1
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Cui X, Li Y, Zhang C, Qi Y, Sun Y, Li W. Multiple HPV integration mode in the cell lines based on long-reads sequencing. Front Microbiol 2023; 14:1294146. [PMID: 38169727 PMCID: PMC10758443 DOI: 10.3389/fmicb.2023.1294146] [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: 09/19/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Background The integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome. Methods In this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines. Results We found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines. Conclusion Elucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.
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Affiliation(s)
- Xiaofang Cui
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
| | | | - Chuanpeng Zhang
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Yanwei Qi
- School of Control and Computer Engineering, North China Electric Power University, Beijing, China
| | | | - Weiyang Li
- Jining Medical University, Jining, Shandong, China
- Department of Bioinformatics, School of Biological Science, Jining Medical University, Rizhao, Shandong, China
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2
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Rao A, Ni Z, Suresh D, Mohanty C, Wang AR, Lee DL, Nickel KP, Varambally SRJ, Lambert PF, Kendziorski C, Iyer G. Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560587. [PMID: 37873389 PMCID: PMC10592929 DOI: 10.1101/2023.10.02.560587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.
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Affiliation(s)
- Aakarsha Rao
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Zijian Ni
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dhruthi Suresh
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
| | - Chitrasen Mohanty
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Albert R. Wang
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Denis L Lee
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Kwangok P. Nickel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Sooryanarayana Randall J. Varambally
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- University of Wisconsin Carbone Cancer Center, Madison, 53705, WI, USA
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gopal Iyer
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53705, USA
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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3
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Zygouras I, Leventakou D, Pouliakis A, Panagiotou S, Tsakogiannis D, Konstantopoulos G, Logotheti E, Samaras M, Kyriakopoulou Z, Beloukas A, Pateras IS, Delides A, Psyrri A, Panayiotides IG, Yiangou M, Kottaridi C. Human Papillomavirus 16 DNA Methylation Patterns and Investigation of Integration Status in Head and Neck Cancer Cases. Int J Mol Sci 2023; 24:14593. [PMID: 37834041 PMCID: PMC10572864 DOI: 10.3390/ijms241914593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Persistent high-risk human papillomavirus (HPV) infection is a pivotal factor in the progression of cervical cancer. In recent years, an increasing interest has emerged in comprehending the influence of HPV on head and neck squamous cell carcinoma (HNSCC). Notably, it is well established that HPV-associated HNSCC show cases with distinct molecular and clinical attributes compared to HPV-negative cases. The present study delves into the epigenetic landscape of HPV16, specifically its L1 gene and untranslated region (UTR), through pyrosequencing, while the HPV16 DNA physical status was evaluated using E2/E6 ratio analysis in HPV16-positive HNSCC FFPE biopsies. Our findings reveal substantial methylation across six sites within the HPV16 L1 gene and seven sites in the UTR. Specifically, methylation percentages of two L1 CpG sites (7136, 7145) exhibit significant associations with tumor histological grade (p < 0.01), while proving concurrent methylation across multiple sites. The HPV16 DNA physical status was not correlated with the methylation of viral genome or tumor characteristics. This is the first study that examines epigenetic modifications and the HPV16 DNA physical status in Greek HNSCC patients. Our findings suggest an orchestrated epigenetic modulation among specific sites, impacting viral gene expression and intricate virus-host interactions.
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Affiliation(s)
- Ioannis Zygouras
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Danai Leventakou
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Abraham Pouliakis
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Styliana Panagiotou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | | | - Georgios Konstantopoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Eirini Logotheti
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Menelaos Samaras
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Zaharoula Kyriakopoulou
- Department of Environment, School of Technology, University of Thessaly, Gaiopolis Campus, 41500 Larissa, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece;
- National AIDS Reference Centre of Southern Greece, School of Public Health, University of West Attica, 11521 Athens, Greece
| | - Ioannis S. Pateras
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Alexandros Delides
- 2nd Department of Otolaryngology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece;
| | - Amanda Psyrri
- 2nd Department of Internal Medicine-Propaedeutic, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece;
| | - Ioannis G. Panayiotides
- 2nd Department of Pathology, University General Hospital “Attikon”, School of Medicine, National and Kapodistrian University of Athens, 12464 Athens, Greece; (D.L.); (A.P.); (M.S.); (I.S.P.); (I.G.P.)
| | - Minas Yiangou
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
| | - Christine Kottaridi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (I.Z.); (S.P.); (G.K.); (E.L.); (M.Y.)
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Lim YX, Mierzwa ML, Sartor MA, D'Silva NJ. Clinical, morphologic and molecular heterogeneity of HPV-associated oropharyngeal cancer. Oncogene 2023; 42:2939-2955. [PMID: 37666939 PMCID: PMC10541327 DOI: 10.1038/s41388-023-02819-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
The incidence of human papillomavirus-positive (HPV+) oropharyngeal squamous cell carcinoma (OPSCC) is rising rapidly and has exceeded cervical cancer to become the most common HPV-induced cancer in developed countries. Since patients with HPV + OPSCC respond very favorably to standard aggressive treatment, the emphasis has changed to reducing treatment intensity. However, recent multi-center clinical trials failed to show non-inferiority of de-escalation strategies on a population basis, highlighting the need to select low-risk patients likely to respond to de-intensified treatments. In contrast, there is a substantial proportion of patients who develop recurrent disease despite aggressive therapy. This supports that HPV + OPSCC is not a homogeneous disease, but comprises distinct subtypes with clinical and biological variations. The overall goal for this review is to identify biomarkers for HPV + OPSCC that may be relevant for patient stratification for personalized treatment. We discuss HPV + OPSCC as a heterogeneous disease from multifaceted perspectives including clinical behavior, tumor morphology, and molecular phenotype. Molecular profiling from bulk tumors as well as single-cell sequencing data are discussed as potential driving factors of heterogeneity between tumor subgroups. Finally, we evaluate key challenges that may impede in-depth investigations of HPV + OPSCC heterogeneity and outline potential future directions, including a section on racial and ethnic differences.
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Affiliation(s)
- Yvonne X Lim
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011N. University Ave, Ann Arbor, MI, USA
| | - Michelle L Mierzwa
- Rogel Cancer Center, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, USA
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biostatistics, School of Public Health, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nisha J D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011N. University Ave, Ann Arbor, MI, USA.
- Rogel Cancer Center, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, USA.
- Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.
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5
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Karimzadeh M, Arlidge C, Rostami A, Lupien M, Bratman SV, Hoffman MM. Human papillomavirus integration transforms chromatin to drive oncogenesis. Genome Biol 2023; 24:142. [PMID: 37365652 DOI: 10.1186/s13059-023-02926-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Human papillomavirus (HPV) drives almost all cervical cancers and up to 70% of head and neck cancers. Frequent integration into the host genome occurs predominantly in tumorigenic types of HPV. We hypothesize that changes in chromatin state at the location of integration can result in changes in gene expression that contribute to the tumorigenicity of HPV. RESULTS We find that viral integration events often occur along with changes in chromatin state and expression of genes near the integration site. We investigate whether introduction of new transcription factor binding sites due to HPV integration could invoke these changes. Some regions within the HPV genome, particularly the position of a conserved CTCF binding site, show enriched chromatin accessibility signal. ChIP-seq reveals that the conserved CTCF binding site within the HPV genome binds CTCF in 4 HPV+ cancer cell lines. Significant changes in CTCF binding pattern and increases in chromatin accessibility occur exclusively within 100 kbp of HPV integration sites. The chromatin changes co-occur with out-sized changes in transcription and alternative splicing of local genes. Analysis of The Cancer Genome Atlas (TCGA) HPV+ tumors indicates that HPV integration upregulates genes which have significantly higher essentiality scores compared to randomly selected upregulated genes from the same tumors. CONCLUSIONS Our results suggest that introduction of a new CTCF binding site due to HPV integration reorganizes chromatin state and upregulates genes essential for tumor viability in some HPV+ tumors. These findings emphasize a newly recognized role of HPV integration in oncogenesis.
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Affiliation(s)
- Mehran Karimzadeh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
| | - Christopher Arlidge
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ariana Rostami
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Scott V Bratman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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6
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Tinhofer I, Staudte S, George S. Liquid biopsy in head neck cancer: ready for clinical routine diagnostics? Curr Opin Oncol 2023; 35:151-157. [PMID: 36966499 DOI: 10.1097/cco.0000000000000935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
PURPOSE OF REVIEW The bodily fluids of patients with solid cancers representing a minimally-invasive source of clinically exploitable biomarkers have attracted an increasing amount of attention in recent years. In patients with head and neck squamous cell carcinoma (HNSCC), cell-free tumour DNA (ctDNA) belongs to the most promising liquid biomarkers for monitoring disease burden and identifying patients at high risk of recurrence. In this review, we highlight recent studies, evaluating the analytical validity and clinical utility of ctDNA as a dynamic biomarker in HNSCC, especially as it relates to risk stratification and contrasting human papilloma virus (HPV+ and HPV-) and carcinomas. RECENT FINDINGS The clinical potential of minimal residual disease monitoring through viral ctDNA in identifying HPV+ oropharyngeal carcinoma patients at higher risk of recurrence has recently been demonstrated. Furthermore, accumulating evidence supports a potential diagnostic value of ctDNA dynamics in HPV-negative HNSCC. Altogether, recent data suggest that ctDNA analysis may be a valuable tool in guiding (de)escalation of surgical interventions as well as adaptation in radiotherapy dosage, both in the definitive and adjuvant settings. SUMMARY Rigorous clinical trials with patient-relevant endpoints are critical in order to demonstrate that treatment decisions based on ctDNA dynamics result in better outcomes in HNSCC.
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Affiliation(s)
- Ingeborg Tinhofer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
| | - Stephanie Staudte
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
| | - Stephen George
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
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7
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McInnis C, Bhatia S, Vijaykumar B, Tian Q, Sun Y, Leistritz-Edwards D, Quinn CT, Uppaluri R, Egloff AM, Srinivasan L, Pregibon DC, Coyle AJ, Hanna GJ. Identification of HPV16 E1 and E2-specific T cells in the oropharyngeal cancer tumor microenvironment. J Immunother Cancer 2023; 11:jitc-2023-006721. [PMID: 36990508 PMCID: PMC10069587 DOI: 10.1136/jitc-2023-006721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND High-risk human papillomavirus (HPV) is a primary cause of an increasing number of oropharyngeal squamous cell carcinomas (OPSCCs). The viral etiology of these cancers provides the opportunity for antigen-directed therapies that are restricted in scope compared with cancers without viral components. However, specific virally-encoded epitopes and their corresponding immune responses are not fully defined. METHODS To understand the OPSCC immune landscape, we conducted a comprehensive single-cell analysis of HPV16+ and HPV33+ primary tumors and metastatic lymph nodes. We used single-cell analysis with encoded peptide-human leukocyte antigen (HLA) tetramers to analyze HPV16+ and HPV33+ OPSCC tumors, characterizing the ex vivo cellular responses to HPV-derived antigens presented in major Class I and Class II HLA alleles. RESULTS We identified robust cytotoxic T-cell responses to HPV16 proteins E1 and E2 that were shared across multiple patients, particularly in HLA-A*01:01 and HLA-B*08:01. Responses to E2 were associated with loss of E2 expression in at least one tumor, indicating the functional capacity of these E2-recognizing T cells and many of these interactions validated in a functional assay. Conversely, cellular responses to E6 and E7 were limited in quantity and cytotoxic capacity, and tumor E6 and E7 expression persisted. CONCLUSIONS These data highlight antigenicity beyond HPV16 E6 and E7 and nominate candidates for antigen-directed therapies.
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Affiliation(s)
| | - Shilpa Bhatia
- Repertoire Immune Medicines, Cambridge, Massachusetts, USA
| | | | - Qiaomu Tian
- Repertoire Immune Medicines, Cambridge, Massachusetts, USA
| | - Yanbo Sun
- Repertoire Immune Medicines, Cambridge, Massachusetts, USA
| | | | - Charles T Quinn
- Center for Head and Neck Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ravi Uppaluri
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ann Marie Egloff
- Division of Otolaryngology-Head and Neck Surgery, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | | | | | - Glenn J Hanna
- Center for Head and Neck Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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8
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Vani NV, Madhanagopal R, Swaminathan R, Ganesan TS. Dynamics of oral human papillomavirus infection in healthy population and head and neck cancer. Cancer Med 2023. [PMID: 36846921 DOI: 10.1002/cam4.5686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
The recent increase in high-risk human papillomavirus (HR-HPV)-associated oral and oropharyngeal cancers has gained considerable importance due to their distinct clinical and molecular characteristics. However, the natural history of oral HPV from acquisition to persistence and malignant transformation is still unclear. The global prevalence of oral HPV infection in healthy individuals ranges from 0.67% to 35%, while 31%-38.5% in head and neck cancer (HNC). The persistence rate of oral HR-HPV infection is 5.5% -12.8% globally. India has the highest HNC burden due to apparent differences in predisposing factors compared with the West. The prevalence of oral HPV in healthy individuals and its contribution to HNC is less evident in Indian studies. HR-HPV-associated HNC in this region accounts for 26%, with an active infection in 8%-15% of these tumors. There is a lack of concordance in the expression of p16 as a surrogate marker for HPV detection in HNC because of differences in behavioral risk factors. Due to a lack of evidence, treatment de-escalation cannot be implemented despite the improved outcome of HPV-associated oropharyngeal cancers. This review critically analyzes the existing literature on the dynamics of oral HPV infection and HPV-associated HNC, identifying potential avenues for future research. A better understanding of the oncogenic role of HR-HPV in HNC will help to formulate novel therapeutic approaches and is expected to have a significant public health impact as preventive strategies can be implemented.
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Affiliation(s)
- N V Vani
- Epidemiology, Biostatistics, and Tumour Registry, Cancer Institute (WIA), Chennai, India
| | - R Madhanagopal
- Epidemiology, Biostatistics, and Tumour Registry, Cancer Institute (WIA), Chennai, India
| | - R Swaminathan
- Epidemiology, Biostatistics, and Tumour Registry, Cancer Institute (WIA), Chennai, India
| | - T S Ganesan
- Medical Oncology, Cancer Institute (WIA), Chennai, India
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9
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Boilesen DR, Neckermann P, Willert T, Müller MD, Schrödel S, Pertl C, Thirion C, Asbach B, Wagner R, Holst PJ. Efficacy and Synergy with Cisplatin of an Adenovirus Vectored Therapeutic E1E2E6E7 Vaccine against HPV Genome-Positive C3 Cancers in Mice. Cancer Immunol Res 2023; 11:261-275. [PMID: 36534088 DOI: 10.1158/2326-6066.cir-22-0174] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 08/25/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Human papillomavirus (HPV) infections are the main cause of cervical and oropharyngeal cancers. As prophylactic vaccines have no curative effect, an efficient therapy would be highly desired. Most therapeutic vaccine candidates target only a small subset of HPV regulatory proteins, namely, E6 and E7, and are therefore restricted in the breadth of their immune response. However, research has suggested E1 and E2 as promising targets to fight HPV+ cancer. Here, we report the design of adenoviral vectors efficiently expressing HPV16 E1 and E2 in addition to transformation-deficient E6 and E7. Vaccination elicited vigorous CD4+ and CD8+ T-cell responses against all encoded HPV16 proteins in outbred mice and against E1 and E7 in C57BL/6 mice. Therapeutic vaccination of C3 tumor-bearing mice led to significantly reduced tumor growth and enhanced survival for both small and established tumors. Tumor biopsies revealed increased numbers of tumor-infiltrating CD8+ T cells in treated mice. Cisplatin enhanced the effect of therapeutic vaccination, accompanied by enhanced infiltration of dendritic cells into the tumor. CD8+ T cells were identified as effector cells in T-cell depletion assays, seemingly under regulation by FoxP3+CD4+ regulatory T cells. Finally, therapeutic vaccination with Ad-Ii-E1E2E6E7 exhibited significantly enhanced survival compared with vaccination with two peptides each harboring a known E6/E7 epitope. We hypothesize that this difference could be due to the induction of additional T-cell responses against E1. These results support the use of this novel vaccine candidate targeting an extended set of antigens (Ad-Ii-E1E2E6E7), in combination with cisplatin, as an advanced strategy to combat HPV+ cancers.
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Affiliation(s)
- Ditte Rahbæk Boilesen
- Centre for Medical Parasitology, The Panum Institute, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,InProTher ApS, Copenhagen, Denmark
| | - Patrick Neckermann
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | | | - Mikkel Dons Müller
- Centre for Medical Parasitology, The Panum Institute, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,InProTher ApS, Copenhagen, Denmark
| | | | | | | | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany.,Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Peter Johannes Holst
- Centre for Medical Parasitology, The Panum Institute, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,InProTher ApS, Copenhagen, Denmark
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Prétet JL, Dalstein V, Touzé A, Beby-Defaux A, Soussan P, Jacquin É, Birembaut P, Clavel C, Mougin C, Rousseau A, Lacau Saint Guily J. High levels of HPV16-L1 antibody but not HPV16 DNA load or integration predict oropharyngeal patient outcome: The Papillophar study. Clin Exp Med 2023; 23:87-96. [PMID: 35199231 DOI: 10.1007/s10238-022-00796-2] [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: 09/30/2021] [Accepted: 01/18/2022] [Indexed: 11/30/2022]
Abstract
The incidence of oropharyngeal cancers (OPC) is increasing in the world. Among OPC, those induced by human papillomaviruses have a better prognosis than non-HPV-associated OPC. The objective of this study was to highlight the relevance of HPV16 load, HPV16 DNA integration and HPV16-L1 serology on progression-free survival and overall survival of OPC patients. The PAPILLOPHAR cohort consists of 362 patients with oropharyngeal squamous cell carcinomas prospectively followed up for 5 years after treatment. Tumor biopsies and sera were collected at inclusion to investigate tumor HPV DNA/RNA characteristics and HPV16 L1 serology, respectively. Twenty-seven percent of tumor biopsies were HPV DNA- and RNA-positive and HPV16 represented 93% of HPV-positive cases. Among them, neither HPV16 viral load nor HPV16 DNA integration was associated with overall survival (OS) or progression-free survival (PFS). In contrast, high anti-HPV16 L1 antibody titers were significantly associated with a better OS and PFS. This study reveals that HPV16 load and integration are not relevant prognosis biomarkers in OPC patients.Clinical Relevance: High levels of HPV16 L1 antibodies may be useful to predict OPC patient outcome following treatment.ClinicalTrials.gov Identifier: NCT00918710, May 2017.
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Affiliation(s)
- Jean-Luc Prétet
- Laboratoire de Biologie Cellulaire Et Moléculaire, PC-Bio, EA3181, UBFC, Université de Franche-Comté, CNR Papillomavirus, Centre Hospitalier Régional Universitaire, CHRU Besancon, Boulevard A Fleming, 25030, Besançon Cedex, France.
| | - Véronique Dalstein
- Inserm UMR-S 1250 P3Cell, Université de Reims Champagne-Ardenne, SFR CAP-Santé, 51092, Reims, France.,Laboratoire de Biopathologie, CHU Maison Blanche, Reims, France
| | - Antoine Touzé
- UMR INRAE ISP Équipe Biologie Des Infections À Polyomavirus, Faculté Des Sciences, Pharmaceutiques 31 avenue Monge, 37200, Tours, France
| | - Agnès Beby-Defaux
- Service de Virologie, CHU de Poitiers, Faculté de Médecine Et de Pharmacie de Poitiers, EA 4331 LITEC, Université de Poitiers, Poitiers, France
| | - Patrick Soussan
- Laboratoire de Virologie, Hôpital Tenon, CRSA Inserm U 938 Sorbonne University, Paris, France
| | - Élise Jacquin
- Laboratoire de Biologie Cellulaire Et Moléculaire, PC-Bio, EA3181, UBFC, Université de Franche-Comté, CNR Papillomavirus, Centre Hospitalier Régional Universitaire, CHRU Besancon, Boulevard A Fleming, 25030, Besançon Cedex, France.,INSERM UMR-S 1193, Faculté de Pharmacie, Châtenay-Malabry, France
| | - Philippe Birembaut
- Inserm UMR-S 1250 P3Cell, Université de Reims Champagne-Ardenne, SFR CAP-Santé, 51092, Reims, France.,Laboratoire de Biopathologie, CHU Maison Blanche, Reims, France
| | - Christine Clavel
- Inserm UMR-S 1250 P3Cell, Université de Reims Champagne-Ardenne, SFR CAP-Santé, 51092, Reims, France.,Laboratoire de Biopathologie, CHU Maison Blanche, Reims, France
| | - Christiane Mougin
- Laboratoire de Biologie Cellulaire Et Moléculaire, PC-Bio, EA3181, UBFC, Université de Franche-Comté, CNR Papillomavirus, Centre Hospitalier Régional Universitaire, CHRU Besancon, Boulevard A Fleming, 25030, Besançon Cedex, France.,INSERM UMR1098, Univ. Bourgogne Franche-Comté, 25000, Besançon Cedex, France
| | - Alexandra Rousseau
- Research Platform Paris-East (URCEST-CRC-CRB), Assistance Publique-Hôpitaux de Paris, Sorbonne University, Paris, France
| | - Jean Lacau Saint Guily
- Department of Otolaryngology, HNS, Tenon Hospital, APHP and Sorbonne University, Paris, France.,Department of OL-HNS, Rothschild Foundation Hospital and Sorbonne University, Paris, France
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11
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Papini C, Wang Z, Kudalkar SN, Schrank TP, Tang S, Sasaki T, Wu C, Tejada B, Ziegler SJ, Xiong Y, Issaeva N, Yarbrough WG, Anderson KS. Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer. iScience 2022; 25:105077. [PMID: 36164654 PMCID: PMC9508485 DOI: 10.1016/j.isci.2022.105077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 12/03/2022] Open
Abstract
APOBEC3 family members are cytidine deaminases catalyzing conversion of cytidine to uracil. Many studies have established a link between APOBEC3 expression and cancer development and progression, especially APOBEC3A (A3A) and APOBEC3B (A3B). Preclinical studies with human papillomavirus positive (HPV+) head and neck squamous cell carcinoma (HNSCC) and clinical trial specimens revealed induction of A3B, but not A3A expression after demethylation. We examined the kinetic features of the cytidine deaminase activity for full length A3B and found that longer substrates and a purine at −2 position favored by A3B, whereas A3A prefers shorter substrates and an adenine or thymine at −2 position. The importance and biological significance of A3B catalytic activity rather than A3A and a preference for purine at the −2 position was also established in HPV+ HNSCCs. Our study explored factors influencing formation of A3A and A3B-related cancer mutations that are essential for understanding APOBEC3-related carcinogenesis and facilitating drug discovery. A3B is upregulated after 5-AzaC treatment and related to 5-AzaC sensitivity in HPV+ HNSCC Full-length A3B prefers longer substrates and a purine at −2 site biochemically A3B also prefers a purine at −2 site in both HPV+ and HPV− HNSCC cells A3B signature at -2 site linked to poor patient survival in HPV+ HNSCC low smokers
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Affiliation(s)
- Christina Papini
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Zechen Wang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Shalley N Kudalkar
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Travis Parke Schrank
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Su Tang
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA
| | - Cory Wu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Brandon Tejada
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Samantha J Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Wendell G Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Lab Medicine, Lineberger Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karen S Anderson
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., New Haven, CT 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Kakavandi S, Goudarzi H, Faghihloo E. Evaluation of genotypes of human papilloma virus in cervical cancer samples collected from 2010 to 2020. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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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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Novel Antigenic Targets of HPV Therapeutic Vaccines. Vaccines (Basel) 2021; 9:vaccines9111262. [PMID: 34835193 PMCID: PMC8621534 DOI: 10.3390/vaccines9111262] [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: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 01/01/2023] Open
Abstract
Human papillomavirus (HPV) infection is the cause of the majority of cervical cancers and head and neck cancers worldwide. Although prophylactic vaccines and cervical cancer screening programs have shown efficacy in preventing HPV-associated cervical cancer, cervical cancer is still a major cause of morbidity and mortality, especially in third world countries. Furthermore, head and neck cancer cases caused by HPV infection and associated mortality are increasing. The need for better therapy is clear, and therapeutic vaccination generating cytotoxic T cells against HPV proteins is a promising strategy. This review covers the current scene of HPV therapeutic vaccines in clinical development and discusses relevant considerations for the design of future HPV therapeutic vaccines and clinical trials, such as HPV protein expression patterns, immunogenicity, and exhaustion in relation to the different stages and types of HPV-associated lesions and cancers. Ultimately, while the majority of the HPV therapeutic vaccines currently in clinical testing target the two HPV oncoproteins E6 and E7, we suggest that there is a need to include more HPV antigens in future HPV therapeutic vaccines to increase efficacy and find that especially E1 and E2 could be promising novel targets.
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