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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wijesekera A, Weeramange CE, Vasani S, Kenny L, Knowland E, Seneviratne J, Punyadeera C. Surveillance of human papillomavirus through salivary diagnostics - A roadmap to early detection of oropharyngeal cancer men. Tumour Virus Res 2024; 17:200278. [PMID: 38442788 PMCID: PMC10937231 DOI: 10.1016/j.tvr.2024.200278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Human papillomavirus (HPV) is the most common sexually transmitted disease. Certain strains have the potential to cause malignancy in multiple anatomical sites if not cleared by the immune system. In most infected people, HPV is cleared within two years. However, HPV may persist in susceptible individuals with certain risk factors, eventually leading to malignancy. New evidence suggests that over 75% of all oropharyngeal cancers (OPC) are directly attributable to HPV. It is estimated that prophylactic HPV vaccination alone may take at least 25 years to have a significant impact on reducing the incidence of OPC. The temporal link between detection of oral HPV, persistence of the infection and the subsequent development of OPC have been well established. Moreover, men have threefold higher risk than women for acquiring HPV-OPC. This comprehensive review focuses on OPC development in men, highlighting the risk factors associated with malignant transformation of HPV-OPC. Current evidence is insufficient to determine whether early identification of at-risk demographics, screening, and prompt diagnosis result in improved outcomes. Hitherto, the effectiveness of an oral HPV screening program in this regard has not been investigated. Nevertheless, the potential to emulate the success of the cervical screening program remains a very real possibility.
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Affiliation(s)
- Akila Wijesekera
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Queensland, Australia; Royal Brisbane and Women's Hospital, Queensland, Australia.
| | - Chameera Ekanayake Weeramange
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Queensland, Australia
| | - Sarju Vasani
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Queensland, Australia; Royal Brisbane and Women's Hospital, Queensland, Australia
| | - Liz Kenny
- Royal Brisbane and Women's Hospital, Queensland, Australia; Faculty of Medicine, University of Queensland, Queensland, Australia
| | - Emma Knowland
- Metro North Sexual Health and HIV Service, Queensland, Australia
| | | | - Chamindie Punyadeera
- Griffith Institute for Drug Discovery, School of Environment and Science, Griffith University, Queensland, Australia; Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.
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3
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Gameiro SF, Salnikov MY, Zeng PYF, Barrett JW, Nichols AC, Mymryk JS. HPV16 Intratypic Variants in Head and Neck Cancers: A North American Perspective. Viruses 2023; 15:2411. [PMID: 38140652 PMCID: PMC10747106 DOI: 10.3390/v15122411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Human papillomavirus (HPV) is the major causative agent for cervical and many head and neck cancers (HNCs). HPVs randomly acquire single nucleotide polymorphisms (SNPs) that may become established via positive selection. Within an HPV type, viral isolates differing by <2% in the L1 region are termed "variants" and classified based on combinations of SNPs. Studies in cervical cancer demonstrate clear differences between HPV16 intratypic variants in terms of persistence of infection, tumor histology, cancer risk, and death. Much less is known about the frequency of HPV16 variants in HNC, and their effects on clinical outcomes. We combined HPV16 positive (HPV16+) HNC samples from a local Southwestern Ontario, Canada cohort with those from the Cancer Genome Atlas to create a larger North American cohort of 149 cases with clinical data and determined the distribution of intratypic variants and their impact on clinical outcomes. Most isolates were lineage A, sublineage A1, or A2, with roughly half exhibiting the T350G polymorphism in E6. Univariable analysis identified significant differences between 350T and 350G intratypic variants in clinical T, N, and O staging, as well as disease-free survival. Multivariable analysis failed to identify any clinical factor as a statistically significant covariate for disease-free survival differences between 350T and 350G. Significant differences in several measures of B-cell mediated immune response were also observed between 350T and 350G intratypic variants. We suggest that HPV genetic variation may be associated with HNC clinical characteristics and may have prognostic value.
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Affiliation(s)
- Steven F. Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
| | - Mikhail Y. Salnikov
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
| | - Peter Y. F. Zeng
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
| | - John W. Barrett
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Anthony C. Nichols
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Oncology, The University of Western Ontario, London, ON N6A 5W9, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada; (S.F.G.); (M.Y.S.)
- Department of Pathology and Laboratory Medicine, The University of Western Ontario, London, ON N6A 5C1, Canada; (P.Y.F.Z.); (A.C.N.)
- Department of Otolaryngology, The University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Oncology, The University of Western Ontario, London, ON N6A 5W9, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6A 5W9, Canada
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Klein S, Wuerdemann N, Demers I, Kopp C, Quantius J, Charpentier A, Tolkach Y, Brinker K, Sharma SJ, George J, Hess J, Stögbauer F, Lacko M, Struijlaart M, van den Hout MFCM, Wagner S, Wittekindt C, Langer C, Arens C, Buettner R, Quaas A, Reinhardt HC, Speel EJ, Klussmann JP. Predicting HPV association using deep learning and regular H&E stains allows granular stratification of oropharyngeal cancer patients. NPJ Digit Med 2023; 6:152. [PMID: 37598255 PMCID: PMC10439941 DOI: 10.1038/s41746-023-00901-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Human Papilloma Virus (HPV)-associated oropharyngeal squamous cell cancer (OPSCC) represents an OPSCC subgroup with an overall good prognosis with a rising incidence in Western countries. Multiple lines of evidence suggest that HPV-associated tumors are not a homogeneous tumor entity, underlining the need for accurate prognostic biomarkers. In this retrospective, multi-institutional study involving 906 patients from four centers and one database, we developed a deep learning algorithm (OPSCCnet), to analyze standard H&E stains for the calculation of a patient-level score associated with prognosis, comparing it to combined HPV-DNA and p16-status. When comparing OPSCCnet to HPV-status, the algorithm showed a good overall performance with a mean area under the receiver operator curve (AUROC) = 0.83 (95% CI = 0.77-0.9) for the test cohort (n = 639), which could be increased to AUROC = 0.88 by filtering cases using a fixed threshold on the variance of the probability of the HPV-positive class - a potential surrogate marker of HPV-heterogeneity. OPSCCnet could be used as a screening tool, outperforming gold standard HPV testing (OPSCCnet: five-year survival rate: 96% [95% CI = 90-100%]; HPV testing: five-year survival rate: 80% [95% CI = 71-90%]). This could be confirmed using a multivariate analysis of a three-tier threshold (OPSCCnet: high HR = 0.15 [95% CI = 0.05-0.44], intermediate HR = 0.58 [95% CI = 0.34-0.98] p = 0.043, Cox proportional hazards model, n = 211; HPV testing: HR = 0.29 [95% CI = 0.15-0.54] p < 0.001, Cox proportional hazards model, n = 211). Collectively, our findings indicate that by analyzing standard gigapixel hematoxylin and eosin (H&E) histological whole-slide images, OPSCCnet demonstrated superior performance over p16/HPV-DNA testing in various clinical scenarios, particularly in accurately stratifying these patients.
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Affiliation(s)
- Sebastian Klein
- Department of Hematology and Stem Cell Transplantation, University Duisburg-Essen, University Hospital Essen, Essen, Germany.
- Institute of Pathology, Medical Faculty, University Hospital Cologne, Cologne, Germany.
| | - Nora Wuerdemann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Medical Faculty, Cologne, Germany
| | - Imke Demers
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christopher Kopp
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Jennifer Quantius
- Institute of Pathology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Arthur Charpentier
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Medical Faculty, Cologne, Germany
| | - Yuri Tolkach
- Institute of Pathology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Klaus Brinker
- Hamm-Lippstadt University of Applied Sciences, Hamm, Germany
| | - Shachi Jenny Sharma
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Medical Faculty, Cologne, Germany
| | - Julie George
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Department of Translational Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Jochen Hess
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabian Stögbauer
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, Germany, and Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
- Institute of Pathology, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Martin Lacko
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marijn Struijlaart
- Department of Otorhinolaryngology and Head and Neck Surgery, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Mari F C M van den Hout
- Department of Pathology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Steffen Wagner
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Claus Wittekindt
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
- Clinic of Otorhinolaryngology, Head and Neck Surgery, Klinikum Dortmund, University of Witten/Herdecke, Faculty for Health, Department of Human Medicine, Witten, Germany
| | - Christine Langer
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Christoph Arens
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany
| | - Reinhard Buettner
- Institute of Pathology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Duisburg-Essen, University Hospital Essen, Essen, Germany
- West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ernst-Jan Speel
- Department of Pathology, GROW - School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jens Peter Klussmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Medical Faculty, Cologne, Germany
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Cochicho D, Nunes A, Sobral D, Gomes JP, Esteves S, Mendonça J, Vieira L, Martins L, Cunha M, Montalvão P, Magalhães M, Gil da Costa RM, Félix A. Distribution and Clinical Significance of HPV16 Variants in Head and Neck Squamous Cell Carcinomas: Data from a Portuguese Cohort and Systematic Review. Pathobiology 2023; 90:333-343. [PMID: 37040716 DOI: 10.1159/000529723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/10/2023] [Indexed: 04/13/2023] Open
Abstract
INTRODUCTION Genomic variants of the human papillomavirus type 16 (HPV16) are thought to play differential roles in the susceptibility to head and neck squamous cell carcinomas (HNSCC) and its biological behaviour. This study aimed to establish the prevalence of HPV16 variants in an HNSCC cohort and associate them with clinical pathological characteristics and patient survival. METHODS We retrieved samples and clinical data from 68 HNSCC patients. DNA samples were available from tumour biopsy at the time of the primary diagnosis. Targeted next-generation sequencing was used to obtain whole-genome sequences, and variants were established based on phylogenetic classification. RESULTS 74% of samples clustered in lineage A, 5.7% in lineage B, 2.9% in lineage C, and 17.1% in lineage D. Comparative genome analysis revealed 243 single nucleotide variations. Of these, one hundred were previously reported, according to our systematic review. No significant associations with clinical pathological variables or patient survival were observed. The E6 amino acid variations E31G, L83V, and D25E and E7 N29S, associated with cervical cancer, were not observed, except for N29S in a single patient. CONCLUSION These results provide a comprehensive genomic map of HPV16 in HSNCC, highlighting tissue-specific characteristics which will help design tailored therapies for cancer patients.
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Affiliation(s)
- Daniela Cochicho
- Research Department, NOVA Medical School University, Lisbon, Portugal,
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal,
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Daniel Sobral
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Susana Esteves
- Clinical Research Unit, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Joana Mendonça
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luis Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Martins
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Mario Cunha
- Virology Laboratory from Clinical Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Pedro Montalvão
- Otorhinolaryngology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Miguel Magalhães
- Otorhinolaryngology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
| | - Rui M Gil da Costa
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
- Post-graduate Programme in Adult Health (PPGSAD), University Hospital (HUUFMA) and Morphology Department, Federal University of Maranhão, São Luís, Brazil
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto), Porto Comprehensive Cancer Center (Porto.CCC), Porto, Portugal
| | - Ana Félix
- Research Department, NOVA Medical School University, Lisbon, Portugal
- Pathology Department, IPOLFG Portuguese Oncology Institute Francisco Gentil, Lisbon, Portugal
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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Guerendiain D, Mühr LSA, Grigorescu R, Holden MTG, Cuschieri K. Mapping HPV 16 Sub-Lineages in Anal Cancer and Implications for Disease Outcomes. Diagnostics (Basel) 2022; 12. [PMID: 36553229 DOI: 10.3390/diagnostics12123222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The incidence of anal cancer is rising worldwide. As identified in cervical cancer management, an improvement in the early detection and management of anal pre-cancer is essential. In other cancers associated with human papillomavirus (HPV), HPV 16 sub-lineages have been shown to be associated with disease status and prognosis. However, in anal cancer, they have been under-explored. A total of 119 HPV 16-positive anal cancer lesions diagnosed between 2009 and 2018 in Scotland and 134 HPV 16-positive residual rectal swabs from asymptomatic men collected in 2016/7 were whole genome sequenced. The association of HPV 16 sub-lineages with underlying disease status (cancer vs. asymptomatic) and overall survival in anal cancer samples was assessed (comparing A1 vs non-A1 sub-lineages). A1 was the dominant sub-lineage present in the anal cancer (76.5%) and the asymptomatic (76.1%) cohorts. A2 was the second most dominant sub-lineage in both groups (16.8% and 17.2%, respectively). We did not observe significant associations of sub-lineage with demographics, clinical variables or survival (A1 vs. non-A1 sub-lineages (HR 0.83, 0.28-2.46 p = 0.743)). HPV 16 sub-lineages do to not appear to cluster with disease vs asymptomatic carriage or be independently associated with outcomes in anal cancer patients. Further international studies on anal HPV sub-lineage mapping will help to determine whether this is a consistent observation.
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King KM, Rajadhyaksha EV, Tobey IG, Van Doorslaer K. Synonymous nucleotide changes drive papillomavirus evolution. Tumour Virus Res 2022; 14:200248. [PMID: 36265836 PMCID: PMC9589209 DOI: 10.1016/j.tvr.2022.200248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Papillomaviruses have been evolving alongside their hosts for at least 450 million years. This review will discuss some of the insights gained into the evolution of this diverse family of viruses. Papillomavirus evolution is constrained by pervasive purifying selection to maximize viral fitness. Yet these viruses need to adapt to changes in their environment, e.g., the host immune system. It has long been known that these viruses evolved a codon usage that doesn't match the infected host. Here we discuss how papillomavirus genomes evolve by acquiring synonymous changes that allow the virus to avoid detection by the host innate immune system without changing the encoded proteins and associated fitness loss. We discuss the implications of studying viral evolution, lifecycle, and cancer progression.
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Affiliation(s)
- Kelly M. King
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Esha Vikram Rajadhyaksha
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA,Department of Physiology and Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Isabelle G. Tobey
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA,Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA,The BIO5 Institute, The Department of Immunobiology, Genetics Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Arizona, USA,Corresponding author. School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
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