1
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Diniz CHDP, Henrique T, Stefanini ACB, De Castro TB, Tajara EH. Cetuximab chemotherapy resistance: Insight into the homeostatic evolution of head and neck cancer (Review). Oncol Rep 2024; 51:80. [PMID: 38639184 PMCID: PMC11056821 DOI: 10.3892/or.2024.8739] [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: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 04/20/2024] Open
Abstract
The complex evolution of genetic alterations in cancer that occurs in vivo is a selective process involving numerous factors and mechanisms. Chemotherapeutic agents that prevent the growth and spread of cancer cells induce selective pressure, leading to rapid artificial selection of resistant subclones. This rapid evolution is possible because antineoplastic drugs promote alterations in tumor‑cell metabolism, thus creating a bottleneck event. The few resistant cells that survive in this new environment obtain differential reproductive success that enables them to pass down the newly selected resistant gene pool. The present review aims to summarize key findings of tumor evolution, epithelial‑mesenchymal transition and resistance to cetuximab therapy in head and neck squamous cell carcinoma.
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Affiliation(s)
- Carlos Henrique De Paula Diniz
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
| | - Ana Carolina B. Stefanini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Department of Experimental Research, Albert Einstein Education and Research Israeli Institute, IIEPAE, São Paulo, SP 05652-900, Brazil
| | - Tialfi Bergamin De Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Microbial Pathogenesis Department, School of Dentistry, University of Maryland, Baltimore, MD 21201, USA
| | - Eloiza H. Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, SP 15090-000, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP 05508-090, Brazil
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2
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Yu L, Majerciak V, Lobanov A, Mirza S, Band V, Liu H, Cam M, Hughes SH, Lowy DR, Zheng ZM. HPV oncogenes expressed from only one of multiple integrated HPV DNA copies drive clonal cell expansion in cervical cancer. mBio 2024; 15:e0072924. [PMID: 38624210 PMCID: PMC11077993 DOI: 10.1128/mbio.00729-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
The integration of HPV DNA into human chromosomes plays a pivotal role in the onset of papillomavirus-related cancers. HPV DNA integration often occurs by linearizing the viral DNA in the E1/E2 region, resulting in the loss of a critical viral early polyadenylation signal (PAS), which is essential for the polyadenylation of the E6E7 bicistronic transcripts and for the expression of the viral E6 and E7 oncogenes. Here, we provide compelling evidence that, despite the presence of numerous integrated viral DNA copies, virus-host fusion transcripts originate from only a single integrated HPV DNA in HPV16 and HPV18 cervical cancers and cervical cancer-derived cell lines. The host genomic elements neighboring the integrated HPV DNA are critical for the efficient expression of the viral oncogenes that leads to clonal cell expansion. The fusion RNAs that are produced use a host RNA polyadenylation signal downstream of the integration site, and almost all involve splicing to host sequences. In cell culture, siRNAs specifically targeting the host portion of the virus-host fusion transcripts effectively silenced viral E6 and E7 expression. This, in turn, inhibited cell growth and promoted cell senescence in HPV16+ CaSki and HPV18+ HeLa cells. Showing that HPV E6 and E7 expression from a single integration site is instrumental in clonal cell expansion sheds new light on the mechanisms of HPV-induced carcinogenesis and could be used for the development of precision medicine tailored to combat HPV-related malignancies. IMPORTANCE Persistent oncogenic HPV infections lead to viral DNA integration into the human genome and the development of cervical, anogenital, and oropharyngeal cancers. The expression of the viral E6 and E7 oncogenes plays a key role in cell transformation and tumorigenesis. However, how E6 and E7 could be expressed from the integrated viral DNA which often lacks a viral polyadenylation signal in the cancer cells remains unknown. By analyzing the integrated HPV DNA sites and expressed HPV RNAs in cervical cancer tissues and cell lines, we show that HPV oncogenes are expressed from only one of multiple chromosomal HPV DNA integrated copies. A host polyadenylation signal downstream of the integrated viral DNA is used for polyadenylation and stabilization of the virus-host chimeric RNAs, making the oncogenic transcripts targetable by siRNAs. This observation provides further understanding of the tumorigenic mechanism of HPV integration and suggests possible therapeutic strategies for the development of precision medicine for HPV cancers.
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Affiliation(s)
- Lulu Yu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Vladimir Majerciak
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Sameer Mirza
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Haibin Liu
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR), National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Douglas R. Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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3
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Chatterjee S, Starrett GJ. Microhomology-mediated repair machinery and its relationship with HPV-mediated oncogenesis. J Med Virol 2024; 96:e29674. [PMID: 38757834 DOI: 10.1002/jmv.29674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Human Papillomaviruses (HPV) are a diverse family of non-enveloped dsDNA viruses that infect the skin and mucosal epithelia. Persistent HPV infections can lead to cancer frequently involving integration of the virus into the host genome, leading to sustained oncogene expression and loss of capsid and genome maintenance proteins. Microhomology-mediated double-strand break repair, a DNA double-stranded breaks repair pathway present in many organisms, was initially thought to be a backup but it's now seen as vital, especially in homologous recombination-deficient contexts. Increasing evidence has identified microhomology (MH) near HPV integration junctions, suggesting MH-mediated repair pathways drive integration. In this comprehensive review, we present a detailed summary of both the mechanisms underlying MH-mediated repair and the evidence for its involvement in HPV integration in cancer. Lastly, we highlight the involvement of these processes in the integration of other DNA viruses and the broader implications on virus lifecycles and host innate immune response.
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Affiliation(s)
- Subhajit Chatterjee
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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4
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Jones KM, Bryan A, McCunn E, Lantz PE, Blalock H, Ojeda IC, Mehta K, Cosper PF. The Causes and Consequences of DNA Damage and Chromosomal Instability Induced by Human Papillomavirus. Cancers (Basel) 2024; 16:1662. [PMID: 38730612 PMCID: PMC11083350 DOI: 10.3390/cancers16091662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
High-risk human papillomaviruses (HPVs) are the main cause of cervical, oropharyngeal, and anogenital cancers, which are all treated with definitive chemoradiation therapy when locally advanced. HPV proteins are known to exploit the host DNA damage response to enable viral replication and the epithelial differentiation protocol. This has far-reaching consequences for the host genome, as the DNA damage response is critical for the maintenance of genomic stability. HPV+ cells therefore have increased DNA damage, leading to widespread genomic instability, a hallmark of cancer, which can contribute to tumorigenesis. Following transformation, high-risk HPV oncoproteins induce chromosomal instability, or chromosome missegregation during mitosis, which is associated with a further increase in DNA damage, particularly due to micronuclei and double-strand break formation. Thus, HPV induces significant DNA damage and activation of the DNA damage response in multiple contexts, which likely affects radiation sensitivity and efficacy. Here, we review how HPV activates the DNA damage response, how it induces chromosome missegregation and micronuclei formation, and discuss how these factors may affect radiation response. Understanding how HPV affects the DNA damage response in the context of radiation therapy may help determine potential mechanisms to improve therapeutic response.
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Affiliation(s)
- Kathryn M. Jones
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Ava Bryan
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Emily McCunn
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Pate E. Lantz
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
| | - Hunter Blalock
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Isabel C. Ojeda
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Kavi Mehta
- Department of Comparative Biosciences, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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5
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Sastre-Garau X, Estrada-Virrueta L, Radvanyi F. HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas. Cancers (Basel) 2024; 16:1584. [PMID: 38672666 PMCID: PMC11048798 DOI: 10.3390/cancers16081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
In HPV-associated carcinomas, some examples of cancer-related genes altered by viral insertion and corresponding to potential therapeutic targets have been described, but no quantitative assessment of these events, including poorly recurrent targets, has been reported to date. To document these occurrences, we built and analyzed a database comprised of 1455 cases, including HPV genotypes and tumor localizations. Host DNA sequences targeted by viral integration were classified as "non-recurrent" (one single reported case; 838 loci), "weakly recurrent" (two reported cases; 82 loci), and highly recurrent (≥3 cases; 43 loci). Whereas the overall rate of cancer-related target genes was 3.3% in the Gencode database, this rate increased to 6.5% in "non-recurrent", 11.4% in "weakly recurrent", and 40.1% in "highly recurrent" genes targeted by integration (p = 4.9 × 10-4). This rate was also significantly higher in tumors associated with high-risk HPV16/18/45 than other genotypes. Among the genes targeted by HPV insertion, 30.2% corresponded to direct or indirect druggable targets, a rate rising to 50% in "highly recurrent" targets. Using data from the literature and the DepMap 23Q4 release database, we found that genes targeted by viral insertion could be new candidates potentially involved in HPV-associated oncogenesis. A more systematic characterization of HPV/host fusion DNA sequences in HPV-associated cancers should provide a better knowledge of HPV-driven carcinogenesis and favor the development of personalize patient treatments.
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Affiliation(s)
- Xavier Sastre-Garau
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, 94010 Créteil, France
| | - Lilia Estrada-Virrueta
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
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6
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Tabatabaeian H, Bai Y, Huang R, Chaurasia A, Darido C. Navigating therapeutic strategies: HPV classification in head and neck cancer. Br J Cancer 2024:10.1038/s41416-024-02655-1. [PMID: 38643337 DOI: 10.1038/s41416-024-02655-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 04/22/2024] Open
Abstract
The World Health Organisation recognised human papillomavirus (HPV) as the cause of multiple cancers, including head and neck cancers. HPV is a double-stranded DNA virus, and its viral gene expression can be controlled after infection by cellular and viral promoters. In cancer cells, the HPV genome is detected as either integrated into the host genome, episomal (extrachromosomal), or a mixture of integrated and episomal. Viral integration requires the breakage of both viral and host DNA, and the integration rate correlates with the level of DNA damage. Interestingly, patients with HPV-positive head and neck cancers generally have a good prognosis except for a group of patients with fully integrated HPV who show worst clinical outcomes. Those patients present with lowered expression of viral genes and limited infiltration of cytotoxic T cells. An impediment to effective therapy applications in the clinic is the sole testing for HPV positivity without considering the HPV integration status. This review will discuss HPV integration as a potential determinant of response to therapies in head and neck cancers and highlight to the field a novel therapeutic avenue that would reduce the cancer burden and improve patient survival.
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Affiliation(s)
| | - Yuchen Bai
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Ruihong Huang
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia
| | - Akhilanand Chaurasia
- Department of Oral Medicine and Radiology, Faculty of Dental Sciences King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Charbel Darido
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.
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7
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Yarbrough WG, Schrank TP, Burtness BA, Issaeva N. De-Escalated Therapy and Early Treatment of Recurrences in HPV-Associated Head and Neck Cancer: The Potential for Biomarkers to Revolutionize Personalized Therapy. Viruses 2024; 16:536. [PMID: 38675879 PMCID: PMC11053602 DOI: 10.3390/v16040536] [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: 02/19/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Human papillomavirus-associated (HPV+) head and neck squamous cell carcinoma (HNSCC) is the most common HPV-associated cancer in the United States, with a rapid increase in incidence over the last two decades. The burden of HPV+ HNSCC is likely to continue to rise, and given the long latency between infection and the development of HPV+ HNSCC, it is estimated that the effect of the HPV vaccine will not be reflected in HNSCC prevalence until 2060. Efforts have begun to decrease morbidity of standard therapies for this disease, and its improved characterization is being leveraged to identify and target molecular vulnerabilities. Companion biomarkers for new therapies will identify responsive tumors. A more basic understanding of two mechanisms of HPV carcinogenesis in the head and neck has identified subtypes of HPV+ HNSCC that correlate with different carcinogenic programs and that identify tumors with good or poor prognosis. Current development of biomarkers that reliably identify these two subtypes, as well as biomarkers that can detect recurrent disease at an earlier time, will have immediate clinical application.
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Affiliation(s)
- Wendell G. Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, Chapel Hill, NC 27599, USA; (T.P.S.); (N.I.)
- Department of Pathology and Lab Medicine, UNC School of Medicine, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC 27599, USA
| | - Travis P. Schrank
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, Chapel Hill, NC 27599, USA; (T.P.S.); (N.I.)
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC 27599, USA
| | - Barbara A. Burtness
- Department of Medicine, Medical Oncology, Yale School of Medicine, New Haven, CT 06510, USA;
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, UNC School of Medicine, Chapel Hill, NC 27599, USA; (T.P.S.); (N.I.)
- Department of Pathology and Lab Medicine, UNC School of Medicine, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC 27599, USA
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8
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Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O'Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet 2024; 111:544-561. [PMID: 38307027 PMCID: PMC10940022 DOI: 10.1016/j.ajhg.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 02/04/2024] Open
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cancer cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and our study applies long-read sequencing to this important chromosomal rearrangement type. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes, and only one BFB breakpoint showed chromothripsis. Five cell lines have a chromosomal region 11q BFB event, with YAP1-BIRC3-BIRC2 amplification. Indeed, YAP1 amplification is associated with a 10-year-earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that individuals with cervical cancer and YAP1-BIRC3-BIRC2 amplification, especially those of African ancestry, might benefit from targeted therapy. In summary, we uncovered valuable insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse G Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tim O'Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Laksh Malik
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Mary Carrington
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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9
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Xu S, Shi C, Zhou R, Han Y, Li N, Qu C, Xia R, Zhang C, Hu Y, Tian Z, Liu S, Wang L, Li J, Zhang Z. Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma. Clin Transl Med 2024; 14:e1556. [PMID: 38279874 PMCID: PMC10819103 DOI: 10.1002/ctm2.1556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND METHODS High-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing. RESULTS HPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process. CONCLUSIONS HPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.
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Affiliation(s)
- Shengming Xu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Chaoji Shi
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Rong Zhou
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Yong Han
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - NianNian Li
- Department of BioinfomaticsSequantaShanghaiChina
| | - Chuxiang Qu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Ronghui Xia
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Chunye Zhang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Yuhua Hu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhen Tian
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Shuli Liu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Lizhen Wang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Jiang Li
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
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10
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Wan M, Yang X, He L, Meng H. Elucidating the clonal relationship of esophageal second primary tumors in patients with laryngeal squamous cell carcinoma. Infect Agent Cancer 2023; 18:75. [PMID: 38017473 PMCID: PMC10685475 DOI: 10.1186/s13027-023-00558-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023] Open
Abstract
Laryngeal cancer ranks as the second most prevalent upper airway malignancy, following Lung cancer. Although some progress has been made in managing laryngeal cancer, the 5-year survival rate is disappointing. The gradual increase in the incidence of second primary tumors (SPTs) plays a crucial role in determining survival outcomes during long-term follow-up, and the esophagus was the most common site with a worse prognosis. In clinical practice, the treatment of esophageal second primary tumors (ESPT) in patients with laryngeal squamous cell carcinoma (LSCC) has always been challenging. For patients with synchronous tumors, several treatment modalities, such as radiotherapy, chemotherapy and potentially curative surgery are necessary but are typically poorly tolerated. Secondary cancer therapy options for metachronous patients are always constrained by index cancer treatment indications. Therefore, understanding the clonal origin of the second primary tumor may be an important issue in the treatment of patients. LSCC cells demonstrate genetic instability because of two distinct aetiologies (human papillomavirus (HPV)-negative and HPV-positive) disease. Various etiologies exhibit distinct oncogenic mechanisms, which subsequently impact the tissue microenvironment. The condition of the tissue microenvironment plays a crucial role in determining the destiny and clonal makeup of mutant cells during the initial stages of tumorigenesis. This review focuses on the genetic advances of LSCC, the current research status of SPT, and the influence of key carcinogenesis of HPV-positive and HPV-negative LSCC on clonal evolution of ESPT cells. The objective is to gain a comprehensive understanding of the molecular basis underlying the clonal origins of SPT, thereby offering novel perspectives for future investigations in this field.
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Affiliation(s)
- Meixuan Wan
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Xinxin Yang
- Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Lin He
- Department of Stomatology, Heilongjiang Province Hospital, Harbin, 150081, China
| | - Hongxue Meng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
- Precision Medicine Center, Harbin Medical University Cancer Hospital, Harbin, 150081, China.
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11
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Gauthier MA, Kadam A, Leveque G, Golabi N, Zeitouni A, Richardson K, Mascarella M, Sadeghi N, Loganathan SK. Long-read sequencing of oropharyngeal squamous cell carcinoma tumors reveal diverse patterns of high-risk Human Papillomavirus integration. Front Oncol 2023; 13:1264646. [PMID: 37916168 PMCID: PMC10616875 DOI: 10.3389/fonc.2023.1264646] [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: 07/21/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction In North America and in most European countries, Human Papillomavirus (HPV) is responsible for over 70% of oropharyngeal squamous cell carcinomas. The burden of OPSCC, in high-income countries, has been steadily increasing over the past 20 years. As a result, in the USA and in the UK, the burden of HPV-related oropharyngeal squamous cell carcinoma in men has now surpassed that of cervical cancer in women. However, the oncogenic impact of high-risk HPV integration in oropharyngeal squamous cell carcinomas hasn't been extensively studied. The present study aimed to explore the patterns of HPV integration in oropharyngeal squamous cell carcinomas and to assess the feasibility and reliability of long-read sequencing technology in detecting viral integration events in oropharyngeal head and neck cancers. Methods A cohort of eight HPV-positive OPSCC pre-treatment patient tumors (four males and four females), were selected. All patients received a p16INK4A positive OPSCC diagnosis and were treated at the McGill University Health Centre, a quaternary center in Montreal. A minimum of 20mg of tumor tissue was used for DNA extraction. Extracted DNA was subjected to Nanopore long-read sequencing to detect and analyze for the presence of high-risk HPV sequences. PCR and Sanger sequencing experiments were performed to confirm Nanopore long-read sequencing readings. Results Nanopore long-read sequencing showed that seven out of eight patient samples displayed either integrated or episomal high-risk HPV sequences. Out of these seven samples, four displayed verifiable integration events upon bioinformatic analysis. Integration confirmation experiments were designed for all four samples using PCR-based methods. Sanger sequencing was also performed. Four distinct HPV integration patterns were identified: concatemer chromosomal integration in a single chromosome, bi-chromosomal concatemer integration, single chromosome complete integration and bi-chromosomal complete integration. HPV concatemer integration also proved more common than full HPV integration events. Conclusion and relevance Long-read sequencing technologies can be effectively used to assess HPV integration patterns in OPSCC tumors. Clinically, more research should be conducted on the prognostication value of high-risk HPV integration in OPSCC tumors using long-read sequencing technology.
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Affiliation(s)
- Marc-Andre Gauthier
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Adway Kadam
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Gary Leveque
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Nahid Golabi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Anthony Zeitouni
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Keith Richardson
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Marco Mascarella
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Nader Sadeghi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Oncology, McGill University, Montreal, QC, Canada
| | - Sampath Kumar Loganathan
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Experimental Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Experimental Medicine, Department of Biochemistry and Goodman Cancer Research Institute, McGill University, Montreal, QC, Canada
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12
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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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13
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Zhang X, Zhu WY, Shen SY, Shen JH, Chen XD. Biological roles of RNA m7G modification and its implications in cancer. Biol Direct 2023; 18:58. [PMID: 37710294 PMCID: PMC10500781 DOI: 10.1186/s13062-023-00414-5] [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: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 09/16/2023] Open
Abstract
M7G modification, known as one of the common post-transcriptional modifications of RNA, is present in many different types of RNAs. With the accurate identification of m7G modifications within RNAs, their functional roles in the regulation of gene expression and different physiological functions have been revealed. In addition, there is growing evidence that m7G modifications are crucial in the emergence of cancer. Here, we review the most recent findings regarding the detection techniques, distribution, biological functions and Regulators of m7G. We also summarize the connections between m7G modifications and cancer development, drug resistance, and tumor microenvironment as well as we discuss the research's future directions and trends.
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Affiliation(s)
- Xin Zhang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Wen-Yan Zhu
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Shu-Yi Shen
- Department of Dermatology, the First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jia-Hao Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xiao-Dong Chen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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14
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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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15
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Chen B, Zhao L, Yang R, Xu T. Advances in molecular mechanism of HPV16 E5 oncoprotein carcinogenesis. Arch Biochem Biophys 2023; 745:109716. [PMID: 37553047 DOI: 10.1016/j.abb.2023.109716] [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: 05/16/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/10/2023]
Abstract
For a considerable duration, cervical cancer has posed a significant risk to the well-being and survival of women. The emergence and progression of cervical cancer have garnered extensive attention, with prolonged chronic infection of HPV serving as a crucial etiological factor. Consequently, investigating the molecular mechanism underlying HPV-induced cervical cancer has become a prominent research area. The HPV molecule is composed of a long control region (LCR), an early coding region and a late coding region.The early coding region encompasses E1, E2, E4, E5, E6, E7, while the late coding region comprises L1 and L2 ORF.The investigation into the molecular structure and function of HPV has garnered significant attention, with the aim of elucidating the carcinogenic mechanism of HPV and identifying potential targets for the treatment of cervical cancer. Research has demonstrated that the HPV gene and its encoded protein play a crucial role in the invasion and malignant transformation of host cells. Consequently, understanding the function of HPV oncoprotein is of paramount importance in comprehending the pathogenesis of cervical cancer. E6 and E7, the primary HPV oncogenic proteins, have been the subject of extensive study. Moreover, a number of contemporary investigations have demonstrated the significant involvement of HPV16 E5 oncoprotein in the malignant conversion of healthy cells through its regulation of cell proliferation, differentiation, and apoptosis via diverse pathways, albeit the precise molecular mechanism remains unclear. This manuscript aims to provide a comprehensive account of the molecular structure and life cycle of HPV.The HPV E5 oncoprotein mechanism modulates cellular processes such as proliferation, differentiation, apoptosis, and energy metabolism through its interaction with cell growth factor receptors and other cellular proteins. This mechanism is crucial for the survival, adhesion, migration, and invasion of tumor cells in the early stages of carcinogenesis. Recent studies have identified the HPV E5 oncoprotein as a promising therapeutic target for early-stage cervical cancer, thus offering a novel approach for treatment.
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Affiliation(s)
- Biqing Chen
- The Second Hospital of Jilin University, Changchun, China
| | - Liping Zhao
- The Second Hospital of Jilin University, Changchun, China
| | - Rulin Yang
- The Second Hospital of Jilin University, Changchun, China
| | - Tianmin Xu
- The Second Hospital of Jilin University, Changchun, China.
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16
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Song C, Chen X, Tang C, Xue P, Jiang Y, Qiao Y. Artificial intelligence for HPV status prediction based on disease-specific images in head and neck cancer: A systematic review and meta-analysis. J Med Virol 2023; 95:e29080. [PMID: 37691329 DOI: 10.1002/jmv.29080] [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: 04/07/2023] [Revised: 07/14/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023]
Abstract
Accurate early detection of the human papillomavirus (HPV) status in head and neck cancer (HNC) is crucial to identify at-risk populations, stratify patients, personalized treatment options, and predict prognosis. Artificial intelligence (AI) is an emerging tool to dissect imaging features. This systematic review and meta-analysis aimed to evaluate the performance of AI to predict the HPV positivity through the HPV-associated diseased images in HNC patients. A systematic literature search was conducted in databases including Ovid-MEDLINE, Embase, and Web of Science Core Collection for studies continuously published from inception up to October 30, 2022. Search strategies included keywords such as "artificial intelligence," "head and neck cancer," "HPV," and "sensitivity & specificity." Duplicates, articles without HPV predictions, letters, scientific reports, conference abstracts, or reviews were excluded. Binary diagnostic data were then extracted to generate contingency tables and then used to calculate the pooled sensitivity (SE), specificity (SP), area under the curve (AUC), and their 95% confidence interval (CI). A random-effects model was used for meta-analysis, four subgroup analyses were further explored. Totally, 22 original studies were included in the systematic review, 15 of which were eligible to generate 33 contingency tables for meta-analysis. The pooled SE and SP for all studies were 79% (95% CI: 75-82%) and 74% (95% CI: 69-78%) respectively, with an AUC of 0.83 (95% CI: 0.79-0.86). When only selecting one contingency table with the highest accuracy from each study, our analysis revealed a pooled SE of 79% (95% CI: 75-83%), SP of 75% (95% CI: 69-79%), and an AUC of 0.84 (95% CI: 0.81-0.87). The respective heterogeneities were moderate (I2 for SE and SP were 51.70% and 51.01%) and only low (35.99% and 21.44%). This evidence-based study showed an acceptable and promising performance for AI algorithms to predict HPV status in HNC but was not comparable to the routine p16 immunohistochemistry. The exploitation and optimization of AI algorithms warrant further research. Compared with previous studies, future studies anticipate to make progress in the selection of databases, improvement of international reporting guidelines, and application of high-quality deep learning algorithms.
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Affiliation(s)
- Cheng Song
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xu Chen
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Tang
- Shenzhen Maternity & Child Healthcare Hospital, Shenzhen, China
| | - Peng Xue
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Jiang
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Youlin Qiao
- School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Rodriguez I, Rossi NM, Keskus A, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley K, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.21.23294276. [PMID: 37662332 PMCID: PMC10473792 DOI: 10.1101/2023.08.21.23294276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved targeted therapeutics, and is the most common cause of cancer death in low-resource countries. We characterized 19 cervical and four head and neck cell lines using long-read DNA and RNA sequencing and identified the HPV types, HPV integration sites, chromosomal alterations, and cancer driver mutations. Structural variation analysis revealed telomeric deletions associated with DNA inversions resulting from breakage-fusion-bridge (BFB) cycles. BFB is a common mechanism of chromosomal alterations in cancer, and this is one of the first analyses of these events using long-read sequencing. Analysis of the inversion sites revealed staggered ends consistent with exonuclease digestion of the DNA after breakage. Some BFB events are complex, involving inter- or intra-chromosomal insertions or rearrangements. None of the BFB breakpoints had telomere sequences added to resolve the dicentric chromosomes and only one BFB breakpoint showed chromothripsis. Five cell lines have a Chr11q BFB event, with YAP1/BIRC2/BIRC3 gene amplification. Indeed, YAP1 amplification is associated with a 10-year earlier age of diagnosis of cervical cancer and is three times more common in African American women. This suggests that cervical cancer patients with YAP1/BIRC2/BIRC3-amplification, especially those of African American ancestry, might benefit from targeted therapy. In summary, we uncovered new insights into the mechanisms and consequences of BFB cycles in cervical cancer using long-read sequencing.
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Affiliation(s)
- Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Ayse Keskus
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Hong Lou
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jesica Godinez Paredes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Rose Milano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Nina Rao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Sonam Tulsyan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Joseph F. Boland
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Wen Luo
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jia Liu
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Tim O’Hanlon
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jazmyn Bess
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vera Mukhina
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medical Center, Baltimore, MD, USA
| | - Daria Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical System, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Laksh Malik
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Kimberley Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, USA and Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, Maryland, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Meredith Yeager
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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18
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Schrank TP, Kothari A, Weir WH, Stepp WH, Rehmani H, Liu X, Wang X, Sewell A, Li X, Tasoulas J, Kim S, Yarbrough G, Xie Y, Flamand Y, Marur S, Hayward MC, Wu D, Burtness B, Anderson KS, Baldwin AS, Yarbrough WG, Issaeva N. Noncanonical HPV carcinogenesis drives radiosensitization of head and neck tumors. Proc Natl Acad Sci U S A 2023; 120:e2216532120. [PMID: 37523561 PMCID: PMC10410762 DOI: 10.1073/pnas.2216532120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/07/2023] [Indexed: 08/02/2023] Open
Abstract
We analyzed transcriptional data from 104 HPV+ (Human papillomavirus) HNSCC (head and neck squamous cell carcinoma) tumors together with two publicly available sources to identify highly robust transcriptional programs (modules) which could be detected consistently despite heterogeneous sequencing and quantification methodologies. Among 22 modules identified, we found a single module that naturally subclassifies HPV+ HNSCC tumors based on a bimodal pattern of gene expression, clusters all atypical features of HPV+ HNSCC biology into a single subclass, and predicts patient outcome in four independent cohorts. The subclass-defining gene set was strongly correlated with Nuclear factor kappa B (NF-κB) target expression. Tumors with high expression of this NF-κB module were rarely associated with activating PIK3CA alterations or viral integration, and also expressed higher levels of HPHPV E2 and had decreased APOBEC mutagenesis. Alternatively, they harbored inactivating alterations of key regulators of NF-κB, TNF receptor associated factor 3 (TRAF3), and cylindromatosis (CYLD), as well as retinoblastoma protein (RB1). HPV+ HNSCC cells in culture with experimental depletion of TRAF3 or CYLD displayed increased expression of the subclass-defining genes, as well as robust radio-sensitization, thus recapitulating both the tumor transcriptional state and improved treatment response observed in patient data. Across all gene sets investigated, methylation to expression correlations were the strongest for the subclass-defining, NF-κB-related genes. Increased tumor-infiltrating CD4+ T cells and increased Estrogen receptors alpha (ERα) expression were identified in NF-κB active tumors. Based on the relatively high rates of cure in HPV+ HNSCC, deintensification of therapy to reduce treatment-related morbidity is being studied at many institutions. Tumor subclassification based on oncogenic subtypes may help guide the selection of therapeutic intensity or modality for patients with HPV+ HNSCC.
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Affiliation(s)
- Travis P. Schrank
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Aditi Kothari
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - William H. Weir
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Wesley H. Stepp
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Hina Rehmani
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Xinyi Liu
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL60612
- University of Illinois Cancer Center, Chicago, IL60612
| | - Xiaowei Wang
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL60612
- University of Illinois Cancer Center, Chicago, IL60612
| | - Andrew Sewell
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Xue Li
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Jason Tasoulas
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Sulgi Kim
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Gray Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Yue Xie
- Dana Farber Cancer Institute Eastern Cooperative Oncology Group and the American College of Radiology Imaging Network Biostatistics Center, Boston, MA02109
| | - Yael Flamand
- Dana Farber Cancer Institute Eastern Cooperative Oncology Group and the American College of Radiology Imaging Network Biostatistics Center, Boston, MA02109
| | - Shanthi Marur
- Johns Hopkins Univ/Sidney Kimmel Cancer Center, Baltimore, MD21231
| | - Michele C. Hayward
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Di Wu
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, The University of North Carolina School of Medicine at Chapel Hill, Chapel Hill, NC27599
| | - Barbara Burtness
- Department of Internal Medicine and Yale Cancer Center, New Haven, CT06510
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
| | - Albert S. Baldwin
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Wendell G. Yarbrough
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Natalia Issaeva
- Department of Otolaryngology/Head and Neck Surgery, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Department of Pathology and Lab Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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19
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Sun P, Wei P, Liu H, Wu J, Gross ND, Sikora AG, Wei Q, Shete S, Zafereo ME, Liu J, Li G. GWAS-identified telomere length associated genetic variants predict risk of recurrence of HPV-positive oropharyngeal cancer after definitive radiotherapy. EBioMedicine 2023; 94:104722. [PMID: 37487414 PMCID: PMC10382868 DOI: 10.1016/j.ebiom.2023.104722] [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: 05/13/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Lymphocyte telomere length (LTL)-related genetic variants may modulate LTL and affect recurrence of squamous cell carcinoma of the oropharynx (SCCOP). METHODS A total of 1013 patients with incident SCCOP were recruited and genotyped for 16 genome-wide association study (GWAS)-identified TL-related polymorphisms. Of these patients, 489 had tumour HPV16 status determination. Univariate and multivariate analyses were performed to evaluate associations. FINDINGS Of the 16 TL-related polymorphisms, four were significantly associated with LTL: rs1920116, rs3027234, rs6772228, and rs11125529, and the patients with putatively favourable genotypes had approximately 1.5-3 times the likelihood of shorter LTL compared with patients with the corresponding risk genotypes. Moreover, patients with one to four favourable genotypes of the four combined polymorphisms had approximately 3-11 times the likelihood of shorter LTL compared with patients with no favourable genotype. The four LTL-related polymorphisms were significantly associated with approximately 40% reduced risk (for favourable genotypes) or doubled risk (for risk genotypes) of recurrence, and similar but more pronounced associations were observed in patients with tumour HPV16-positive SCCOP. Similarly, patients with one to four risk genotypes had significantly approximately 2.5-4 times increased recurrence risk compared with patients with no risk genotype, and similar but more pronounced associations were observed in patients with tumour HPV16-positive SCCOP. INTERPRETATION Four LTL-related polymorphisms individually or jointly modify LTL and risk of recurrence of SCCOP, particularly HPV-positive SCCOP. These LTL-related polymorphisms could have potential to further stratify patients with HPV-positive SCCOP for individualized treatment and better survival. FUNDING Not applicable.
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Affiliation(s)
- Peng Sun
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA; Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Hongliang Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Neil D Gross
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Andrew G Sikora
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Qingyi Wei
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA; Department of Imaging Physics, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Mark E Zafereo
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA
| | - Jisheng Liu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA; Department of Epidemiology, The University of Texas MD Anderson Cancer Centre, Houston, TX 77030, USA.
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20
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Allevato MM, Smith JD, Brenner MJ, Chinn SB. Tumor-Derived Exosomes and the Role of Liquid Biopsy in Human Papillomavirus Oropharyngeal Squamous Cell Carcinoma. Cancer J 2023; 29:230-237. [PMID: 37471614 PMCID: PMC10372688 DOI: 10.1097/ppo.0000000000000671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
ABSTRACT The global incidence of human papillomavirus-positive (HPV+) head and neck squamous cell carcinoma (HNSCC) has surged in recent decades, with HPV+ HNSCC accounting for >70% of oropharynx cancers in the United States. Its incidence in men has surpassed that of HPV+ cervical cancer in women, and reliable assays are needed for early detection and to monitor response to therapy. Human papillomavirus-positive OPSCC has a more favorable response to therapy and prognosis than HPV-negative (HPV-) HNSCC, motivating regimens to deintensify curative surgery or chemoradiotherapy protocols. A barrier to deintensifying and personalizing therapy is lack of reliable predictive biomarkers. Furthermore, HPV- HNSCC survival rates are static without reliable surveillance biomarkers available. The emergence of circulating plasma-based biomarkers reflecting the tumor-immune microenvironment heralds a new era in HNSCC diagnosis and therapy. We review evidence on tumor-derived extracellular vesicles (exosomes) as biomarkers for diagnosis, prognostication, and treatment in HPV+ and HPV- HNSCC.
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Affiliation(s)
- Michael M. Allevato
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Joshua D. Smith
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michael J. Brenner
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Steven B. Chinn
- Department of Otolaryngology—Head and Neck Surgery, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Rogel Cancer Center, University of Michigan Health System, Ann Arbor, Michigan, USA
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21
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Chihu-Amparan L, Pedroza-Saavedra A, Gutierrez-Xicotencatl L. The Immune Response Generated against HPV Infection in Men and Its Implications in the Diagnosis of Cancer. Microorganisms 2023; 11:1609. [PMID: 37375112 DOI: 10.3390/microorganisms11061609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Human papillomavirus (HPV) infection is associated with precancerous lesions and cancer of the genital tract both in women and men. The high incidence of cervical cancer worldwide focused the research on this infection mainly in women and to a lesser extent in men. In this review, we summarized epidemiological, immunological, and diagnostic data associated with HPV and cancer in men. We presented an overview of the main characteristics of HPV and infection in men that are associated with different types of cancer but also associated with male infertility. Men are considered important vectors of HPV transmission to women; therefore, identifying the sexual and social behavioral risk factors associated with HPV infection in men is critical to understand the etiology of the disease. It is also essential to describe how the immune response develops in men during HPV infection or when vaccinated, since this knowledge could help to control the viral transmission to women, decreasing the incidence of cervical cancer, but also could reduce other HPV-associated cancers among men who have sex with men (MSM). Finally, we summarized the methods used over time to detect and genotype HPV genomes, as well as some diagnostic tests that use cellular and viral biomarkers that were identified in HPV-related cancers.
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Affiliation(s)
- Lilia Chihu-Amparan
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
| | - Adolfo Pedroza-Saavedra
- Center of Research for Infection Diseases, National Institute of Public Health, Cuernavaca 62100, Morelos, Mexico
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22
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Fazlalipour M, Ghoreshi ZAS, Molaei HR, Arefinia N. The Role of DNA Viruses in Human Cancer. Cancer Inform 2023; 22:11769351231154186. [PMID: 37363356 PMCID: PMC10286548 DOI: 10.1177/11769351231154186] [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: 09/08/2022] [Accepted: 01/03/2023] [Indexed: 06/28/2023] Open
Abstract
This review discusses the possible involvement of infections-associated cancers in humans, with virus infections contributing 15% to 20% of total cancer cases in humans. DNA virus encoded proteins interact with host cellular signaling pathways and control proliferation, cell death and genomic integrity viral oncoproteins are known to bind cellular Deubiquitinates (DUBs) such as cyclindromatosis tumor suppressor, ubiquitin-specific proteases 7, 11, 15 and 20, and A-20 to improve their intracellular stability and cellular signaling pathways and finally transformation. Human papillomaviruses (cervical carcinoma, oral cancer and laryngeal cancer); human polyomaviruses (mesotheliomas, brain tumors); Epstein-Barr virus (B-cell lymphoproliferative diseases and nasopharyngeal carcinoma); Kaposi's Sarcoma Herpesvirus (Kaposi's Sarcoma and primary effusion lymphomas); hepatitis B (hepatocellular carcinoma (HCC)) cause up to 20% of malignancies around the world.
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Affiliation(s)
- Mehdi Fazlalipour
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran (IPI), Tehran, Iran
- Research Center for Emerging and Reemerging Infectious diseases, Pasteur Institute of Iran (IPI), Tehran, Iran
| | | | - Hamid Reza Molaei
- Department of Medical Bacteriology and Virology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Nasir Arefinia
- Student Research Committee, Jiroft University of Medical Sciences, Jiroft, Iran
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23
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Modic Z, Cemazar M, Markelc B, Cör A, Sersa G, Kranjc Brezar S, Jesenko T. HPV-positive murine oral squamous cell carcinoma: development and characterization of a new mouse tumor model for immunological studies. J Transl Med 2023; 21:376. [PMID: 37296466 PMCID: PMC10257320 DOI: 10.1186/s12967-023-04221-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Infection with high-risk human papillomavirus (HPV) strains is one of the risk factors for the development of oral squamous cell carcinoma (OSCC). Some patients with HPV-positive OSCC have a better prognosis and respond better to various treatment modalities, including radiotherapy or immunotherapy. However, since HPV can only infect human cells, there are only a few immunocompetent mouse models available that enable immunological studies. Therefore, the aim of our study was to develop a transplantable immunocompetent mouse model of HPV-positive OSCC and characterize it in vitro and in vivo. METHODS Two monoclonal HPV-positive OSCC mouse cell lines were established by inducing the expression of HPV-16 oncogenes E6 and E7 in the MOC1 OSCC cell line using retroviral transduction. After confirming stable expression of HPV-16 E6 and E7 with quantitative real-time PCR and immunofluorescence staining, the cell lines were further characterized in vitro using proliferation assay, wound healing assay, clonogenic assay and RNA sequencing. In addition, tumor models were characterized in vivo in C57Bl/6NCrl mice in terms of their histological properties, tumor growth kinetics, and radiosensitivity. Furthermore, immunofluorescence staining of blood vessels, hypoxic areas, proliferating cells and immune cells was performed to characterize the tumor microenvironment of all three tumor models. RESULTS Characterization of the resulting MOC1-HPV cell lines and tumor models confirmed stable expression of HPV-16 oncogenes and differences in cell morphology, in vitro migration capacity, and tumor microenvironment characteristics. Although the cell lines did not differ in their intrinsic radiosensitivity, one of the HPV-positive tumor models, MOC1-HPV K1, showed a significantly longer growth delay after irradiation with a single dose of 15 Gy compared to parental MOC1 tumors. Consistent with this, MOC1-HPV K1 tumors had a lower percentage of hypoxic tumor area and a higher percentage of proliferating cells. Characteristics of the newly developed HPV-positive OSCC tumor models correlate with the transcriptomic profile of MOC1-HPV cell lines. CONCLUSIONS In conclusion, we developed and characterized a novel immunocompetent mouse model of HPV-positive OSCC that exhibits increased radiosensitivity and enables studies of immune-based treatment approaches in HPV-positive OSCC.
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Affiliation(s)
- Ziva Modic
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia.
- Faculty of Health Sciences, University of Primorska, Polje 42, Izola, Slovenia.
| | - Bostjan Markelc
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia
| | - Andrej Cör
- Department of Research, Valdoltra Orthopedic Hospital, Jadranska cesta 31, Ankaran, Slovenia
- Faculty of Education, University of Primorska, Cankarjeva pot 5, Koper, Slovenia
| | - Gregor Sersa
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Health Sciences, University of Ljubljana, Zdravstvena pot 5, Ljubljana, Slovenia
| | - Simona Kranjc Brezar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia
| | - Tanja Jesenko
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Zaloska cesta 2, Ljubljana, Slovenia.
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, Ljubljana, Slovenia.
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24
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Rossi NM, Dai J, Xie Y, Wangsa D, Heselmeyer-Haddad K, Lou H, Boland JF, Yeager M, Orozco R, Freites EA, Mirabello L, Gharzouzi E, Dean M. Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis. Cancer Res 2023; 83:1768-1781. [PMID: 36971511 PMCID: PMC10239328 DOI: 10.1158/0008-5472.can-22-3030] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
SIGNIFICANCE Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.
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Affiliation(s)
- Nicole M. Rossi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Jieqiong Dai
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yi Xie
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Darawalee Wangsa
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerstin Heselmeyer-Haddad
- Center for Cancer Research, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Lou
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F. Boland
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Leidos Biomedical Research, Inc., National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Enrique Alvirez Freites
- Hospital Central Universitario “Dr. Antonio M Pineda,” Barquisimeto, Lara State, Venezuela, and Universidad Andino de Cusco, Cusco, Perú
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
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25
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Chiliquinga AJ, Acosta B, Ogonaga-Borja I, Villarruel-Melquiades F, de la Garza J, Gariglio P, Ocádiz-Delgado R, Ramírez A, Sánchez-Pérez Y, García-Cuellar CM, Bañuelos C, Camacho J. Ion Channels as Potential Tools for the Diagnosis, Prognosis, and Treatment of HPV-Associated Cancers. Cells 2023; 12:1376. [PMID: 37408210 DOI: 10.3390/cells12101376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/19/2023] [Accepted: 05/05/2023] [Indexed: 07/07/2023] Open
Abstract
The human papilloma virus (HPV) group comprises approximately 200 genetic types that have a special affinity for epithelial tissues and can vary from producing benign symptoms to developing into complicated pathologies, such as cancer. The HPV replicative cycle affects various cellular and molecular processes, including DNA insertions and methylation and relevant pathways related to pRb and p53, as well as ion channel expression or function. Ion channels are responsible for the flow of ions across cell membranes and play very important roles in human physiology, including the regulation of ion homeostasis, electrical excitability, and cell signaling. However, when ion channel function or expression is altered, the channels can trigger a wide range of channelopathies, including cancer. In consequence, the up- or down-regulation of ion channels in cancer makes them attractive molecular markers for the diagnosis, prognosis, and treatment of the disease. Interestingly, the activity or expression of several ion channels is dysregulated in HPV-associated cancers. Here, we review the status of ion channels and their regulation in HPV-associated cancers and discuss the potential molecular mechanisms involved. Understanding the dynamics of ion channels in these cancers should help to improve early diagnosis, prognosis, and treatment in the benefit of HPV-associated cancer patients.
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Affiliation(s)
| | - Brenda Acosta
- Grupo de Investigación de Ciencias en Red, Universidad Técnica del Norte, Ibarra 100105, Ecuador
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Ingrid Ogonaga-Borja
- Grupo de Investigación de Ciencias en Red, Universidad Técnica del Norte, Ibarra 100105, Ecuador
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Fernanda Villarruel-Melquiades
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Jaime de la Garza
- Unidad de Oncología Torácica y Laboratorio de Medicina Personalizada, Instituto Nacional de Cancerología (INCan), Tlalpan, Ciudad de Mexico CP 14080, Mexico
| | - Patricio Gariglio
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Rodolfo Ocádiz-Delgado
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Ana Ramírez
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Tijuana 22390, Mexico
| | - Yesennia Sánchez-Pérez
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), Tlalpan, Ciudad de Mexico CP 14080, Mexico
| | - Claudia M García-Cuellar
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), Tlalpan, Ciudad de Mexico CP 14080, Mexico
| | - Cecilia Bañuelos
- Programa Transdisciplinario en Desarrollo Científico y Tecnológico para la Sociedad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
| | - Javier Camacho
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de Mexico CP 07360, Mexico
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26
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Zeng X, Wang Y, Liu B, Rao X, Cao C, Peng F, Zhi W, Wu P, Peng T, Wei Y, Chu T, Xu M, Xu Y, Ding W, Li G, Lin S, Wu P. Multi-omics data reveals novel impacts of human papillomavirus integration on the epigenomic and transcriptomic signatures of cervical tumorigenesis. J Med Virol 2023; 95:e28789. [PMID: 37212325 DOI: 10.1002/jmv.28789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023]
Abstract
Integration of human papilloma virus (HPV) DNA into the human genome may progressively contribute to cervical carcinogenesis. To explore how HPV integration affects gene expression by altering DNA methylation during carcinogenesis, we analyzed a multiomics dataset for cervical cancer. We obtained multiomics data by HPV-capture sequencing, RNA sequencing, and Whole Genome Bisulfite Sequencing from 50 patients with cervical cancer. We detected 985 and 485 HPV-integration sites in matched tumor and adjacent paratumor tissues. Of these, LINC00486 (n = 19), LINC02425 (n = 11), LLPH (n = 11), PROS1 (n = 5), KLF5 (n = 4), LINC00392 (n = 3), MIR205HG (n = 3) and NRG1 (n = 3) were identified as high-frequency HPV-integrated genes, including five novel recurrent genes. Patients at clinical stage II had the highest number of HPV integrations. E6 and E7 genes of HPV16 but not HPV18 showed significantly fewer breakpoints than random distribution. HPV integrations occurring in exons were associated with altered gene expression in tumor tissues but not in paratumor tissues. A list of HPV-integrated genes regulated at transcriptomic or epigenetic level was reported. We also carefully checked the candidate genes with regulation pattern correlated in both levels. HPV fragments integrated at MIR205HG mainly came from the L1 gene of HPV16. RNA expression of PROS1 was downregulated when HPV integrated in its upstream region. RNA expression of MIR205HG was elevated when HPV integrated into its enhancer. The promoter methylation levels of PROS1 and MIR205HG were all negatively correlated with their gene expressions. Further experimental validations proved that upregulation of MIR205HG could promote the proliferative and migrative abilities of cervical cancer cells. Our data provides a new atlas for epigenetic and transcriptomic regulations regarding HPV integrations in cervical cancer genome. We demonstrate that HPV integration may affect gene expression by altering methylation levels of MIR205HG and PROS1. Our study provides novel biological and clinical insights into HPV-induced cervical cancer.
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Affiliation(s)
- Xi Zeng
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuyouye Wang
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinjie Rao
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fang Peng
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wenhua Zhi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ye Wei
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guoliang Li
- Key Laboratory of Smart Farming for Agricultural Animals and Hubei Key Laboratory of Agricultural Bioinformatics, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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27
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Mima M, Okabe A, Hoshii T, Nakagawa T, Kurokawa T, Kondo S, Mizokami H, Fukuyo M, Fujiki R, Rahmutulla B, Yoshizaki T, Hanazawa T, Misawa K, Kaneda A. Tumorigenic activation around HPV integrated sites in head and neck squamous cell carcinoma. Int J Cancer 2023; 152:1847-1862. [PMID: 36650703 DOI: 10.1002/ijc.34439] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Human papillomavirus (HPV) is causally involved in the development of head and neck squamous cell carcinoma (HNSCC). The integration of HPV drives tumorigenesis through expression of oncogenic viral genes as well as genomic alterations in surrounding regions. To elucidate involvement of epigenetic dysregulation in tumorigenesis, we here performed integrated analyses of the epigenome, transcriptome and interactome using ChIP-seq, RNA-seq and Hi-C and 4C-seq for HPV(+) HNSCCs. We analyzed clinical HNSCC using The Cancer Genome Atlas data and found that genes neighboring HPV integration sites were significantly upregulated and were correlated with oncogenic phenotypes in HPV(+) HNSCCs. While we found four HPV integration sites in HPV(+) HNSCC cell line UPCI-SCC-090 through target enrichment sequencing, 4C-seq revealed 0.5 to 40 Mb of HPV-interacting regions (HPVIRs) where host genomic regions interacted with integrated HPV genomes. While 9% of the HPVIRs were amplified and activated epigenetically forming super-enhancers, the remaining non-amplified regions were found to show a significant increase in H3K27ac levels and an upregulation of genes associated with GO terms, for example, Signaling by WNT and Cell Cycle. Among those genes, ITPR3 was significantly upregulated, involving UPCI-SCC-090-specific super-enhancer formation around the ITPR3 promoter and in the 80-kb-downstream region. The knockdown of ITPR3 by siRNA or CRISPR deletions of the distant enhancer region led to a significant suppression of cell proliferation. The epigenetic activation of HPVIRs was also confirmed in other cell lines, UM-SCC-47 and UM-SCC-104. These data indicate that epigenetic activation in HPVIRs contributes, at least partially, to genesis of HPV(+) HNSCC.
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Affiliation(s)
- Masato Mima
- Department of Otorhinolaryngology, Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takuya Nakagawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoru Kondo
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Harue Mizokami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomokazu Yoshizaki
- Division of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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28
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Aguayo F, Perez-Dominguez F, Osorio JC, Oliva C, Calaf GM. PI3K/AKT/mTOR Signaling Pathway in HPV-Driven Head and Neck Carcinogenesis: Therapeutic Implications. BIOLOGY 2023; 12:biology12050672. [PMID: 37237486 DOI: 10.3390/biology12050672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
High-risk human papillomaviruses (HR-HPVs) are the causal agents of cervical, anogenital and a subset of head and neck carcinomas (HNCs). Indeed, oropharyngeal cancers are a type of HNC highly associated with HR-HPV infections and constitute a specific clinical entity. The oncogenic mechanism of HR-HPV involves E6/E7 oncoprotein overexpression for promoting cell immortalization and transformation, through the downregulation of p53 and pRB tumor suppressor proteins, among other cellular targets. Additionally, E6/E7 proteins are involved in promoting PI3K/AKT/mTOR signaling pathway alterations. In this review, we address the relationship between HR-HPV and PI3K/AKT/mTOR signaling pathway activation in HNC with an emphasis on its therapeutic importance.
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Affiliation(s)
- Francisco Aguayo
- Departamento de Biomedicina, Facultad de Medicina, Universidad de Tarapacá, Arica 1000000, Chile
| | - Francisco Perez-Dominguez
- Laboratorio de Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Julio C Osorio
- Laboratorio de Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Carolina Oliva
- Laboratorio de Oncovirología, Programa de Virología, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, Santiago 8380000, Chile
| | - Gloria M Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
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29
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Chen Y, Wang Y, Zhou P, Huang H, Li R, Zeng Z, Cui Z, Tian R, Jin Z, Liu J, Huang Z, Li L, Huang Z, Tian X, Yu M, Hu Z. VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:300-310. [PMID: 36804047 PMCID: PMC10626058 DOI: 10.1016/j.gpb.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein-Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.
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Affiliation(s)
- Ye Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Yuyan Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Ping Zhou
- Department of Obstetrics and Gynecology, Dongguan Maternal and Child Health Care Hospital, Dongguan 523000, China
| | - Hao Huang
- Office of Scientific Research & Development, Sun Yat-sen University, Guangzhou 510000, China
| | - Rui Li
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhen Zeng
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Rui Tian
- Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhuang Jin
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Jiashuo Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhaoyue Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Lifang Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zheying Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
| | - Meiying Yu
- Department of Pathology, the Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China.
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan 430062, China; Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China.
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30
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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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31
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Sofiani VH, Veisi P, Rukerd MRZ, Ghazi R, Nakhaie M. The complexity of human papilloma virus in cancers: a narrative review. Infect Agent Cancer 2023; 18:13. [PMID: 36843070 PMCID: PMC9969657 DOI: 10.1186/s13027-023-00488-w] [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: 08/17/2022] [Accepted: 02/09/2023] [Indexed: 02/27/2023] Open
Abstract
Among human tumorigenic viruses, the role of Human papillomavirus (HPV) has been proven as one of the most important oncoviruses that are associated with a large number of cancers. Most cancers of the genital area such cervical and anal cancer as are caused by HPV, and in many other cancers, such as colorectal, gastric, liver, esophageal, urinary bladder, and head and neck cancers, it is considered as one of the important risk factors. Our search was conducted for published researches between 2000 and 2022 by using several international databases including Scopus, PubMed, and Web of Science as well as Google scholar. We also evaluated additional evidence from relevant published articles. It has been demonstrated that HPV can promote tumorigenesis via focusing on genes, proteins, and signaling pathways, by using E6 and E7 oncoproteins and inhibiting two crucial tumor suppressors, P53 and Rb. The following study was performed to investigate different malignant cancers under the influence of HPV infection and changes in molecular factors caused by HPV infection.
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Affiliation(s)
- Vahideh Hamidi Sofiani
- grid.411747.00000 0004 0418 0096Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Parsa Veisi
- grid.411747.00000 0004 0418 0096Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammad Rezaei Zadeh Rukerd
- grid.412105.30000 0001 2092 9755Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Ghazi
- Department of Biotechnology, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Mohsen Nakhaie
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran.
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32
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Yeh TJ, Luo CW, Du JS, Huang CT, Wang MH, Chuang TM, Gau YC, Cho SF, Liu YC, Hsiao HH, Chen LT, Pan MR, Wang HC, Moi SH. Deciphering the Functions of Telomerase Reverse Transcriptase in Head and Neck Cancer. Biomedicines 2023; 11:691. [PMID: 36979671 PMCID: PMC10044978 DOI: 10.3390/biomedicines11030691] [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: 02/09/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/30/2023] Open
Abstract
Head and neck cancers (HNCs) are among the ten leading malignancies worldwide. Despite significant progress in all therapeutic modalities, predictive biomarkers, and targeted therapies for HNCs are limited and the survival rate is unsatisfactory. The importance of telomere maintenance via telomerase reactivation in carcinogenesis has been demonstrated in recent decades. Several mechanisms could activate telomerase reverse transcriptase (TERT), the most common of which is promoter alternation. Two major hotspot TERT promoter mutations (C228T and C250T) have been reported in different malignancies such as melanoma, genitourinary cancers, CNS tumors, hepatocellular carcinoma, thyroid cancers, sarcomas, and HNCs. The frequencies of TERT promoter mutations vary widely across tumors and is quite high in HNCs (11.9-64.7%). These mutations have been reported to be more enriched in oral cavity SCCs and HPV-negative tumors. The association between TERT promoter mutations and poor survival has also been demonstrated. Till now, several therapeutic strategies targeting telomerase have been developed although only a few drugs have been used in clinical trials. Here, we briefly review and summarize our current understanding and evidence of TERT promoter mutations in HNC patients.
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Affiliation(s)
- Tsung-Jang Yeh
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chi-Wen Luo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Department of Cosmetic Science and Institute of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan 717, Taiwan
| | - Jeng-Shiun Du
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chien-Tzu Huang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Min-Hung Wang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tzer-Ming Chuang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yuh-Ching Gau
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shih-Feng Cho
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Yi-Chang Liu
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hui-Hua Hsiao
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Li-Tzong Chen
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Hui-Ching Wang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N. A deep learning approach reveals unexplored landscape of viral expression in cancer. Nat Commun 2023; 14:785. [PMID: 36774364 PMCID: PMC9922274 DOI: 10.1038/s41467-023-36336-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/25/2023] [Indexed: 02/13/2023] Open
Abstract
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
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Affiliation(s)
| | - Ying Ye
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel E Schäffer
- The Wistar Institute, Philadelphia, PA, 19104, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Xue Hao
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | - Konstantinos Tsingas
- The Wistar Institute, Philadelphia, PA, 19104, USA.,University of Pennsylvania, Philadelphia, PA, USA
| | | | - Qi Long
- University of Pennsylvania, Philadelphia, PA, USA
| | - Quaid Morris
- Computational and Systems Biology, Sloan Kettering Institute, New York City, NY, 10065, USA
| | - Rugang Zhang
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Practical Application of Circulating Tumor-Related DNA of Human Papillomavirus in Liquid Biopsy to Evaluate the Molecular Response in Patients with Oropharyngeal Cancer. Cancers (Basel) 2023; 15:cancers15041047. [PMID: 36831390 PMCID: PMC9953792 DOI: 10.3390/cancers15041047] [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: 01/09/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Recent findings have shown that human papillomavirus (HPV) DNA is present in the blood as a tumor-specific biomarker (circulating tumor-related HPV; ctHPV) in patients with HPV-related oropharyngeal cancer (HPV-related OPC). The molecular response (MR) in patients with HPV-related OPC can be defined as the change in the number of ctHPV copies in relation to its initial quantity. The optimal model for assessing the MR using a liquid biopsy (LB) should be based on the E6/E7 sequences of the viral genome. MR assessment can help to evaluate the intensity of ongoing treatments in relation to the tumor response. The evaluation of the residual disease at the end of therapy may also be performed by MR assessment. If a partial MR (pMR) is found, caution is indicated and a subsequent LB should be considered, due to the likelihood of disease progression. Complete radiological and clinical responses together with a complete MR (cMR) convincingly indicate a low risk of treatment failure. Moreover, molecular recurrence (Mrec) during a follow-up, confirmed in two consecutive assays, even despite the lack of any other clinical or radiological symptoms of progression, indicates patients at high risk of disease recurrence. In conclusion, MR by ctHPV assessment may hasten the early detection of disease progression, at any stage of the management of the patient with HPV-related OPC.
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DNA Damage Response Mechanisms in Head and Neck Cancer: Significant Implications for Therapy and Survival. Int J Mol Sci 2023; 24:ijms24032760. [PMID: 36769087 PMCID: PMC9917521 DOI: 10.3390/ijms24032760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Head and neck cancer (HNC) is a term collectively used to describe a heterogeneous group of tumors that arise in the oral cavity, larynx, nasopharynx, oropharynx, and hypopharynx, and represents the sixth most common type of malignancy worldwide. Despite advances in multimodality treatment, the disease has a recurrence rate of around 50%, and the prognosis of metastatic patients remains poor. HNCs are characterized by a high degree of genomic instability, which involves a vicious circle of accumulating DNA damage, defective DNA damage repair (DDR), and replication stress. Nonetheless, the damage that is induced on tumor cells by chemo and radiotherapy relies on defective DDR processes for a successful response to treatment, and may play an important role in the development of novel and more effective therapies. This review summarizes the current knowledge on the genes and proteins that appear to be deregulated in DDR pathways, their implication in HNC pathogenesis, and the rationale behind targeting these genes and pathways for the development of new therapies. We give particular emphasis on the therapeutic targets that have shown promising results at the pre-clinical stage and on those that have so far been associated with a therapeutic advantage in the clinical setting.
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36
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Treating Head and Neck Cancer in the Age of Immunotherapy: A 2023 Update. Drugs 2023; 83:217-248. [PMID: 36645621 DOI: 10.1007/s40265-023-01835-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Most patients diagnosed with head and neck squamous cell carcinoma (HNSCC) will present with locally advanced disease, requiring multimodality therapy. While this approach has a curative intent, a significant subset of these patients will develop locoregional failure and/or distant metastases. The prognosis of these patients is poor, and therapeutic options other than palliative chemotherapy are urgently needed. Epidermal growth factor receptor (EGFR) overexpression is an important factor in the pathogenesis of HNSCC, and a decade ago, the EGFR targeting monoclonal antibody cetuximab was approved for the treatment of late-stage HNSCC in different settings. In 2016, the anti-programmed death-1 (PD-1) immune checkpoint inhibitors nivolumab and pembrolizumab were both approved for the treatment of patients with recurrent or metastatic HNSCC with disease progression on or after platinum-containing chemotherapy, and in 2019, pembrolizumab was approved for first-line treatment (either as monotherapy in PD-L1 expressing tumors, or in combination with chemotherapy). Currently, trials are ongoing to include immune checkpoint inhibition in the (neo)adjuvant treatment of HNSCC as well as in novel combinations with other drugs in the recurrent/metastatic setting to improve response rates and survival and help overcome resistance mechanisms to immune checkpoint blockade. This article provides a comprehensive review of the management of head and neck cancers in the current era of immunotherapy.
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37
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Rajendra S, Sharma P. Causal Link of Human Papillomavirus in Barrett Esophagus and Adenocarcinoma: Are We There Yet? Cancers (Basel) 2023; 15:cancers15030873. [PMID: 36765833 PMCID: PMC9913573 DOI: 10.3390/cancers15030873] [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: 11/27/2022] [Revised: 01/07/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Esophageal cancer is a relatively common malignancy worldwide with a high mortality (5-year survival of <15%). Despite screening, surveillance, improved imaging and treatment, the exponential rise in OAC continues. The strongest risk factors for OAC are chronic heartburn and metaplastic transformation of the lower third of the esophagus (Barrett's esophagus). The risk profile includes Caucasian race, male gender older age, obesity and smoking. Although the tumor risk in BO has been progressively revised downwards, the exponential rise in OAC remains unchecked. This paradox points to an unidentified missing link. Relatively recently, we provided the world's initial data for a strong association of biologically relevant hr-HPV with BD and OAC. Since then, systematic reviews and meta-analysis have documented HPV DNA prevalence rates in OAC of between 13 to 35%. In this review, we provide some evidence for a probable causal relationship between hr-HPV and OAC. This is challenging given the multifactorial etiology and long latency. Increasingly, high-risk HPV (hr-HPV) is regarded as a risk factor for OAC. This discovery will aid identification of a sub-group of high-risk progressors to esophageal cancer by surveillance and the development of effective preventive strategies including vaccination.
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Affiliation(s)
- Shanmugarajah Rajendra
- Gastro-Intestinal Viral Oncology Group, Ingham Institute for Applied Medical Research, Liverpool, Sydney, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
- Department of Gastroenterology & Hepatology, Bankstown-Lidcombe Hospital, South-Western Sydney Local Health Network, Bankstown, Sydney, NSW 2200, Australia
- Correspondence: ; Tel.: +61-(0)-2-9722-8814; Fax: +61-(0)-9722-8570
| | - Prateek Sharma
- Division of Gastroenterology and Hepatology, Veterans Affairs Medical Center, Kansas City, MO 64128, USA
- School of Medicine, University of Kansas, Kansas City, MO 66160, USA
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38
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Ferris RL, Westra W. Oropharyngeal Carcinoma with a Special Focus on HPV-Related Squamous Cell Carcinoma. ANNUAL REVIEW OF PATHOLOGY 2023; 18:515-535. [PMID: 36693202 DOI: 10.1146/annurev-pathmechdis-031521-041424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV-OPSCC) has one of the most rapidly increasing incidences of any cancer in high-income countries. The most recent (8th) edition of the Union for International Cancer Control/American Joint Committee on Cancer staging system separates HPV-OPSCC from its HPV-negative counterpart to account for the improved prognosis seen in the former. Indeed, owing to its improved prognosis and greater prevalence in younger individuals, numerous ongoing trials are examining the potential for treatment deintensification as a means to improve quality of life while maintaining acceptable survival outcomes. Owing to the distinct biology of HPV-OPSCCs, targeted therapies and immunotherapies have become an area of particular interest. Importantly, OPSCC is often detected at an advanced stage, highlighting the need for diagnostic biomarkers to aid in earlier detection. In this review, we highlight important advances in the epidemiology, pathology, diagnosis, and clinical management of HPV-OPSCC and underscore the need for a progressive understanding of the molecular basis of this disease toward early detection and precision care.
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Affiliation(s)
| | - William Westra
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, New York, USA
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Kusakabe M, Taguchi A, Tanikawa M, Hoshi D, Tsuchimochi S, Qian X, Toyohara Y, Kawata A, Wagatsuma R, Yamaguchi K, Yamamoto Y, Ikemura M, Sone K, Mori-Uchino M, Matsunaga H, Tsuruga T, Nagamatsu T, Kukimoto I, Wada-Hiraike O, Kawazu M, Ushiku T, Takeyama H, Oda K, Kawana K, Hippo Y, Osuga Y. Application of organoid culture from HPV18-positive small cell carcinoma of the uterine cervix for precision medicine. Cancer Med 2023; 12:8476-8489. [PMID: 36691316 PMCID: PMC10134306 DOI: 10.1002/cam4.5588] [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: 09/16/2022] [Revised: 11/27/2022] [Accepted: 12/17/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Small cell carcinoma of the uterine cervix (SCCC) is a rare and highly malignant human papillomavirus (HPV)-associated cancer in which human genes related to the integration site can serve as a target for precision medicine. The aim of our study was to establish a workflow for precision medicine of HPV-associated cancer using patient-derived organoid. METHODS Organoid was established from the biopsy of a patient diagnosed with HPV18-positive SCCC. Therapeutic targets were identified by whole exome sequencing (WES) and RNA-seq analysis. Drug sensitivity testing was performed using organoids and organoid-derived mouse xenograft model. RESULTS WES revealed that both the original tumor and organoid had 19 somatic variants in common, including the KRAS p.G12D pathogenic variant. Meanwhile, RNA-seq revealed that HPV18 was integrated into chromosome 8 at 8q24.21 with increased expression of the proto-oncogene MYC. Drug sensitivity testing revealed that a KRAS pathway inhibitor exerted strong anti-cancer effects on the SCCC organoid compared to a MYC inhibitor, which were also confirmed in the xenograft model. CONCLUSION In this study, we confirmed two strategies for identifying therapeutic targets of HPV-derived SCCC, WES for identifying pathogenic variants and RNA sequencing for identifying HPV integration sites. Organoid culture is an effective tool for unveiling the oncogenic process of rare tumors and can be a breakthrough for the development of precision medicine for patients with HPV-positive SCCC.
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Affiliation(s)
- Misako Kusakabe
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ayumi Taguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Michihiro Tanikawa
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Hoshi
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Saki Tsuchimochi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Xi Qian
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Toyohara
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Kawata
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,CBBD-OIL, AIST-Waseda University, Tokyo, Japan
| | - Kohei Yamaguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoko Yamamoto
- Department of Surgical Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenbun Sone
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mayuyo Mori-Uchino
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Tetsushi Tsuruga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,CBBD-OIL, AIST-Waseda University, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Katsutoshi Oda
- Division of Integrative Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Nihon University School of Medicine, Tokyo, Japan
| | - Yoshitaka Hippo
- Department of Molecular Carcinogenesis, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Goon P, Sudhoff H, Goerner M. Hit and run oncogeneses in head and neck cancers requires greater investigation. J Med Virol 2023; 95:e28254. [PMID: 36284485 DOI: 10.1002/jmv.28254] [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: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023]
Abstract
Head and neck cancers are unique in so far that two major oncogenic viruses, Epstein Barr virus (EBV) and Human papillomavirus (HPV) infect adjacent anatomy and cause nasopharyngeal and oropharyngeal cancers, respectively. Dominant recognized carcinogens are alcohol and tobacco but some head and neck cancers have been found to have mixed carcinogens (including betel leaf, areca nuts, slaked lime, viruses, etc.) involved in their oncogenesis and conversely, groups of patients with unknown or less dominant carcinogens involved in their development. These cancers may have had viral involvement in the past but then lost most of their viral nucleic acids (be they DNA and/or RNA) below a detection threshold, thus rendering them virus-negative. Some of these virus-negative tumors appear to have mutagenic signatures associated with virus-positive cancers, for example, from the APOBEC defense mechanism which is known to mutate viral nucleic acids as well as cause collateral damage to host DNA, with subsequent development of strongly viral prejudiced mutational signatures. These mechanisms are likely to be less efficient at oncogenesis than traditional EBV and HPV oncogenes directly driving mutagenesis, thus accounting for the smaller frequencies of these cancers found. More profound investigations of these unusual tumors are warranted to dissect out these mechanistic pathways.
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Affiliation(s)
- Peter Goon
- Department of Medicine, Division of Dermatology, Yong Loo Ling School of Medicine, National University Hospital, National University of Singapore, Singapore
| | - Holger Sudhoff
- Department of Otolaryngology & Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Bielefeld, Germany
| | - Martin Goerner
- Department of Haematology, Oncology and Palliative Medicine, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Bielefeld, Germany
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Huang Y, Zou D, Guo M, He M, He H, Li X, Zheng Q, Li Q, Mao Z. HPV and radiosensitivity of cervical cancer: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1405. [PMID: 36660629 PMCID: PMC9843372 DOI: 10.21037/atm-22-5930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Background and Objective Cervical cancer (CC), the most common gynecological malignancy, is divided into two categories: human papillomavirus-related [HPV positive (HPV+)] and non-HPV-related [HPV negative (HPV-)]. Compared with HPV- CC, HPV+ CC has better radiosensitivity and prognosis. We conducted a literature search and summarized relevant studies to explore the detailed mechanisms by which HPV+ improves the prognosis of CC compared to HPV-. Methods PubMed was used to search the literature on human papillomavirus, cervical cancer, and radiotherapy up to June 2022. Key Content and Findings Compared with HPV- CC, HPV+ CC has better radiotherapy outcomes and better prognosis. HPV improves the radiotherapy sensitivity of CC by inhibiting damaged DNA repair, increasing cell cycle arrest, reducing hypoxia, increasing cellular immune response, and other mechanisms. However, the effect of HPV on radiotherapy sensitivity of CC is not consistent and is affected by HPV type, viral load, and many other factors. Partial HPV+ CCs, due to hypoxia and other factors, are resistant to radiotherapy and have a poor prognosis. HPV- CC has poor radiotherapy sensitivity and poor prognosis. With the spread of the vaccine, HPV- CC will gradually increase, which is a cause for concern. Conclusions The radiosensitivity was significantly increased in patients with HPV+ CC, compared to HPV- patients. HPV improves the radiotherapy sensitivity of cervical cancer through a number of pathways. Meanwhile, the relationship between HPV and radiotherapy sensitivity is influenced by a number of factors. Some HPV+ CCs showed radiotherapy resistance, and HPV- CCs deserve further attention.
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Affiliation(s)
- Yue Huang
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Dongling Zou
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Mingfang Guo
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Misi He
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Hao He
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Xiuying Li
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Qian Zheng
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Qiaoling Li
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
| | - Zejia Mao
- Department of Gynecological Cancer Center, Affiliated Cancer Hospital of Chongqing University, Chongqing, China
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Khan A, Das BC, Abiha U, Sisodiya S, Chikara A, Nazir SU, Das AM, Rodrigues AG, Passari AK, Tanwar P, Hussain S, Rashid S, Rashid S. Insights into the role of complement regulatory proteins in HPV mediated cervical carcinogenesis. Semin Cancer Biol 2022; 86:583-589. [PMID: 34087416 DOI: 10.1016/j.semcancer.2021.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 01/27/2023]
Abstract
The persistent infection of high-risk Human papillomavirus (HR-HPV) induced cervical cancer remains a challenge in women worldwide including India. Recent advances in cancer research have paved the way for advanced cancer treatment modalities including immunotherapy by manipulating the function or number of cytotoxic T cells. It is well established that anaphylatoxins like C3a and C5a of complement system influence tumor growth by evading apoptosis leading to progression of cancer. The role of the complement system, particularly the complement regulatory proteins (CRPs) which are important determinants of immune response play a crucial role in carcinogenesis. In a tumor microenvironment (TME) assisted suppression of immune effector cells may be achieved through CRPs. However, recent advances in pharmacogenomics including drug designing and combination of these approaches have provided a holistic understanding of signaling pathways and their crosstalk, to regulate cellular communications.This review describes the role of complement system; particularly CRPs in HPV induced cervical carcinogenesis which may be used for designing anti- HPV or cervical cancer therapeutics.
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Affiliation(s)
- Asiya Khan
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India; Laboratory Oncology Unit, Rotary Cancer Center, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Bhudev C Das
- Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR), Health & Allied Sciences Amity University, Noida, India
| | - Umme Abiha
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | - Sandeep Sisodiya
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Ministry of Health & Family Welfare, Noida, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Atul Chikara
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Ministry of Health & Family Welfare, Noida, India; Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Sheeraz Un Nazir
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Ministry of Health & Family Welfare, Noida, India
| | - Ankan M Das
- Amity Institute of Public Health, Amity University, Noida, India
| | - Alexandre Gomes Rodrigues
- Alpha & Omega Labor, Messe-Alle, 23, 04158, Leipzig, Germany; University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173, Hannover, Germany
| | - Ajit Kumar Passari
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Pranay Tanwar
- Laboratory Oncology Unit, Rotary Cancer Center, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Showket Hussain
- Division of Molecular Oncology & Molecular Diagnostics, ICMR-National Institute of Cancer Prevention and Research, Ministry of Health & Family Welfare, Noida, India.
| | - Sabia Rashid
- Queen Elizabeth Hospital & King's College Hospital, Stadium Road, London, United Kingdom.
| | - Shazia Rashid
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
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Toal TW, Estrada-Florez AP, Polanco-Echeverry GM, Sahasrabudhe RM, Lott PC, Suarez-Olaya JJ, Guevara-Tique AA, Rocha S, Morales-Arana A, Castro-Valencia F, Urayama S, Kirane A, Wei D, Rios-Sarabia N, Medrano R, Mantilla A, Echeverry de Polanco M, Torres J, Bohorquez-Lozano ME, Carvajal-Carmona LG. Multiregional Sequencing Analysis Reveals Extensive Genetic Heterogeneity in Gastric Tumors from Latinos. CANCER RESEARCH COMMUNICATIONS 2022; 2:1487-1496. [PMID: 36970058 PMCID: PMC10035402 DOI: 10.1158/2767-9764.crc-22-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
UNLABELLED Gastric cancer is a leading cause of cancer mortality and health disparities in Latinos. We evaluated gastric intratumoral heterogeneity using multiregional sequencing of >700 cancer genes in 115 tumor biopsies from 32 patients, 29 who were Latinos. Analyses focused on comparisons with The Cancer Genome Atlas (TCGA) and on mutation clonality, druggability, and signatures. We found that only approximately 30% of all mutations were clonal and that only 61% of the known TCGA gastric cancer drivers harbored clonal mutations. Multiple clonal mutations were found in new candidate gastric cancer drivers such as EYS, FAT4, PCDHA1, RAD50, EXO1, RECQL4, and FSIP2. The genomically stable (GS) molecular subtype, which has the worse prognosis, was identified in 48% of our Latino patients, a fraction that was >2.3-fold higher than in TCGA Asian and White patients. Only a third of all tumors harbored clonal pathogenic mutations in druggable genes, with most (93%) GS tumors lacking actionable clonal mutations. Mutation signature analyses revealed that, in microsatellite-stable (MSS) tumors, DNA repair mutations were common for both tumor initiation and progression, while tobacco, POLE, and inflammation signatures likely initiate carcinogenesis. MSS tumor progression was likely driven by aging- and aflatoxin-associated mutations, as these latter changes were usually nonclonal. In microsatellite-unstable tumors, nonclonal tobacco-associated mutations were common. Our study, therefore, contributed to advancing gastric cancer molecular diagnostics and suggests clonal status is important to understanding gastric tumorigenesis. Our findings of a higher frequency of a poor prognosis associated molecular subtype in Latinos and a possible new aflatoxin gastric cancer etiology also advance cancer disparities research. SIGNIFICANCE Our study contributes to advancing our knowledge of gastric carcinogenesis, diagnostics, and cancer health disparities.
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Affiliation(s)
- Ted W. Toal
- Genome Center, University of California, Davis, California
| | - Ana P. Estrada-Florez
- Genome Center, University of California, Davis, California
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | | | | | - Paul C. Lott
- Genome Center, University of California, Davis, California
| | - John J. Suarez-Olaya
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Alix A. Guevara-Tique
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Sienna Rocha
- Genome Center, University of California, Davis, California
| | | | - Fabian Castro-Valencia
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Shiro Urayama
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Division of Gastroenterology & Hepatology, University of California, Davis, California
| | - Amanda Kirane
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | - Dongguang Wei
- Department of Pathology and Laboratory Medicine, University of California, Davis, California
| | - Nora Rios-Sarabia
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Rafael Medrano
- Departamento de Sarcomas y Tubo Digestivo Alto, Unidad Medica de Alta Especialidad en Oncología Instituto Mexicano del Seguro Social (IMSS), México City, México
| | - Alejandra Mantilla
- Departamento de Patología, Unidad Medica de Alta Especialidad en Oncología, Instituto Mexicano del Seguro Social (IMSS), México City, México
| | | | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas y Parasitarias, Unidad Médica de Alta Especialidad en Pediatría, Instituto Mexicano del Seguro Social, México City, México
| | - Mabel E. Bohorquez-Lozano
- Grupo de Citogenética, Filogenia y Evolución de las Poblaciones, Universidad del Tolima, Ibagué, Colombia
| | - Luis G. Carvajal-Carmona
- Genome Center, University of California, Davis, California
- UC Davis Comprehensive Cancer Center, Sacramento, California
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, California
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Ramberg IMS. Human papillomavirus-related neoplasia of the ocular adnexa. Acta Ophthalmol 2022; 100 Suppl 272:3-33. [PMID: 36203222 PMCID: PMC9827891 DOI: 10.1111/aos.15244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 08/21/2022] [Indexed: 01/12/2023]
Abstract
Human papillomaviruses (HPV) are involved in approximately 5% of solid cancers worldwide. The mucosotropic genotypes infect the stratified epithelium of various locations, where persistent infection may lead to invasive carcinomas. While the causative role of HPV in certain anogenital and head and neck carcinomas is well established, the role of HPV in carcinomas arising in the mucosal membranes of the ocular adnexal tissue (the lacrimal drainage system and the conjunctiva) has been a topic of great uncertainty. Therefore, we conducted a series of studies to assess the correlation between HPV and carcinomas arising in the mucosa of the ocular adnexal tissue and characterize the clinical, histopathological, and genomic features of the tumors in the context of HPV status in a Danish nationwide cohort. We collected clinical and histopathological data and tumor specimens from patients with carcinomas of the conjunctiva and the lacrimal drainage system, and their potential precursors, identified in Danish nationwide registries. The HPV status of the tumors was determined by the combined use of HPV DNA polymerase chain reaction (PCR), HPV E6/E7 mRNA in-situ hybridization, and p16 immunohistochemistry. The genomic profile was investigated by high-throughput DNA sequencing targeting 523 cancer-relevant genes. The literature to date on carcinomas of the lacrimal drainage system and the conjunctiva was summarized. In the Danish cohort, 67% of all carcinomas of the lacrimal drainage system and 21% of all conjunctival carcinomas were HPV-positive. HPV16 was the most frequently implicated genotype. A full-thickness expression of the viral oncogenes E6 and E7 was evident in almost all HPV DNA-positive cases. The HPV-positive carcinomas of the conjunctiva and the lacrimal drainage system shared histopathological and genomic features distinct from their HPV-negative counterparts. The HPV-positive carcinomas were characterized by a non-keratinizing morphology, p16 overexpression, high transcriptional activity of HPV E6/E7, and frequent pathogenic variants in the PI3K-AKT signaling cascade. In contrast, the HPV-negative carcinomas were characterized by a keratinizing morphology, lack of p16 and E6/E7 expression, and frequent somatic pathogenic variants in TP53, CDKN2A, and RB1. Among the patients with conjunctival tumors, HPV positivity was associated with a younger age at diagnosis and a higher risk of recurrence. In conclusion, the results support an etiological role of HPV in a subset of conjunctival and LDS carcinomas and their precursor lesions. Our investigations have shown that the HPV-positive carcinomas of the ocular adnexa share genomic and phenotypic characteristics with HPV-positive carcinomas of other anatomical locations. Therefore, these patients may be eligible for inclusion in future basket trials and future treatment regimens tailored to the more frequently occurring HPV-positive carcinomas of other locations. Future research will further elucidate the diagnostic, prognostic, and predictive role of HPV in these carcinomas.
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The Drivers, Mechanisms, and Consequences of Genome Instability in HPV-Driven Cancers. Cancers (Basel) 2022; 14:cancers14194623. [PMID: 36230545 PMCID: PMC9564061 DOI: 10.3390/cancers14194623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Cells infected with high-risk human papillomaviruses (HPV) can accumulate DNA damage and eventually transform into HPV-driven cancers. Genome instability, or the progressive accumulation of DNA alterations (e.g., mutations), in HPV-infected cells is directly induced by the HPV genes and indirectly promoted by HPV infection through the consequences of chronic infection maintenance, increased cell growth, and accumulation of damaging mutations in genes that themselves affect genome instability. While the HPV genome typically exists as a separate entity within cells, genome instability increases the chances of HPV integrating within the host (human) genome, which is common in HPV-induced cancers. The DNA regions surrounding HPV integrations are unstable and can undergo complex alterations that affect both human and HPV genes. This review discusses HPV-dependent and -independent drivers and mechanisms of genome instability in HPV-driven cancers, both globally and around sites of HPV integration, and describes the changes induced in the tumour genome. Abstract Human papillomavirus (HPV) is the causative driver of cervical cancer and a contributing risk factor of head and neck cancer and several anogenital cancers. HPV’s ability to induce genome instability contributes to its oncogenicity. HPV genes can induce genome instability in several ways, including modulating the cell cycle to favour proliferation, interacting with DNA damage repair pathways to bring high-fidelity repair pathways to viral episomes and away from the host genome, inducing DNA-damaging oxidative stress, and altering the length of telomeres. In addition, the presence of a chronic viral infection can lead to immune responses that also cause genome instability of the infected tissue. The HPV genome can become integrated into the host genome during HPV-induced tumorigenesis. Viral integration requires double-stranded breaks on the DNA; therefore, regions around the integration event are prone to structural alterations and themselves are targets of genome instability. In this review, we present the mechanisms by which HPV-dependent and -independent genome instability is initiated and maintained in HPV-driven cancers, both across the genome and at regions of HPV integration.
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Direct Comparison of HPV16 Viral Genomic Integration, Copy Loss, and Structural Variants in Oropharyngeal and Uterine Cervical Cancers Reveal Distinct Relationships to E2 Disruption and Somatic Alteration. Cancers (Basel) 2022; 14:cancers14184488. [PMID: 36139648 PMCID: PMC9496734 DOI: 10.3390/cancers14184488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Squamous cell carcinoma of the oropharynx caused by HPV type 16 (HPV16+ OPSCC) is the most common HPV-associated malignancy in the USA and has many molecular differences from uterine cervical squamous cell carcinoma (UCSCC). Our understanding of HPV oncogenesis relied on studies of UCSCC revealing a consensus model reliant on HPV integration with a loss of E2. Here, we compare patterns of HPV integration in UCSCC and OPSCC by analysis of affinity capture sequencing of the HPV16 genome in 104 OPSCC and 44 UCSCC tumors. These cohorts were contemporaneously sequenced using an identical strategy. Integration was identified using discordant read pair clustering and assembly-based approaches. Viral integration sites, structural variants, and copy losses were examined. While large-scale deep losses of HPV16 genes were common in UCSCC and were associated with E2 loss, deep copy losses of the HPV16 genome were infrequent in HPV16+ OPSCC. Similarly, structural variants within HPV16 favored E2 loss in UCSCC but not OPSCC. HPV16 integration sites were non-random, with recurrent integration hot-spots identified. OPSCC tumors had many more integration sites per tumor when compared to UCSCC and had more integration sites in genomic regions with high gene density. These data show that viral integration and E2 disruption are distinct in UCSCC and OPSCC. Our findings also add to growing literature suggesting that HPV tumorigenesis in OPSCC does not follow the model developed based on UCSCC.
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Katerji M, Bertucci A, Filippov V, Vazquez M, Chen X, Duerksen-Hughes PJ. Proton-induced DNA damage promotes integration of foreign plasmid DNA into human genome. Front Oncol 2022; 12:928545. [PMID: 36119491 PMCID: PMC9478911 DOI: 10.3389/fonc.2022.928545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/16/2022] [Indexed: 11/20/2022] Open
Abstract
High-risk human papillomaviruses (HPVs) cause virtually all cervical cancer cases and are also associated with other types of anogenital and oropharyngeal cancers. Normally, HPV exists as a circular episomal DNA in the infected cell. However, in some instances, it integrates into the human genome in such a way as to enable increased expression of viral oncogenes, thereby leading to carcinogenesis. Since viral integration requires breaks in both viral and human genomes, DNA damage likely plays a key role in this critical process. One potentially significant source of DNA damage is exposure to elevated doses of ionizing radiation. Natural background radiation is ubiquitous; however, some populations, including radiological workers, radiotherapy patients, and astronauts, are exposed to significantly higher radiation doses, as well as to different types of radiation such as particle radiation. We hypothesize that ionizing radiation-induced DNA damage facilitates the integration of HPV into the human genome, increasing the risk of developing HPV-related cancers in the exposed population. To test this, we first determined the kinetics of DNA damage in keratinocytes exposed to ionizing radiation (protons) by assessing γ-H2AX foci formation using immunofluorescence (direct damage), and also measured ROS and 8-oxoG levels via DCFDA and Avidin-FITC (indirect damage).As anticipated, direct DNA damage was observed promptly, within 30 min, whereas indirect DNA damage was delayed due to the time required for ROS to accumulate and cause oxidative damage. Although radiation was lethal at high doses, we were able to establish an experimental system where radiation exposure (protons and X-rays) induced DNA damage dose-dependently without causing major cytotoxic effects as assessed by several cytotoxicity assays. Most importantly, we explored the impact of radiation exposure on integration frequency using a clonogenic assay and demonstrated that as predicted, proton-induced DNA damage promotes the integration of HPV-like foreign DNA in oral keratinocytes. Overall, the insights gained from this work enable us to better understand the contribution of radiation exposure and DNA damage to HPV-mediated carcinogenesis and direct us toward strategies aimed at preventing malignancies in HPV-infected individuals.
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Affiliation(s)
- Meghri Katerji
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Antonella Bertucci
- Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Valery Filippov
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Marcelo Vazquez
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- Department of Radiation Medicine, Loma Linda University Medical Center, Loma Linda, CA, United States
| | - Xin Chen
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA, United States
| | - Penelope J. Duerksen-Hughes
- Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, United States
- *Correspondence: Penelope J. Duerksen-Hughes,
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Labarge B, Hennessy M, Zhang L, Goldrich D, Chartrand S, Purnell C, Wright S, Goldenberg D, Broach JR. Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer. Mol Cancer Res 2022; 20:1420-1428. [PMID: 35657601 PMCID: PMC9437566 DOI: 10.1158/1541-7786.mcr-21-0831] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/29/2022] [Accepted: 05/31/2022] [Indexed: 01/07/2023]
Abstract
Human papillomavirus (HPV)-positive head and neck cancers, predominantly oropharyngeal squamous cell carcinoma (OPSCC), exhibit epidemiologic, clinical, and molecular characteristics distinct from those OPSCCs lacking HPV. We applied a combination of whole-genome sequencing and optical genome mapping to interrogate the genome structure of HPV-positive OPSCCs. We found that the virus had integrated in the host genome in two thirds of the tumors examined but resided solely extrachromosomally in the other third. Integration of the virus occurred at essentially random sites within the genome. Focal amplification of the virus and the genomic sequences surrounding it often occurred subsequent to integration, with the number of tandem repeats in the chromosome accounting for the increased copy number of the genome sequences flanking the site of integration. In all cases, viral integration correlated with pervasive genome-wide somatic alterations at sites distinct from that of viral integration and comprised multiple insertions, deletions, translocations, inversions, and point mutations. Few or no somatic mutations were present in tumors with only episomal HPV. Our data could be interpreted by positing that episomal HPV is captured in the host genome following an episode of global genome instability during tumor development. Viral integration correlated with higher grade tumors, which may be explained by the associated extensive mutation of the genome and suggests that HPV integration status may inform prognosis. IMPLICATIONS Our results indicate that HPV integration in head and neck cancer correlates with extensive pangenomic structural variation, which may have prognostic implications.
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Affiliation(s)
- Brandon Labarge
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Max Hennessy
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Lijun Zhang
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldrich
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania.,Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania
| | - Scott Chartrand
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Carson Purnell
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Sage Wright
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania
| | - David Goldenberg
- Department of Otolaryngology, Penn State College of Medicine, Hershey, Pennsylvania
| | - James R. Broach
- Institute for Personalized Medicine, Penn State College of Medicine, Hershey, Pennsylvania.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania.,Corresponding Author: James R. Broach, Department of Biochemistry, Penn State College of Medicine, Hershey, PA 17033. Phone: 717-531-8586; E-mail:
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The HPV Induced Cancer Resource (THInCR): a Suite of Tools for Investigating HPV-Dependent Human Carcinogenesis. mSphere 2022; 7:e0031722. [PMID: 35950764 PMCID: PMC9429961 DOI: 10.1128/msphere.00317-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human papillomaviruses (HPVs) are highly infectious and cause the most common sexually transmitted viral infections. They induce hyperproliferation of squamous epithelial tissue, often forming warts. Virally encoded proteins reprogram gene expression and cell growth to create an optimal environment for viral replication. In addition to their normal roles in infection, functional alterations induced by viral proteins establish conditions that frequently contribute to human carcinogenesis. In fact, ~5% of human cancers are caused by HPVs, with virtually all cervical squamous cell carcinomas (CESC) and an increasing number of head and neck squamous cell carcinomas (HNSC) attributed to HPV infection. The Cancer Genome Atlas (TCGA) molecularly characterized thousands of primary human cancer samples in many cancer types, including CESC and HNSC, and created a comprehensive atlas of genomic, epigenomic, and transcriptomic data. This publicly available genome-wide information provides an unprecedented opportunity to expand the knowledge of the role that HPV plays in human carcinogenesis. While many tools exist to mine these data, few, if any, focus on the comparison of HPV-positive cancers with their HPV-negative counterparts or adjacent normal control tissue. We have constructed a suite of web-based tools, The HPV Induced Cancer Resource (THInCR), to utilize TCGA data for research related to HPV-induced CESC and HNSC. These tools allow investigators to gain greater biological and medical insights by exploring the impacts of HPV on cellular gene expression (mRNA and microRNA), altered gene methylation, and associations with patient survival and immune landscape features. These tools are accessible at https://thincr.ca/. IMPORTANCE The suite of analytical tools of THInCR provides the opportunity to investigate the roles that candidate target genes identified in cell lines or other model systems contribute to in actual HPV-dependent human cancers and is based on large-scale TCGA data sets. Expression of target genes, including both mRNA and microRNA, can be correlated with HPV gene expression, epigenetic changes in DNA methylation, patient survival, and numerous immune features, like leukocyte infiltration, interferon gamma response, T cell response, etc. Data from these analyses may immediately provide evidence to validate in vitro observations, reveal insights into mechanisms of virus-mediated alterations in cell growth, behavior, gene expression, and innate and adaptive immunity and may help hypothesis generation for further investigations.
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50
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Park NJY, Park CSY, Jeong JY, Kim M, Yoo SH, Chong GO, Hong DG, Park JY. Strategic Significance of Low Viral Load of Human Papillomavirus in Uterine Cervical Cytology Specimens. Diagnostics (Basel) 2022; 12:diagnostics12081855. [PMID: 36010208 PMCID: PMC9406681 DOI: 10.3390/diagnostics12081855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Infection with high-risk (HR) Human Papillomavirus (HPV) is associated with the development of precancerous lesions or invasive carcinoma of the uterine cervix. Thus, the high viral load (VL) of HR-HPV DNA currently serves as a representative quantitative marker for cervical cancer. However, the clinical significance of low HPV DNA VL remains undetermined. This study aimed to evaluate the clinical association between the low HPV DNA VL and cytology/histologic diagnosis of cervical samples. We searched the electronic medical databases for the resultant analyses of HPV genotyping among patients who underwent treatment for any cervical lesion or who had undergone gynecological examinations with any positive HPV results according to the national cancer screening service between 2015 and 2016. HPV testing with genotyping and semi-quantitative VL measurement was conducted using an AnyplexTM II H28 Detection assay (H28 assay, Seegene, Seoul, Republic of Korea). The H28 assay is a multiplex semi-quantitative real-time PCR test using the tagging of oligonucleotide cleavage and extension (TOCE) technology. The VL was semi-quantified as high (3+; positive signal before 31 PCR cycles), intermediate (2+; positive between 31 and 39 PCR cycles), or low (1+; positive after 40 PCR cycles). Out of 5940 HPV VL analyses, 356 assays (5.99%) were reported as low VL (1+) of HPV DNA. Matched cytology diagnoses were mostly negative findings (n = 347, 97.5%), except for seven cases of atypical squamous cells of undetermined significance (1.9%) and two cases of atypical glandular cells (0.6%). During the follow-up periods, abnormal cytologic diagnoses were identified, including one case of high-grade squamous intraepithelial lesion (HSIL) and two low-grade squamous intraepithelial lesions (LSILs). The matched, confirmative histologic diagnosis of HSIL cytology was compatible with chronic inflammation, wherein the two LSILs had regular check-ups. None revealed clinically concerned outcomes associated with HPV-related squamous lesions. The cytology was most likely negative for malignancy when the VL of HPV DNA was low (1+). Additional strategic monitoring and management may thus be unnecessary.
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Affiliation(s)
- Nora Jee-Young Park
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea; (N.J.-Y.P.); (J.Y.J.); (M.K.)
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41405, Korea;
- KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, Kyungpook National University, Daegu 41566, Korea
| | | | - Ji Yun Jeong
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea; (N.J.-Y.P.); (J.Y.J.); (M.K.)
| | - Moonsik Kim
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea; (N.J.-Y.P.); (J.Y.J.); (M.K.)
| | - Su Hyun Yoo
- Department of Pathology, National Police Hospital, Seoul 05715, Korea;
| | - Gun Oh Chong
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41405, Korea;
- KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, Kyungpook National University, Daegu 41566, Korea
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea;
| | - Dae Gy Hong
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea;
| | - Ji Young Park
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea; (N.J.-Y.P.); (J.Y.J.); (M.K.)
- Correspondence: ; Tel.: +82-53-200-3405; Fax: +82-53-200-3399
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