(P = .01). Amino acid substitutions (D32N/E, E36Q, H85Y, and E120D in E6 and N29H/S and R77C in E7) were predicted to have an effect on conserved structural and functional residues, and five amino acid substitutions (H85Y, E36Q, I34L, and D32E in E6; R77C in E7) would potentially change the secondary structure. "6329G>T," a potential binding site for TATA-binding protein, is the most common in LCR variants. A4 (Asian) was associated with an increased risk of HSIL compared to A1-3(P = .009). The H85/E120 in E6 and N29 in HPV16 E7 might play a critical role in carcinogenesis by disrupting p53 and Rb degradation due to affecting their interaction, respectively. In a word, the findings in this study provide preventative and therapeutic interventions of HPV16 -related cervical lesions/cancer.
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Affiliation(s)
- Junwei Zhao
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiacheng Zhu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Maternal and Child Health Research Institute, BGI-Shenzhen, Shenzhen, China
| | - Junhan Guo
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tailin Zhu
- School of Physics HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Jixing Zhong
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Min Liu
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yetian Ruan
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shujie Liao
- Shujie Liao Cancer Biology Research Center, Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Li
- Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, Shanghai, China
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14
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Zhou C, Tuong ZK, Frazer IH. Papillomavirus Immune Evasion Strategies Target the Infected Cell and the Local Immune System. Front Oncol 2019; 9:682. [PMID: 31428574 PMCID: PMC6688195 DOI: 10.3389/fonc.2019.00682] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Persistent infection with human papillomavirus (HPV) initiates ~5% of all human cancers, and particularly cervical and oropharyngeal cancers. HPV vaccines prevent HPV infection, but do not eliminate existing HPV infections. Papillomaviruses induce hyperproliferation of epithelial cells. In this review we discuss how hyperproliferation renders epithelial cells less sensitive to immune attack, and impacts upon the efficiency of the local immune system. These observations have significance for the design of therapeutic HPV cancer immunotherapies.
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Affiliation(s)
- Chenhao Zhou
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Zewen Kelvin Tuong
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Ian Hector Frazer
- Faculty of Medicine, The University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, QLD, Australia
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