1
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Wang H, Hang X, Wang H, Peng J, Yu H, Wang L. Label/immobilization-free Cas12a-based electrochemiluminescence biosensor for sensitive DNA detection. Talanta 2024; 275:126114. [PMID: 38631265 DOI: 10.1016/j.talanta.2024.126114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Electrochemiluminescence (ECL) is one of the most sensitive techniques in the field of diagnostics. However, they typically require luminescent labeling and electrode surface biological modification, which is a time-consuming and laborious process involving multiple steps and may also lead to low reaction efficiency. Fabricating label/modification-free biosensors has become one of the most attractive parts for simplifying the ECL assays. In this work, the ECL luminophores carbon dots (CDs) were encapsulated in DNA hydrogel in situ by a simple rolling circle amplification (RCA) reaction. Upon binding of the target DNA, active Cas12a induces a collateral cleavage of the hydrogel's ssDNA backbone, resulting in a programmable degradation of the hydrogel and the release of CDs. By directly measuring the released CDs ECL, a simple and rapid label/modification-free detection of the target HPV-16 was realized. It is noted that this method allowed for 0.63 pM HPV-16 DNA detection without any amplification step, and it could take only ∼60 min for a fast test of a human serum sample. These results showed that our label/modification-free ECL biosensor has great potential for use in simple, rapid, and sensitive point-of-care (POC) detection.
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Affiliation(s)
- Honghong Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Xiaomin Hang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Huiyi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jiaxin Peng
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China
| | - Haoming Yu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Li Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, PR China.
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2
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Hong Z, Xiong J, Yang H, Mo YK. Lightweight Low-Rank Adaptation Vision Transformer Framework for Cervical Cancer Detection and Cervix Type Classification. Bioengineering (Basel) 2024; 11:468. [PMID: 38790335 PMCID: PMC11118906 DOI: 10.3390/bioengineering11050468] [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: 03/23/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Cervical cancer is a major health concern worldwide, highlighting the urgent need for better early detection methods to improve outcomes for patients. In this study, we present a novel digital pathology classification approach that combines Low-Rank Adaptation (LoRA) with the Vision Transformer (ViT) model. This method is aimed at making cervix type classification more efficient through a deep learning classifier that does not require as much data. The key innovation is the use of LoRA, which allows for the effective training of the model with smaller datasets, making the most of the ability of ViT to represent visual information. This approach performs better than traditional Convolutional Neural Network (CNN) models, including Residual Networks (ResNets), especially when it comes to performance and the ability to generalize in situations where data are limited. Through thorough experiments and analysis on various dataset sizes, we found that our more streamlined classifier is highly accurate in spotting various cervical anomalies across several cases. This work advances the development of sophisticated computer-aided diagnostic systems, facilitating more rapid and accurate detection of cervical cancer, thereby significantly enhancing patient care outcomes.
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Affiliation(s)
- Zhenchen Hong
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA
| | - Jingwei Xiong
- Graduate Group in Biostatistics, University of California, Davis, CA 95616, USA
| | - Han Yang
- Department of Chemistry, Columbia University, New York, NY 10027, USA;
| | - Yu K. Mo
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA;
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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3
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Wang Y, He M, He T, Ouyang X, Shen X, Shi W, Huang S, Xiang L, Zou D, Jiang W, Yang H. Integrated genomic and transcriptomic analysis reveals the activation of PI3K signaling pathway in HPV-independent cervical cancers. Br J Cancer 2024; 130:987-1000. [PMID: 38253702 PMCID: PMC10951256 DOI: 10.1038/s41416-023-02555-w] [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: 05/16/2023] [Revised: 12/02/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND HPV-independent cervical cancers (HPV-ind CCs) are uncommon with worse prognosis and poorly understood. This study investigated the molecular characteristics of HPV-ind CCs, aiming to explore new strategies for HPV-ind CCs. METHODS HPV status of 1010 cervical cancer patients were detected by RT-PCR, PCR and RNA-sequencing (RNA-seq). Whole exome sequencing (WES) and RNA-seq were performed in identified HPV-ind CCs. The efficacy of PI3Kα inhibitor BYL719 in HPV-ind CCs was evaluated in cell lines, patient-derived organoids (PDOs) and patient-derived xenografts (PDXs). RESULTS Twenty-five CCs were identified as HPV-ind, which were more common seen in older, adenocarcinoma patients and exhibited poorer prognosis as well as higher tumor mutation burden compared to HPV-associated CCs. HPV-ind CCs were featured with highly activated PI3K/AKT signaling pathway, particularly, PIK3CA being the most predominant genomic alteration (36%). BYL719 demonstrated superior tumor suppression in vitro and in vivo. Furthermore, HPV-ind CCs were classified into two subtypes according to distinct prognosis by gene expression profiles, the metabolism subtype and immune subtype. CONCLUSIONS This study reveals the prevalence, clinicopathology, and molecular features of HPV-ind CCs and emphasizes the importance of PIK3CA mutations and PI3K pathway activation in tumorigenesis, which suggests the potential significance of PI3Kα inhibitors in HPV-ind CC patients.
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Affiliation(s)
- Yi Wang
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Misi He
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030, China
- Chongqing Specialized Medical Research Center of Ovarian Cancer, Chongqing, 400030, China
- Organoid Transformational Research Center, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Tiancong He
- Department of Surgical Oncology, Minhang Branch, Fudan University Shanghai Cancer Center, Shanghai, 200240, China
| | - Xueyan Ouyang
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xuxia Shen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Wanling Shi
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shengling Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Libing Xiang
- Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dongling Zou
- Department of Gynecologic Oncology, Chongqing University Cancer Hospital & Chongqing Cancer Institute & Chongqing Cancer Hospital, Chongqing, 400030, China.
- Chongqing Specialized Medical Research Center of Ovarian Cancer, Chongqing, 400030, China.
- Organoid Transformational Research Center, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, China.
| | - Wei Jiang
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Huijuan Yang
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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Prétet JL, Arroyo Mühr LS, Cuschieri K, Fellner MD, Correa RM, Picconi MA, Garland SM, Murray GL, Molano M, Peeters M, Van Gucht S, Lambrecht C, Broeck DV, Padalko E, Arbyn M, Lepiller Q, Brunier A, Silling S, Søreng K, Christiansen IK, Poljak M, Lagheden C, Yilmaz E, Eklund C, Thapa HR, Querec TD, Unger ER, Dillner J. Human papillomavirus negative high grade cervical lesions and cancers: Suggested guidance for HPV testing quality assurance. J Clin Virol 2024; 171:105657. [PMID: 38401369 DOI: 10.1016/j.jcv.2024.105657] [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: 09/12/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Some high-grade cervical lesions and cervical cancers (HSIL+) test negative for human papillomavirus (HPV). The HPV-negative fraction varies between 0.03 % and 15 % between different laboratories. Monitoring and extended re-analysis of HPV-negative HSIL+ could thus be helpful to monitor performance of HPV testing services. We aimed to a) provide a real-life example of a quality assurance (QA) program based on re-analysis of HPV-negative HSIL+ and b) develop international guidance for QA of HPV testing services based on standardized identification of apparently HPV-negative HSIL+ and extended re-analysis, either by the primary laboratory or by a national HPV reference laboratory (NRL). METHODS There were 116 initially HPV-negative cervical specimens (31 histopathology specimens and 85 liquid-based cytology samples) sent to the Swedish HPV Reference Laboratory for re-testing. Based on the results, an international QA guidance was developed through an iterative consensus process. RESULT Standard PCR testing detected HPV in 55.2 % (64/116) of initially "HPV-negative" samples. Whole genome sequencing of PCR-negative samples identified HPV in an additional 7 samples (overall 61.2 % HPV positivity). Reasons for failure to detect HPV in an HSIL+ lesion are listed and guidance to identify cases for extended re-testing, including which information should be included when referring samples to an NRL are presented. CONCLUSION Monitoring the proportion of and reasons for failure to detect HPV in HSIL+ will help support high performance and quality improvement of HPV testing services. We encourage implementation of QA strategies based on re-analysis of "HPV negative" HSIL+ samples.
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Affiliation(s)
- Jean Luc Prétet
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Laila Sara Arroyo Mühr
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Kate Cuschieri
- Scottish HPV Reference Laboratory, Deptartment of Lab Medicine, Royal Infirmary of Edinburgh, Edinburgh, EH16 4SA, UK
| | - María Dolores Fellner
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - Rita Mariel Correa
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - María Alejandra Picconi
- Laboratorio Nacional y Regional de Referencia de Papilomavirus Humanos, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr Malbrán", C1282AFF Buenos Aires, Argentina
| | - Suzanne M Garland
- Royal Women's Hospital, Parkville 3052 VIC, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville 3052 VIC, Australia
| | - Gerald L Murray
- Royal Women's Hospital, Parkville 3052 VIC, Australia; Department of Obstetrics and Gynaecology, University of Melbourne, Parkville 3052 VIC, Australia
| | - Monica Molano
- Royal Women's Hospital, Parkville 3052 VIC, Australia
| | - Michael Peeters
- National Reference Centre for Human Papillomaviruses, Viral Diseases, Infectious Diseases in Humans, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Steven Van Gucht
- National Reference Centre for Human Papillomaviruses, Viral Diseases, Infectious Diseases in Humans, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Charlotte Lambrecht
- National Reference Centre for Human Papillomaviruses, Algemeen Medisch Laboratorium. Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Davy Vanden Broeck
- National Reference Centre for Human Papillomaviruses, Algemeen Medisch Laboratorium. Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Elizaveta Padalko
- National Reference Centre for Human Papillomaviruses, Laboratory of Medical Microbiology, University Hospital Ghent. C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Marc Arbyn
- Unit Cancer Epidemiology, Cancer centre, Sciensano. Rue Juliette Wytsman 14, 1050 Brussels, Belgium
| | - Quentin Lepiller
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Alice Brunier
- French National Papillomavirus Reference Center, CHU de Besançon, EA3181, Université of Franche-Comté, F-25000 Besançon, France
| | - Steffi Silling
- Institute of Virology, National Reference Center for Papilloma- and Polyomaviruses, University of Cologne, Faculty of Medicine and University Hospital of Cologne, 50935 Cologne, Germany
| | - Kristiane Søreng
- Norwegian HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Irene Kraus Christiansen
- Norwegian HPV Reference Laboratory, Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Camilla Lagheden
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Emel Yilmaz
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Carina Eklund
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden
| | - Hem R Thapa
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Troy D Querec
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joakim Dillner
- Swedish National HPV Reference Laboratory, Center for Cervical Cancer Elimination, Karolinska Institutet and Karolinska University Hospital F56, 141 86 Stockholm, Sweden.
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5
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Ye R, Wang A, Bu B, Luo P, Deng W, Zhang X, Yin S. Viral oncogenes, viruses, and cancer: a third-generation sequencing perspective on viral integration into the human genome. Front Oncol 2023; 13:1333812. [PMID: 38188304 PMCID: PMC10768168 DOI: 10.3389/fonc.2023.1333812] [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: 11/07/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
The link between viruses and cancer has intrigued scientists for decades. Certain viruses have been shown to be vital in the development of various cancers by integrating viral DNA into the host genome and activating viral oncogenes. These viruses include the Human Papillomavirus (HPV), Hepatitis B and C Viruses (HBV and HCV), Epstein-Barr Virus (EBV), and Human T-Cell Leukemia Virus (HTLV-1), which are all linked to the development of a myriad of human cancers. Third-generation sequencing technologies have revolutionized our ability to study viral integration events at unprecedented resolution in recent years. They offer long sequencing capabilities along with the ability to map viral integration sites, assess host gene expression, and track clonal evolution in cancer cells. Recently, researchers have been exploring the application of Oxford Nanopore Technologies (ONT) nanopore sequencing and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) sequencing in cancer research. As viral integration is crucial to the development of cancer via viruses, third-generation sequencing would provide a novel approach to studying the relationship interlinking viral oncogenes, viruses, and cancer. This review article explores the molecular mechanisms underlying viral oncogenesis, the role of viruses in cancer development, and the impact of third-generation sequencing on our understanding of viral integration into the human genome.
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Affiliation(s)
- Ruichen Ye
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Einstein Pathology Single-cell & Bioinformatics Laboratory, Bronx, NY, United States
- Stony Brook University, Stony Brook, NY, United States
| | - Angelina Wang
- Tufts Friedman School of Nutrition, Boston, MA, United States
| | - Brady Bu
- Horace Mann School, Bronx, NY, United States
| | - Pengxiang Luo
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjun Deng
- Clinical Proteomics Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Xinyi Zhang
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shanye Yin
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, United States
- Einstein Pathology Single-cell & Bioinformatics Laboratory, Bronx, NY, United States
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Arroyo Mühr LS, Lagheden C, Hassan SS, Eklund C, Dillner J. The International Human Papillomavirus Reference Center: Standardization, collaboration, and quality assurance in HPV research and diagnostics. J Med Virol 2023; 95:e29332. [PMID: 38115556 DOI: 10.1002/jmv.29332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/21/2023]
Abstract
The International Human Papillomavirus (HPV) Reference Center (IHRC) confirms and assigns type numbers to novel HPV types, maintains a reference clone repository, and issues international proficiency panels for HPV screening and genotyping. Furthermore, the Center coordinates the Global HPV Reference Laboratory Network that promotes collaboration and international exchange of experiences among national HPV reference laboratories, to further international standardization and quality assurance in the HPV field. The established HPV types (n = 225) belong to 5 different genera: alpha (n = 65), beta (n = 54), gamma (n = 102), mu (n = 3) and nu (n = 1). Since the last published IHRC overview in 2018, 6 novel types have been established, with 5/6 belonging to the gamma genus and 1/6 to beta genus. Also, 474 reference clones have been provided to 55 different research laboratories and the global proficiency program for HPV genotyping has seen an increasing proficiency (despite a decrease seen in 2019), from 68% proficiency in 2017 to 77.3% in 2022. The first proficiency study for HPV screening found an international proficiency of up to 77%. In summary, increasing complexity of the HPVs and demands on quality assurance in the era of cervical cancer elimination requires international efforts to support proficiency and recognized quality and order among HPV types.
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Affiliation(s)
- Laila Sara Arroyo Mühr
- Department of Clinical Science, Intervention and Technology (CLINTEC), Center for Cervical Cancer Elimination, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Lagheden
- Department of Clinical Science, Intervention and Technology (CLINTEC), Center for Cervical Cancer Elimination, Karolinska Institutet, Stockholm, Sweden
| | - Sadaf S Hassan
- Department of Clinical Science, Intervention and Technology (CLINTEC), Center for Cervical Cancer Elimination, Karolinska Institutet, Stockholm, Sweden
| | - Carina Eklund
- Department of Clinical Science, Intervention and Technology (CLINTEC), Center for Cervical Cancer Elimination, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Clinical Science, Intervention and Technology (CLINTEC), Center for Cervical Cancer Elimination, Karolinska Institutet, Stockholm, Sweden
- Center for Cervical Cancer Elimination, Karolinska University Hospital Huddinge, Stockholm, Sweden
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Friedman CF, Ravichandran V, Miller K, Vanderbilt C, Zhou Q, Iasonos A, Vivek M, Mishra P, Leitao MM, Broach V, Sonoda Y, Kyi C, Zamarin D, O'Cearbhaill RE, Konner J, Berger MF, Weigelt B, Momeni Boroujeni A, Park KJ, Aghajanian C, Solit DB, Donoghue MT. Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets. Clin Cancer Res 2023; 29:4660-4668. [PMID: 37643132 PMCID: PMC10644000 DOI: 10.1158/1078-0432.ccr-23-1078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/29/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023]
Abstract
PURPOSE Tumor genomic profiling is increasingly used to guide treatment strategy in patients with cancer. We integrated tumor genomic, clinical demographic, and treatment response data to assess how prospective tumor-normal sequencing impacted treatment selection in patients with cervical cancer. EXPERIMENTAL DESIGN Cervical cancers were prospectively analyzed using the MSK-IMPACT (Memorial Sloan Kettering Cancer Center - Integrated Mutation Profiling of Actionable Cancer Targets) next-generation sequencing panel. Clinical data, including histology, stage at diagnosis, treatment history, clinical trial enrollment and outcomes, date of last follow-up, and survival status were obtained from medical records. RESULTS A total of 177 patients with cervical cancer (squamous, 69; endocervical adenocarcinoma, 50; gastric type, 22; adenosquamous, 21; and other, 15) underwent MSK-IMPACT testing. The most prevalent genomic alterations were somatic mutations or amplifications in PIK3CA (25%), ERBB2 (12%), KMT2C (10%), and KMT2D (9%). Furthermore, 13% of patients had high tumor mutational burden (TMB >10 mut/Mb), 3 of which were also microsatellite instability-high (MSI-H). Thirty-seven percent of cases had at least one potentially actionable alteration designated as a level 3B mutational event according to the FDA-recognized OncoKB tumor mutation database and treatment classification system. A total of 30 patients (17%) were enrolled on a therapeutic clinical trial, including 18 (10%) who were matched with a study based on their MSK-IMPACT results. Twenty patients (11%) participated in an immune checkpoint inhibition study for metastatic disease; 2 remain progression free at >5 years follow-up. CONCLUSIONS Tumor genomic profiling can facilitate the selection of targeted/immunotherapies, as well as clinical trial enrollment, for patients with cervical cancer.
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Affiliation(s)
- Claire F. Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Vignesh Ravichandran
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathryn Miller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Qin Zhou
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexia Iasonos
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Malavika Vivek
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pamela Mishra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mario M. Leitao
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Vance Broach
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Yukio Sonoda
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of OB/GYN, Weill Cornell Medical College, New York, New York
| | - Chrisann Kyi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Roisin E. O'Cearbhaill
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jason Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni Boroujeni
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay J. Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark T.A. Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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8
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Wang J, Elfström KM, Lagheden C, Eklund C, Sundström K, Sparén P, Dillner J. Impact of cervical screening by human papillomavirus genotype: Population-based estimations. PLoS Med 2023; 20:e1004304. [PMID: 37889928 PMCID: PMC10637721 DOI: 10.1371/journal.pmed.1004304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/10/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Cervical screening programs use testing for human papillomavirus (HPV) genotypes. Different HPV types differ greatly in prevalence and oncogenicity. We estimated the impact of cervical screening and follow-up for each HPV type. METHODS AND FINDINGS For each type of HPV, we calculated the number of women needed to screen (NNS) and number of women needing follow-up (NNF) to detect or prevent one cervical cancer case, using the following individual level input data (i) screening and cancer data for all women aged 25 to 80 years, resident in Sweden during 2004 to 2011 (N = 3,568,938); (ii) HPV type-specific prevalences and screening histories among women with cervical cancer in Sweden in 2002 to 2011(N = 4,254); (iii) HPV 16/18/other HPV prevalences in the population-based HPV screening program (N = 656,607); and (iv) exact HPV genotyping in a population-based cohort (n = 12,527). Historical screening attendance was associated with a 72% reduction of cervical cancer incidence caused by HPV16 (71.6%, 95% confidence interval (CI) [69.1%, 73.9%]) and a 54% reduction of cancer caused by HPV18 (53.8%, 95% CI [40.6%, 63.1%]). One case of HPV16-caused cervical cancer could be prevented for every 5,527 women attending screening (number needed to screen, NNS). Prevention of one case of HPV16-caused cervical cancer required follow-up of 147 HPV16-positive women (number needed to follow-up, NNF). The NNS and NNF were up to 40 to 500 times higher for HPV types commonly screened for with lower oncogenic potential (HPV35,39,51,56,59,66,68). For women below 30 years of age, NNS and NNF for HPV16 were 4,747 and 289, respectively, but >220,000 and >16,000 for HPV35,39,51,56,59,66,68. All estimates were either age-standarized or age-stratified. The primary limitation of our study is that NNS is dependent on the HPV prevalence that can differ between populations and over time. However, it can readily be recalculated in other settings and monitored when HPV type-specific prevalence changes. Other limitations include that in some age groups, there was little data and extrapolations had to be made. Finally, there were very few cervical cancer cases associated with certain HPV types in young age group. CONCLUSIONS In this study, we observed that the impact of cervical cancer screening varies depending on the HPV type screened for. Estimating and monitoring the impact of screening by HPV type can facilitate the design of effective and efficient HPV-based cervical screening programs. TRIAL REGISTRATION ClinicalTrials.gov with numbers NCT00479375, NCT01511328.
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Affiliation(s)
- Jiangrong Wang
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - K. Miriam Elfström
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Camilla Lagheden
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Carina Eklund
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Sundström
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Pär Sparén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Division of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology and Cancer Diagnostics, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
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9
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Aitmanaitė L, Širmonaitis K, Russo G. Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap. Int J Mol Sci 2023; 24:13786. [PMID: 37762088 PMCID: PMC10531294 DOI: 10.3390/ijms241813786] [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: 08/07/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.
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Affiliation(s)
| | | | - Giancarlo Russo
- EMBL Partnership Institute for Gene Editing, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (L.A.); (K.Š.)
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10
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Yilmaz E, Lagheden C, Ghaderi M, Wang J, Dillner J, Elfström KM. Assessment of Human Papillomavirus Non-16/18, Type-Specific Risk for Cervical Intraepithelial Neoplasia Grade 3 or Worse Among Women With Cervical Atypical Glandular Cells. Obstet Gynecol 2023; 142:679-687. [PMID: 37535949 DOI: 10.1097/aog.0000000000005286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/25/2023] [Indexed: 08/05/2023]
Abstract
OBJECTIVE To evaluate the risk for cervical intraepithelial neoplasia grade 3 (CIN 3) or worse (including adenocarcinoma in situ [AIS] and invasive cervical cancer) associated with non-16/18 human papillomavirus (HPV) types (other HPV) among women with atypical glandular cells (AGC) in cervical cytology. METHODS This population-based cohort study evaluates the risk of CIN 3 or worse associated with other HPV types. Human papillomavirus genotyping was performed on Pap tests collected in Sweden from 341 women with AGC that were positive for other HPV types from February 17, 2014, to December 31, 2018. The women were followed for histopathologic outcomes using comprehensive registry linkages until December 31, 2019. Cumulative incidence proportions of CIN 3 or worse by specific HPV type were calculated using 1-minus Kaplan-Meier function. Hazard ratios (HRs) for CIN 3 or worse were generated using multivariate Cox regression. RESULTS Of 341 women, 134 (39.3%) had CIN 3-AIS, but there were only five (1.5%) women in the cohort with invasive cervical cancer. Human papillomavirus 45 preceded 80.0% of invasive cervical cancer cases. Among women positive for HPV33, 82.9% (95% CI 58.0-97.3%) had CIN 3 or worse during follow-up. Positivity for HPV31 conferred the highest HR for CIN 3 or worse relative to other types, both in primary cytology and primary HPV screening (HR 2.71, 95% CI 1.47-5.00 and HR 3.41, 95% CI 1.95-5.96, respectively). CONCLUSION Among non-16/18 HPV types in AGC, HPV31 and 33 had the highest risk for CIN 3 or worse, whereas most of the women with invasive cancer were positive for HPV45. Extended HPV genotyping may be helpful for the management of AGC.
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Affiliation(s)
- Emel Yilmaz
- Center for Cervical Cancer Elimination, Department of Clinical Pathology and Cancer Diagnostics, Medical Diagnostics Karolinska, Karolinska University Hospital, Huddinge, and the Division for of Cervical Cancer Elimination, Department of Clinical Science, Intervention and Technology, CLINTEC, Karolinska Institutet, Stockholm, Sweden
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11
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Mittelstadt S, Kelemen O, Admard J, Gschwind A, Koch A, Wörz S, Oberlechner E, Engler T, Bonzheim I, Staebler A, Weidner N, Stubenrauch F, Iftner T, Riess O, Schroeder C, Kommoss S, Ossowski S. Detection of circulating cell-free HPV DNA of 13 HPV types for patients with cervical cancer as potential biomarker to monitor therapy response and to detect relapse. Br J Cancer 2023; 128:2097-2103. [PMID: 36973448 DOI: 10.1038/s41416-023-02233-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND HPV-related cervical cancer (CC) is the fourth most frequent cancer in women worldwide. Cell-free tumour DNA is a potent biomarker to detect treatment response, residual disease, and relapse. We investigated the potential use of cell-free circulating HPV-DNA (cfHPV-DNA) in plasma of patients with CC. METHODS cfHPV-DNA levels were measured using a highly sensitive next-generation sequencing-based approach targeting a panel of 13 high-risk HPV types. RESULTS Sequencing was performed in 69 blood samples collected from 35 patients, of which 26 were treatment-naive when the first liquid biopsy sample was retrieved. cfHPV-DNA was successfully detected in 22/26 (85%) cases. A significant correlation between tumour burden and cfHPV-DNA levels was observed: cfHPV-DNA was detectable in all treatment-naive patients with advanced-stage disease (17/17, FIGO IB3-IVB) and in 5/9 patients with early-stage disease (FIGO IA-IB2). Sequential samples revealed a decrease of cfHPV-DNA levels in 7 patients corresponding treatment response and an increase in a patient with relapse. CONCLUSIONS In this proof-of-concept study we demonstrated the potential of cfHPV-DNA as a biomarker for therapy monitoring in patients with primary and recurrent CC. Our findings facilitate the development of a sensitive and precise, non-invasive, inexpensive, and easily accessible tool in CC diagnosis, therapy monitoring and follow-up.
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Affiliation(s)
- Suzana Mittelstadt
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany.
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - André Koch
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Sarah Wörz
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Ernst Oberlechner
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Annette Staebler
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Nicola Weidner
- Department of Radiooncology, University Hospital Tübingen, Tübingen, Germany
| | - Frank Stubenrauch
- Institute for Medical Virology and Epidemiology of Viral Disease, University Hospital Tübingen, Tübingen, Germany
| | - Thomas Iftner
- Institute for Medical Virology and Epidemiology of Viral Disease, University Hospital Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), partner site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Kommoss
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), partner site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
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12
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Leiendecker L, Neumann T, Jung PS, Cronin SM, Steinacker TL, Schleiffer A, Schutzbier M, Mechtler K, Kervarrec T, Laurent E, Bachiri K, Coyaud E, Murali R, Busam KJ, Itzinger-Monshi B, Kirnbauer R, Cerroni L, Calonje E, Rütten A, Stubenrauch F, Griewank KG, Wiesner T, Obenauf AC. Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers. Cancer Discov 2023; 13:70-84. [PMID: 36213965 PMCID: PMC9827110 DOI: 10.1158/2159-8290.cd-22-0489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/24/2022] [Accepted: 10/04/2022] [Indexed: 01/13/2023]
Abstract
The skin is exposed to viral pathogens, but whether they contribute to the oncogenesis of skin cancers has not been systematically explored. Here we investigated 19 skin tumor types by analyzing off-target reads from commonly available next-generation sequencing data for viral pathogens. We identified human papillomavirus 42 (HPV42) in 96% (n = 45/47) of digital papillary adenocarcinoma (DPA), an aggressive cancer occurring on the fingers and toes. We show that HPV42, so far considered a nononcogenic, "low-risk" HPV, recapitulates the molecular hallmarks of oncogenic, "high-risk" HPVs. Using machine learning, we find that HPV-driven transformation elicits a germ cell-like transcriptional program conserved throughout all HPV-driven cancers (DPA, cervical carcinoma, and head and neck cancer). We further show that this germ cell-like transcriptional program, even when reduced to the top two genes (CDKN2A and SYCP2), serves as a fingerprint of oncogenic HPVs with implications for early detection, diagnosis, and therapy of all HPV-driven cancers. SIGNIFICANCE We identify HPV42 as a uniform driver of DPA and add a new member to the short list of tumorigenic viruses in humans. We discover that all oncogenic HPVs evoke a germ cell-like transcriptional program with important implications for detecting, diagnosing, and treating all HPV-driven cancers. See related commentary by Starrett et al., p. 17. This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Lukas Leiendecker
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Quantro Therapeutics, Vienna, Austria
| | - Pauline S. Jung
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Shona M. Cronin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Thomas L. Steinacker
- Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Michael Schutzbier
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Institute of Molecular Biotechnology (IMBA), Vienna BioCenter (VBC), Vienna, Austria.,The Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences (GMI), Vienna BioCenter (VBC), Vienna, Austria
| | - Thibault Kervarrec
- Department of Pathology, University Hospital Center of Tours, University of Tours, Tours, France
| | - Estelle Laurent
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Kamel Bachiri
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Etienne Coyaud
- PRISM INSERM U1192, Université de Lille, Villeneuve d'Ascq, France
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J. Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Reinhard Kirnbauer
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Eduardo Calonje
- Department of Dermatopathology, St John's Institute of Dermatology, St Thomas’ Hospital, London, United Kingdom
| | - Arno Rütten
- Dermatopathology Friedrichshafen, Friedrichshafen, Germany
| | - Frank Stubenrauch
- University Hospital Tuebingen, Institute for Medical Virology and Epidemiology of Viral Diseases, Tuebingen, Germany
| | - Klaus G. Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg, German Cancer Consortium (DKTK), Partner Site, Essen, Germany
| | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Department of Pathology, Medical University of Vienna, Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.,Corresponding Authors: Anna C. Obenauf, Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria. Phone: 0043-179-730; E-mail: ; and Thomas Wiesner, Department of Dermatology, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria. Phone: 0043-1404-0077-100; E-mail:
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13
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Padavu S, Aichpure P, Krishna Kumar B, Kumar A, Ratho R, Sonkusare S, Karunasagar I, Karunasagar I, Rai P. An insight into clinical and laboratory detections for screening and diagnosis of cervical cancer. Expert Rev Mol Diagn 2023; 23:29-40. [PMID: 36697264 DOI: 10.1080/14737159.2023.2173580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Cervical cancer is the most frequent malignancy among women caused by an unresolved long-term infection with distinct human papillomavirus (HPV) genotypes. It is the fourth most common form of cancer among women worldwide. The two oncogenic genotypes, HPV 16 and 18, are responsible for >70% of all cervical cancers worldwide. Cervical cancer is one of the most successfully preventable and treatable forms of cancer if detected early. AREAS COVERED In this review article, we have summarizedsummarised the different approaches used in clinical diagnosis and research laboratories to detect HPV-related changes associated with cervical cancer for a better understanding of the advantages and limitations of these tests. EXPERT OPINION Despite the well-known screening strategies for cervical cancer, developing nations lack effective implementation due to various factors. With the current rate of cervical cancer cases, precise and timely identification of HPV can significantly impact the prevention and efficient management of cervical cancer. Cervical cancer is the most common gynecological cancer in developing countries. The primary screening test with cytology and molecular testing of HPV is important for preventing cervical cancer. To address these issues, several point-of-care assays have been developed to facilitate rapid screening of HPV with the least turnaround time.
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Affiliation(s)
- Shruthi Padavu
- Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru-575018, Karnataka, India
| | - Pooja Aichpure
- Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru-575018, Karnataka, India
| | - Ballamoole Krishna Kumar
- Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru-575018, Karnataka, India
| | - Anoop Kumar
- In Vivo Bioassay Laboratory & Animal Facility, National Institute of Biologicals (NIB), Ministry of Health & Family Welfare, Noida, India
| | - RadhaKanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Shipra Sonkusare
- Nitte (Deemed to Be University), Department of Obstetrics & Gynaecology, KS Hegde Medical Academy (KSHEMA), Deralakatte, Mangaluru, India
| | - Indrani Karunasagar
- Nitte (Deemed to Be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangaluru, India
| | - Iddya Karunasagar
- Nitte (Deemed to Be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangaluru, India
| | - Praveen Rai
- Nitte (Deemed to Be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Infectious Diseases, Deralakatte, Mangaluru-575018, Karnataka, India
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14
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Piña-Sánchez P. Human Papillomavirus: Challenges and Opportunities for the Control of Cervical Cancer. Arch Med Res 2022; 53:753-769. [PMID: 36462952 DOI: 10.1016/j.arcmed.2022.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/18/2022] [Indexed: 12/05/2022]
Abstract
Viruses are the most abundant and genetically diverse entities on the planet, infect all life forms and have evolved with their hosts. To date, 263 viral species have been identified that infect humans, of which only seven are considered type I oncogenic. Human papillomavirus (HPV) is the main virus associated with cancer and is responsible for practically all cases of cervical carcinoma. Screening tests for early detection have been available since the 1960s. Undoubtedly, the entailment between knowledge of HPV biology and the natural history of cervical cancer has contributed to the significant advances that have been made for its prevention since the 21st century, with the development of prophylactic vaccines and improved screening strategies. Therefore, it is possible to eradicate invasive cervical cancer as a worldwide public health problem, as proposed by the WHO with the 90-70-90 initiative based on vaccination coverage, screening, and treatment, respectively. In addition, the emerging knowledge of viral biology generates opportunities that will contribute to strengthening prevention and treatment strategies in HPV-associated neoplasms.
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Affiliation(s)
- Patricia Piña-Sánchez
- Laboratorio Molecular de Oncología, Unidad de Investigación Oncológica, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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15
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Basiletti JA, Valls J, Poklépovich T, Fellner MD, Rol M, Alonso R, Correa RM, Colucci MC, Rodríguez de la Peña M, Falabella PG, Saíno A, Campos J, Herrero R, Almonte M, Picconi MA. Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. PLoS One 2022; 17:e0278117. [PMID: 36417453 PMCID: PMC9683586 DOI: 10.1371/journal.pone.0278117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Sensitive and specific genotyping of human papillomaviruses (HPVs) is critical for the surveillance and monitoring of the vaccine effectiveness. Here, HPV genotypes were identified in 137 cervical samples with different histology (79 ≤CIN1 and 58 CIN3+) using Nested-PCR followed by Next-Generation sequencing (NGS) and relative proportions for each genotype in multiple infections were computed. All samples had been previously genotyped by PCR-Reverse Blotting Hybridization (PCR-RBH) thus allowing for a concordance analysis between both techniques. Multiple infections were present in 85% of ≤CIN1 cases compared to only 41% in CIN3+ cases (p<0.001). Among ≤CIN1 cases a towering genotypic diversity was observed, considering both low (LR-) and high risk (HR-) HPV genotypes; while among CIN3+, diversity was lower, HR-HPVs prevailing in most cases, especially HPV16. Furthermore, the predominance of HR-HPV genotypes in the proportions identified in each sample was higher in CIN3+ cases [(HPV16 (62.5%), followed by HPV31 and HPV58 (8.3% each)], than in ≤CIN1 cases [(HPV16 (17.7%), followed by HPV52 (14.7%) and HPV31 (10.3%)]. Agreement between PCR-RBH and NGS was higher than 90% for all genotypes (with an overall Kappa of 0.7), even though NGS identified eighty-nine positive results for HPV genotypes that had not been detected by PCR-RBH, evidencing its greater sensitivity. These results suggest that a reduction in genotypic diversity and/or an increase in the relative proportion of HR-HPVs in multiple infections can be considered as a biomarker for the potential risk of malignant progression.
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Affiliation(s)
- Jorge Alejandro Basiletti
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Joan Valls
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Tomás Poklépovich
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - María Dolores Fellner
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Maryluz Rol
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rafael Alonso
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rita Mariel Correa
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - María Celeste Colucci
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | | | - Paula Gabriela Falabella
- Servicio de Ginecología, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Agustina Saíno
- Servicio de Anatomía Patológica, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, San José, Costa Rica
| | - Maribel Almonte
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - María Alejandra Picconi
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
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16
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Ure AE, Lagheden C, Arroyo Mühr LS. Metatranscriptome analysis in human papillomavirus negative cervical cancers. Sci Rep 2022; 12:15062. [PMID: 36064569 PMCID: PMC9445079 DOI: 10.1038/s41598-022-19008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Human papillomavirus (HPV) negative cancers are associated with symptomatic detection, late-stage diagnosis, and worse prognosis. It is thus essential to investigate all possible infectious agents and biomarkers that could early identify these HPV negative cancers. We aimed to analyze and compare the metatranscriptome present in HPV positive and HPV negative cervical cancers. We analyzed the whole RNA sequencing files from 223 HPV negative cervical cancers (negativity established after confirming cervical cancer diagnosis, sample adequacy and subjecting specimens to PCR and unbiased RNA sequencing), 223 HPV positive tumors and 11 blank paraffin block pools (used as controls) using Kraken2 software. Overall, 84 bacterial genera were detected, with 6/84 genera showing a positive median number of reads/sample and being present in both cervical tumor groups (HPV positive and negative). Viral reads belonged to 63 different viral genera, with 6/63 genera showing a positive median annotated read/sample value. No significant difference among genera was detected except for the presence of alpha-papillomaviruses. Metatranscriptome of bacteria and viruses present in HPV positive and HPV negative cervical cancers show no significant difference, except for HPV. Further studies are needed to early identify this biologically distinct group of cervical cancers.
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Affiliation(s)
- Agustin Enrique Ure
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - Camilla Lagheden
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
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17
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Alirezaei M, Mosawi SH, Afgar A, Zarean M, Movahhed TK, Abbasi V, Fotouhi-Ardakani R. Discrimination of human papillomavirus genotypes using innovative technique nested-high resolution melting. Sci Rep 2022; 12:13943. [PMID: 35977949 PMCID: PMC9382607 DOI: 10.1038/s41598-022-14730-9] [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: 08/17/2021] [Accepted: 06/13/2022] [Indexed: 11/09/2022] Open
Abstract
The prompt detection of human papillomavirus and discrimination of its genotypes by combining conventional methods in new molecular laboratories is essential to achieve the global call of eliminating cervical cancer. After predicting the melting temperature of an approximately 221 bp region of the L1 gene from different HPV genotypes by bioinformatics software, an innovative technique based on the nested- high resolution melting was designed with three approaches and using conventional PCR, qPCR, and diagnostic standards. HPV-positive samples identified by microarray along with diagnostic standards were evaluated by qPCR-HRM and discordant results were subjected to sequencing and analyzed in silico using reference types. In addition to screening for human papillomavirus, nested-qPCR-HRM is one of the modified HRM techniques which can discriminate some genotypes, including 6, 16, 18, 52, 59, 68 and 89. Despite the differences in diagnostic capabilities among HRM, microarray and sequencing, a number of similarities between HRM, and sequencing were diagnostically identified as the gold standard method. However, the bioinformatics analysis and melting temperature studies of the selected region in different HPV genotypes showed that it could be predicted. With numerous HPV genotypes and significant genetic diversity among them, determining the virus genotype is important. Therefore, our goal in this design was to use the specific molecular techniques with several specific primers to increase sensitivity and specificity for discriminating a wide range of HPV genotypes. This approach led to new findings to evaluate the ability of different approaches and procedures in accordance with bioinformatics.
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Affiliation(s)
- Melika Alirezaei
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | | | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Zarean
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tahereh Komeili Movahhed
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Vajiheh Abbasi
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran
| | - Reza Fotouhi-Ardakani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, 3736175513, Iran. .,Department of Medical Biotechnology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
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18
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Ure A, Mukhedkar D, Arroyo Mühr LS. Using HPV-meta for human papillomavirus RNA quality detection. Sci Rep 2022; 12:13058. [PMID: 35906372 PMCID: PMC9338075 DOI: 10.1038/s41598-022-17318-5] [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: 04/26/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
In the era of cervical cancer elimination, accurate and validated pipelines to detect human papillomavirus are essential to elucidate and understand HPV association with human cancers. We aimed to provide an open-source pipeline, “HPV-meta”, to detect HPV transcripts in RNA sequencing data, including several steps to warn operators for possible viral contamination. The “HPV-meta” pipeline automatically performs several steps, starting with quality trimming, human genome filtering, HPV detection (blastx), cut-off settlement (10 reads and 690 bp coverage to make an HPV call) and finishing with fasta sequence generation for HPV positive samples. Fasta sequences can then be aligned to assess sequence diversity among HPV positive samples. All RNA sequencing files (n = 10,908) present in the cancer genome atlas (TCGA) were analyzed. “HPV-meta” identified 25 different HPV types being present in 488/10,904 specimens. Validation of results showed 99.98% agreement (10,902/10,904). Multiple alignment from fasta files warned about high sequence identity between several HPV 18 and 38 positive samples, whose contamination had previously been reported. The “HPV-meta” pipeline is a robust and validated pipeline that detects HPV in RNA sequencing data. Obtaining the fasta files enables contamination investigation, a non very rare occurrence in next generation sequencing.
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Affiliation(s)
- Agustin Ure
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden
| | - Dhananjay Mukhedkar
- Department of Laboratory Medicine, Karolinska Institutet, 141 86, Stockholm, Sweden.,Hopsworks AB, Medborgarplatsen 25, 118 72, Stockholm, Sweden
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Suresh RR, Kulandaisamy AJ, Nesakumar N, Nagarajan S, Lee JH, Rayappan JBB. Graphene Quantum Dots – Hydrothermal Green Synthesis, Material Characterization and Prospects for Cervical Cancer Diagnosis Applications: A Review. ChemistrySelect 2022. [DOI: 10.1002/slct.202200655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Raghavv Raghavender Suresh
- Department of Bioengineering School of Chemical & Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Arockia Jayalatha Kulandaisamy
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Noel Nesakumar
- Department of Bioengineering School of Chemical & Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Saisubramanian Nagarajan
- Center for Research in Infectious Diseases (CRID) School of Chemical and Biotechnology SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology School of Advanced Materials Science & Engineering Biomedical Institute for Convergence at SKKU (BICS) Sungkyunkwan University (SKKU) Suwon 16419 South Korea
| | - John Bosco Balaguru Rayappan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB) SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
- School of Electrical & Electronics Engineering SASTRA Deemed University Thanjavur 613 401 Tamil Nadu India
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20
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Human Papillomavirus and Oral Lesions: What is the Best Diagnostic Method? J Craniofac Surg 2022; 33:e279-e281. [DOI: 10.1097/scs.0000000000008113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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21
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Ma Z, Gharizadeh B, Cai X, Li M, Fellner MD, Basiletti JA, Correa RM, Colucci MC, Baldoni G, Vacchino M, Galarza P, Picconi MA, Wang C. A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections. Infect Agent Cancer 2022; 17:9. [PMID: 35313939 PMCID: PMC8935747 DOI: 10.1186/s13027-022-00420-8] [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: 11/18/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run. METHODS A cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay. RESULTS The assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified. CONCLUSIONS The ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.
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Affiliation(s)
- Zhihai Ma
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Baback Gharizadeh
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA
| | - Xingsheng Cai
- Maijing Gene Medical Technology, No. 9, Spiral 4th Road, International Biological Island, Guangzhou, China
| | - Mengzhen Li
- Maijing Gene Medical Technology, No. 9, Spiral 4th Road, International Biological Island, Guangzhou, China
| | - María Dolores Fellner
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Jorge Alejandro Basiletti
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Rita Mariel Correa
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - María Celeste Colucci
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Gabriela Baldoni
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Martín Vacchino
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Patricia Galarza
- Sexually Transmitted Diseases Service, National Reference Laboratory for STDs, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - María Alejandra Picconi
- Oncogenic Viruses Service, National and Regional HPV Reference Laboratory, National Institute of Infectious Diseases-ANLIS "Dr. Malbrán", Av. Velez Sarsfield 563, C1282AFF, Buenos Aires, Argentina
| | - Chunlin Wang
- Chapter Diagnostics Inc., 1455 Adams Drive, Menlo Park, CA, 94025, USA.
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22
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Regauer S, Reich O, Kashofer K. HPV-negative Squamous Cell Carcinomas of the Cervix With Special Focus on Intraepithelial Precursor Lesions. Am J Surg Pathol 2022; 46:147-158. [PMID: 34387215 DOI: 10.1097/pas.0000000000001778] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Recently, the World Health Organization (WHO) recognized human papilloma virus (HPV)-independent invasive cervical squamous cell carcinoma (SCC) without recognizing the existence of precursor lesions. This is a detailed characterization of 3 preinvasive lesions and 6 invasive SCC negative for HPV-DNA (32 genotypes), HPV-mRNA (14 genotypes) and genomic HPV sequencing. We evaluated histologic features, expression of p16ink4a, p53, CK7, and CK17, aberrations in 50 cancer genes and chromosomal copy number variations. HPV-negative preinvasive lesions were extensive basaloid or highly differentiated keratinizing intraepithelial proliferations of 3 to 20 cell layers thickness, partly with prominent cervical gland involvement. Overall, 2/3 intraepithelial lesions and the in situ component of 1/6 SCC showed p16ink4a block staining, while 1/6 in situ component revealed heterogenous p16ink4a staining. All invasive components of keratinizing SCC were p16ink4a-negative. Preinvasive and invasive SCC showed inconsistent CK7 and CK17 staining. Nuclear p53 overexpression was restricted to the TP53 gene mutated SCC. The highly vascularized peritumoral stroma showed a dense inflammatory infiltrate including plasma cells and intratumoral and peritumoral eosinophilic granulocytes. Inconsistent somatic gene mutations (PIK3CA, STK11, TP53, SMARC2B, and GNAS) occurred predominantly in nonhotspot locations at low mutational frequency in 3/6 SCC. Consistent aberrations included the pathogenic (angiogenic) germline polymorphism Q472H in the KDR gene (7/9 patients), and chromosome 3q gains (4/9 patients). In conclusion, HPV-negative intraepithelial cervical precancerous lesions exist, either as highly differentiated keratinized intraepithelial proliferations reminiscent of differentiated vulvar intraepithelial neoplasia, or undifferentiated basaloid intraepithelial lesions with occasional p16ink4a block staining resembling high-grade squamous intraepithelial lesion. Gains of chromosome 3q, angiogenic germline variants the inflammatory infiltrate may contribute to progression of HPV-negative cervical carcinogenesis.
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Affiliation(s)
| | - Olaf Reich
- Department of Obstetrics and Gynecology, Medical University Graz, Graz, Austria
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23
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Lei J, Arroyo-Mühr LS, Lagheden C, Eklund C, Nordqvist Kleppe S, Elfström M, Andrae B, Sparén P, Dillner J, Sundström K. Human Papillomavirus Infection Determines Prognosis in Cervical Cancer. J Clin Oncol 2022; 40:1522-1528. [PMID: 35077203 DOI: 10.1200/jco.21.01930] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Detection of human papillomavirus (HPV) by polymerase chain reaction in invasive cervical cancer is strongly associated with prognosis but previous studies have not considered sequencing efforts. We aimed to assess the association when also including comprehensive analysis of HPV infection by deep sequencing and a longer follow-up period. MATERIALS AND METHODS We subjected all 392 of 2,845 invasive cervical cancer cases that were polymerase chain reaction-negative for HPV to RNA sequencing on the NovaSeq 6000 platform (Illumina) and identified an additional 169 cases as HPV-positive. We followed all women from date of diagnosis to December 31, 2016, emigration, or death, whichever occurred first. The main outcome was all-cause mortality by December 31, 2016. We calculated 5-year cumulative relative survival ratios compared with the female general population and used Poisson regression to estimate excess hazard ratios of all-cause mortality by infection with any of the 13 most oncogenic (high-risk [hr]) HPV types in the tumor. All models were adjusted for age, time since diagnosis, stage, histology, and education level. RESULTS The 5-year cumulative relative survival ratio was 0.45 (95% CI, 0.39 to 0.51) in the hrHPV-negative group, and 0.74 (95% CI, 0.72 to 0.75) in the hrHPV-positive group. This translated to a statistically significantly 43% lower excess mortality in the hrHPV-positive group compared with the hrHPV-negative (corresponding to an excess hazard ratio 0.57; 95% CI, 0.48 to 0.69). There was no association between HPV risk group, clade, or number of HPV infections and prognosis. CONCLUSION hrHPV status is a strong determinant of cervical cancer prognosis over 15 years after diagnosis, above and beyond other established factors.
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Affiliation(s)
- Jiayao Lei
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laila Sara Arroyo-Mühr
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Camilla Lagheden
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Carina Eklund
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Nordqvist Kleppe
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Miriam Elfström
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Bengt Andrae
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Sparén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Sundström
- Department of Laboratory Medicine, Karolinska Institutet, and Center for Cervical Cancer Prevention, Karolinska University Hospital, Stockholm, Sweden
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24
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Detection and Prevention of Virus Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:21-52. [DOI: 10.1007/978-981-16-8969-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Hortlund M, Mühr LSA, Lagheden C, Hjerpe A, Dillner J. Audit of laboratory sensitivity of human papillomavirus and cytology testing in a cervical screening program. Int J Cancer 2021; 149:2083-2090. [PMID: 34418082 DOI: 10.1002/ijc.33769] [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: 04/28/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/07/2022]
Abstract
The globally recommended public health policy for cervical screening is primary human papillomavirus (HPV) screening with cytology triaging of positives. To ensure optimal quality of laboratory services we have conducted regular audits of cervical smears taken before cervical cancer or cancer in situ (CIN3+) within an HPV-based screening program. The central cervical screening laboratory of Stockholm, Sweden, identified cases of CIN3+ who had had a previous cervical screening test up to 3 years before and randomly selected 300 cervical liquid-based cytology (LBC) samples for auditing. HPV testing with Roche Cobas was performed either at screening or with biobanked samples. HPV negative samples and subsequent biopsies were retrieved and tested with modified general primer HPV PCR and, if still HPV-negative, the LBCs and biopsies were whole genome sequenced. The Cobas 4800 detected HPV in 1020/1052 (97.0%) LBC samples taken before CIN3+. Further analyses found HPV in 28 samples, with nine of those containing HPV types not targeted by the Cobas 4800 test. There were 4 specimens (4/1052, 0.4%) where no HPV was detected. By comparison, the proportion of CIN3+ cases that were positive in a previous cytology were 91.6%. We find that the routine HPV screening test had a sensitivity in the real-life screening program of 97.0%. Regular laboratory audits of cervical samples taken before CIN3+ can be readily performed within a real-life screening program and provide assurance that the laboratory of the real-life program has the expected performance.
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Affiliation(s)
- Maria Hortlund
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Camilla Lagheden
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anders Hjerpe
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Center for Cervical Cancer Prevention, Department of Pathology & Cancer Diagnostics, Medical Diagnostics Karolinska, Karolinska University Hospital, Stockholm, Sweden
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26
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Armstrong SA, Malley R, Wang H, Lenz HJ, Arguello D, El-Deiry WS, Xiu J, Gatalica Z, Hwang JJ, Philip PA, Shields AF, Marshall JL, Salem ME, Weinberg BA. Molecular characterization of squamous cell carcinoma of the anal canal. J Gastrointest Oncol 2021; 12:2423-2437. [PMID: 34790403 DOI: 10.21037/jgo-20-610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 09/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Squamous cell carcinoma of the anal canal (SCCA) is an uncommon malignancy with limited therapeutic options. Nivolumab and pembrolizumab show promising results in patients with SCCA. Human papillomavirus (HPV)-negative tumors are frequently TP53-mutated (TP53-MT) and often resistant to therapy. Methods We present a large molecularly-profiled cohort of SCCA, exploring the underlying biology of SCCA, differences between TP53-wild type (TP53-WT) and TP53-MT tumors, and differences between local and metastatic tumors. SCCA specimens (n=311) underwent multiplatform testing with immunohistochemistry (IHC), in situ hybridization (ISH) and next-generation sequencing (NGS). Tumor mutational burden (TMB) was calculated using only somatic nonsynonymous missense mutations. Chi-square testing was used for comparative analyses. Results The most frequently mutated genes included PIK3CA (28.1%), KMT2D (19.5%), FBXW7 (12%), TP53 (12%) and PTEN (10.8%). The expression of PD-1 was seen in 68.8% and PD-L1 in 40.5% of tumors. High TMB was present in 6.7% of specimens. HER2 IHC was positive in 0.9%, amplification by chromogenic in situ hybridization (CISH) was seen 1.3%, and mutations in ERBB2 were present in 1.8% of tumors. The latter mutation has not been previously described in SCCA. When compared with TP53-WT tumors, TP53-MT tumors had higher rates of CDKN2A, EWSR1, JAK1, FGFR1 and BRAF mutations. PD-1 and PD-L1 expression were similar, and high TMB did not correlate with PD-1 (P=0.50) or PD-L1 (P=0.52) expression. Conclusions Molecular profiling differences between TP53-MT and TP53-WT SCCA indicate different carcinogenic pathways which may influence response to therapy. Low frequency mutations in several druggable genes may provide therapeutic opportunities for patients with SCCA.
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Affiliation(s)
- Samantha A Armstrong
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Rita Malley
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Hongkun Wang
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, CA, USA
| | | | | | | | | | - Jimmy J Hwang
- Department of Hematology/Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Philip A Philip
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI, USA
| | - Anthony F Shields
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI, USA
| | - John L Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
| | - Mohamed E Salem
- Department of Hematology/Oncology, Levine Cancer Institute, Atrium Health, Charlotte, NC, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, USA
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27
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Fernandes A, Viveros-Carreño D, Hoegl J, Ávila M, Pareja R. Human papillomavirus-independent cervical cancer. Int J Gynecol Cancer 2021; 32:1-7. [PMID: 34725203 DOI: 10.1136/ijgc-2021-003014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/18/2021] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is the fourth most frequent cancer in women worldwide, representing nearly 8% of all female cancer deaths every year. The majority of cases of cervical cancer are caused by human papillomavirus (HPV); however, up to 5% of tumors are not associated with HPV-persistent infection and, moreover, the new WHO Female Genital Tumors classification subdivided cervical squamous and adenocarcinomas into HPV-associated and HPV-independent tumors. Based on this new information, the aim of this review is to provide an overview of HPV-independent cervical cancer, evaluating diagnostic techniques, molecular profiles, and clinical outcomes. The HPV-independent tumors are characterized by a differentiated molecular profile with lower proliferative activity, a p53 immunostaining, a decreased expression of cyclin-dependent kinase inhibitor proteins, such as p16, p14, and p27, and alterations in PTEN, p53, KRAS, CTNNB1, ARID1A, and ARID5B HPV-independent tumors are associated with both adenocarcinomas and squamous histologic subtypes, with lymph node involvement in the early stages, more distant metastasis, and generally worse oncological outcomes. Thus far, no specific therapeutic strategies have been developed based on HPV status; however, with advancing knowledge of differences in the molecular profiles and possible targetable alterations, novel approaches may offer potential options in the near future. Investigators should report on clinical outcomes, evaluating the overall response rates to specific treatments, and consider new biomarkers to establish more accurate prognostics factors.
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Affiliation(s)
- Andreina Fernandes
- Laboratorio de Genética Molecular, Instituto de Oncología y Hematología, Caracas, Bolivarian Republic of Venezuela
| | - David Viveros-Carreño
- Department of Gynecologic Oncology, Instituto Nacional de Cancerologia, Bogota, Colombia
| | - Jorge Hoegl
- Obstetrics and Gynecology. Division of Gynecological Oncology, Hospital General del Este "Dr. Domingo Luciani", Caracas, Bolivarian Republic of Venezuela
| | - Maira Ávila
- Laboratorio de Genética Molecular, Instituto de Oncología y Hematología, Caracas, Bolivarian Republic of Venezuela
| | - Rene Pareja
- Department of Gynecologic Oncology, Instituto Nacional de Cancerologia, Bogota, Colombia .,Clínica ASTORGA, Medellín, Colombia
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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics. Sci Rep 2021; 11:18852. [PMID: 34552145 PMCID: PMC8458301 DOI: 10.1038/s41598-021-98452-4] [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: 11/05/2020] [Accepted: 09/06/2021] [Indexed: 11/30/2022] Open
Abstract
Although metagenomics and metatranscriptomics are commonly used to identify bacteria and viruses in human samples, few studies directly compare these strategies. We wished to compare DNA and RNA sequencing of bacterial and viral metagenomes and metatranscriptomes in the human cervix. Total nucleic acids from six human cervical samples were subjected to DNA and RNA sequencing. The effect of DNase-treatment before reverse transcription to cDNA were also analyzed. Similarities and differences in the metagenomic findings with the three different sequencing approaches were evaluated. A higher proportion of human sequences were detected by DNA sequencing (93%) compared to RNA sequencing without (76%) and with prior DNase-treatment (11%). On the contrary, bacterial sequences increased 17 and 91 times. However, the number of detected bacterial genera were less by RNA sequencing, suggesting that only a few contribute to most of the bacterial transcripts. The viral sequences were less by RNA sequencing, still twice as many virus genera were detected, including some RNA viruses that were missed by DNA sequencing. Metatranscriptomics of total cDNA provided improved detection of mainly transcribed bacteria and viruses in cervical swabs as well as detection of RNA viruses, compared to metagenomics.
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29
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Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
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30
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Arroyo Mühr LS, Hultin E, Dillner J. Transcription of human papillomaviruses in nonmelanoma skin cancers of the immunosuppressed. Int J Cancer 2021; 149:1341-1347. [PMID: 33990956 DOI: 10.1002/ijc.33683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022]
Abstract
Nonmelanoma skin cancer (NMSC) has a greatly increased incidence among the immunosuppressed and the DNA of human papillomavirus (HPV) is commonly found in these tumors. To investigate if there are any actively transcribed HPV infections in these tumors, we identified all skin cancers diagnosed after solid organ transplantation in Sweden during 1964-2011 (n = 7614 NMSCs) and requested the diagnostic tumor blocks from the corresponding pathology archives. For the present study, we selected diagnostic specimens from 345 NMSC and performed whole genome transcriptome analysis using NovaSeq (Illumina), in comparison with three cervical cancers. Although we obtained an abundance of high-quality paired reads per sample (median of 35 million reads), only 15 NMSC specimens contained HPV transcription. Three specimens had transcription of oncogenic anogenital HPVs (HPV16 and 56), six tumors had transcription of HPVs from the beta-2 species (three HPV38, two with HPV23 and one with HPV107) and then there was one observation each of transcription of HPVs 3, 26, 57, 147, 158, 168 and of two nonestablished HPV types belonging to the gamma genus. In conclusion, transcription of specific HPV types can be found in NMSC among the immunosuppressed, but this is not common.
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Affiliation(s)
| | - Emilie Hultin
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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31
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First Report of Phodopus sungorus Papillomavirus Type 1 Infection in Roborovski Hamsters ( Phodopus roborovskii). Viruses 2021; 13:v13050739. [PMID: 33922632 PMCID: PMC8145573 DOI: 10.3390/v13050739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 11/17/2022] Open
Abstract
Papillomaviruses (PVs) are considered highly species-specific with cospeciation as the main driving force in their evolution. However, a recent increase in the available PV genome sequences has revealed inconsistencies in virus–host phylogenies, which could be explained by adaptive radiation, recombination, host-switching events and a broad PV host range. Unfortunately, with a relatively low number of animal PVs characterized, understanding these incongruities remains elusive. To improve knowledge of biology and the spread of animal PV, we collected 60 swabs of the anogenital and head and neck regions from a healthy colony of 30 Roborovski hamsters (Phodopus roborovskii) and detected PVs in 44/60 (73.3%) hamster samples. This is the first report of PV infection in Roborovski hamsters. Moreover, Phodopus sungorus papillomavirus type 1 (PsuPV1), previously characterized in Siberian hamsters (Phodopus sungorus), was the only PV detected in Roborovski hamsters. In addition, after a detailed literature search, review and summary of published evidence and construction of a tanglegram linking the cladograms of PVs and their hosts, our findings were discussed in the context of available knowledge on PVs described in at least two different host species.
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32
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Borgfeldt C, Söderlund-Strand A, Flygh LD, Forslund O. HPV73 in cervical cancer and distribution of HPV73 variants in cervical dysplasia. Int J Cancer 2021; 149:936-943. [PMID: 33837548 DOI: 10.1002/ijc.33590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/07/2022]
Abstract
HPV73 is classified as possibly oncogenic and is not recognized by most commercial primary HPV screening platforms. The aim was to determine the prevalence of HPV73 among invasive cervical cancers, formalin-fixed paraffin embedded (FFPE) samples (N = 69), from southern Sweden during 2009 to 2010. Another aim was to determine proportions of HPV73 among Aptima HPV assay negative cervical cancers (N = 9, out of 206 cancers) and of high-grade cytological cervical diagnosis (N = 75, out of 5807 high grade lesions) in liquid-based cytology (LBC) samples collected between 2016 and 2019. We also investigated the distribution of HPV73 variants A1, A2 and B among HPV73-positive cases. HPV73 was detected by multiplex MGP-PCR and Luminex, and HPV73 variants were identified by sequencing PCR amplicons. HPV73 was detected in 2.9% (2/69, 95% CI: 0.18-9.9) of the FFPE cervical cancer series. Among the Aptima HPV-negative LBC samples, HPV73 was present in 55.5% (5/9) of the cancers and 29.3% (22/75) of the different grades of cervical diagnosis. The A1, A2 and B variants were present in 6.9% (2/29), 82.7% (24/29) and 10.3% (3/29) of the HPV73-positive women, respectively. Among the seven HPV73 cancer cases (two FFPE samples and five LBC samples), six A2 and one A1 isolate were detected. In summary, the A2 variant of HPV73 was most common in our region. In addition, the observed prevalence of HPV73 (2.9%) in cervical cancers and its relative high occurrence (55.5%) among Aptima HPV-negative cancers urge that detection of HPV73 should be included in future primary HPV screening programs.
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Affiliation(s)
- Christer Borgfeldt
- Department of Obstetrics & Gynecology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Anna Söderlund-Strand
- Department of Medical Microbiology, Laboratory Medicine Region Skåne, Lund University, Lund, Sweden
| | - Lotten Darlin Flygh
- Division of Surgery, Department of Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Ola Forslund
- Department of Medical Microbiology, Laboratory Medicine Region Skåne, Lund University, Lund, Sweden
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33
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Misclassifications in human papillomavirus databases. Virology 2021; 558:57-66. [PMID: 33730650 DOI: 10.1016/j.virol.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 01/05/2023]
Abstract
We assessed the quality of human papillomavirus (HPV) sequences in GenBank by analyzing the possible presence of chimeras, "wrong-assembled" contigs and errors in taxonomy using an open-source script (HPVChimera_Gb) that compared 25 638 HPV-related nucleotide sequences in GenBank with the 221 numbered HPV types and another 220 complete HPV sequences. There were 110 sequences with taxonomy/naming errors (sequences reported as another HPV type than the one they corresponded to) and 1318 possibly chimeric sequences. Manual analysis found plausible explanations for most of them (e.g. sequence covering an integration site) but 114 sequences appeared to be chimeras (96/114 were already flagged as "unverified" by GenBank) and 13 had taxonomy/naming errors. When comparing all correct HPV sequences in GenBank, there appeared to exist about 800 unique putative HPV types. Systematic and regular work towards eliminating chimeric sequences and taxonomy/naming errors could increase the quality and order in HPV research.
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34
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Hortlund M, van Mol T, Van de Pol F, Bogers J, Dillner J. Human papillomavirus load and genotype analysis improves the prediction of invasive cervical cancer. Int J Cancer 2021; 149:684-691. [PMID: 33586149 DOI: 10.1002/ijc.33519] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/30/2020] [Accepted: 01/11/2021] [Indexed: 01/15/2023]
Abstract
Human papillomavirus (HPV)-based cervical screening is a globally recommended health policy. Different HPV types have different risk for cervical cancer. For optimal HPV screening, the sensitivity and specificity for each HPV type at different viral loads should be known in a screening setting. HPV test results in about 1 million cervical samples analyzed during 2006 to 2014 were compared for 319 women who had developed invasive cervical cancer up to 8.5 years later and for 1911 matched control women. Detection including low viral loads resulted in markedly increased sensitivity for cervical cancer only for HPV types 16 and 18. Testing for HPV types 31, 33, 45 and 52 also increased the sensitivity for prediction of cervical cancer, but for these viruses, detection of low viral load did not further increase sensitivity. HPV types 35, 39, 51, 56, 58, 59, 66 and 68 only predicted occasional additional cervical cancer cases. Testing for HPV16/18 at low viral load plus testing for HPV31, 33, 45 and 52 at >3000 copies/μL predicted 86.5% of cancers occurring within a year after testing, similar to the 89.4% that were predicted by testing for 14 HPV types. By contrast, the type and viral load-restricted testing greatly increased specificity: 6.3% of healthy women tested positive as compared to 11.7% of healthy women testing positive for the 14 HPV types commonly screened for today. Adequate HPV screening sensitivity, with considerable increase in specificity, can be obtained by testing only for HPV16/18/31/33/45/52, with detection of low viral load required only for HPV16/18.
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Affiliation(s)
- Maria Hortlund
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tine van Mol
- Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Frederik Van de Pol
- Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Johannes Bogers
- Laboratory for Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Joakim Dillner
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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35
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Human Papilloma Virus: Current Knowledge and Focus on Oral Health. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6631757. [PMID: 33623784 PMCID: PMC7875628 DOI: 10.1155/2021/6631757] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/05/2021] [Accepted: 01/20/2021] [Indexed: 11/18/2022]
Abstract
The human papilloma virus (HPV) is responsible for different pathological manifestations in humans. This agent gives rise to lesions of different types and in different areas of the organism, including the oral cavity. The aim of this study is to show which are the main diseases for which HPV is responsible and to bring to light some of the interceptive and therapeutic strategies. The analysis was conducted by consulting the major scientific databases with the aim of obtaining information on the characteristics of oral HPV and its management; furthermore, the literature was supported by some clinical cases proposed by the authors. The role of dentistry is essential in the early diagnosis of this type of pathologies and above all in knowing how to direct patients towards a path that can lead to patient management, especially in the event that these lesions have a malignant potential. Enhancing the knowledge and role of dentistry can lead to early diagnosis of this type of injury, intercepting a pathology that could have multiorgan implications.
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