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Karaoğlan BB, Ürün Y. Unveiling the Role of Human Papillomavirus in Urogenital Carcinogenesis a Comprehensive Review. Viruses 2024; 16:667. [PMID: 38793549 PMCID: PMC11125962 DOI: 10.3390/v16050667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/27/2024] [Accepted: 04/09/2024] [Indexed: 05/26/2024] Open
Abstract
Human papillomavirus (HPV), an oncogenic DNA virus, is the most common sexually transmitted virus and significant public health concern globally. Despite the substantial prevalence of HPV infection among men, routine testing remains elusive due to the lack of approved HPV tests and the complexity of detection methods. Various studies have explored the link between HPV and genitourinary cancers, revealing different associations influenced by geographic variation, histological subtype and methodological differences. These findings underscore the importance of further research to elucidate the role of HPV in male urogenital cancers. This comprehensive review delves into the intricate relationship between HPV and male genitourinary cancers, shedding light on the virus's oncogenic mechanisms and its reported prevalence. A deeper understanding of HPV's implications for male health is essential for advancing public health initiatives and reducing the burden of urogenital cancers worldwide.
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Affiliation(s)
- Beliz Bahar Karaoğlan
- Department of Medical Oncology, Ankara University Faculty of Medicine, 06620 Ankara, Türkiye;
- Faculty of Medicine, Department of Internal Medicine, Division of Internal Medicine, Ankara University Cancer Research Institute, 06620 Ankara, Türkiye
| | - Yüksel Ürün
- Department of Medical Oncology, Ankara University Faculty of Medicine, 06620 Ankara, Türkiye;
- Faculty of Medicine, Department of Internal Medicine, Division of Internal Medicine, Ankara University Cancer Research Institute, 06620 Ankara, Türkiye
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2
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Sastre-Garau X, Estrada-Virrueta L, Radvanyi F. HPV DNA Integration at Actionable Cancer-Related Genes Loci in HPV-Associated Carcinomas. Cancers (Basel) 2024; 16:1584. [PMID: 38672666 PMCID: PMC11048798 DOI: 10.3390/cancers16081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
In HPV-associated carcinomas, some examples of cancer-related genes altered by viral insertion and corresponding to potential therapeutic targets have been described, but no quantitative assessment of these events, including poorly recurrent targets, has been reported to date. To document these occurrences, we built and analyzed a database comprised of 1455 cases, including HPV genotypes and tumor localizations. Host DNA sequences targeted by viral integration were classified as "non-recurrent" (one single reported case; 838 loci), "weakly recurrent" (two reported cases; 82 loci), and highly recurrent (≥3 cases; 43 loci). Whereas the overall rate of cancer-related target genes was 3.3% in the Gencode database, this rate increased to 6.5% in "non-recurrent", 11.4% in "weakly recurrent", and 40.1% in "highly recurrent" genes targeted by integration (p = 4.9 × 10-4). This rate was also significantly higher in tumors associated with high-risk HPV16/18/45 than other genotypes. Among the genes targeted by HPV insertion, 30.2% corresponded to direct or indirect druggable targets, a rate rising to 50% in "highly recurrent" targets. Using data from the literature and the DepMap 23Q4 release database, we found that genes targeted by viral insertion could be new candidates potentially involved in HPV-associated oncogenesis. A more systematic characterization of HPV/host fusion DNA sequences in HPV-associated cancers should provide a better knowledge of HPV-driven carcinogenesis and favor the development of personalize patient treatments.
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Affiliation(s)
- Xavier Sastre-Garau
- Department of Pathology, Centre Hospitalier Intercommunal de Créteil, 40, Avenue de Verdun, 94010 Créteil, France
| | - Lilia Estrada-Virrueta
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
| | - François Radvanyi
- Institut Curie, PSL Research University, CNRS, UMR 144, 75005 Paris, France; (L.E.-V.); (F.R.)
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3
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Griffiths CD, Shah M, Shao W, Borgman CA, Janes KA. Three Modes of Viral Adaption by the Heart. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587274. [PMID: 38585853 PMCID: PMC10996681 DOI: 10.1101/2024.03.28.587274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Viruses elicit long-term adaptive responses in the tissues they infect. Understanding viral adaptions in humans is difficult in organs such as the heart, where primary infected material is not routinely collected. In search of asymptomatic infections with accompanying host adaptions, we mined for cardio-pathogenic viruses in the unaligned reads of nearly one thousand human hearts profiled by RNA sequencing. Among virus-positive cases (~20%), we identified three robust adaptions in the host transcriptome related to inflammatory NFκB signaling and post-transcriptional regulation by the p38-MK2 pathway. The adaptions are not determined by the infecting virus, and they recur in infections of human or animal hearts and cultured cardiomyocytes. Adaptions switch states when NFκB or p38-MK2 are perturbed in cells engineered for chronic infection by the cardio-pathogenic virus, coxsackievirus B3. Stratifying viral responses into reversible adaptions adds a targetable systems-level simplification for infections of the heart and perhaps other organs.
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Affiliation(s)
- Cameron D. Griffiths
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Millie Shah
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - William Shao
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Cheryl A. Borgman
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Kevin A. Janes
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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4
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Wilczyński J, Paradowska E, Wilczyński M. High-Grade Serous Ovarian Cancer-A Risk Factor Puzzle and Screening Fugitive. Biomedicines 2024; 12:229. [PMID: 38275400 PMCID: PMC10813374 DOI: 10.3390/biomedicines12010229] [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: 11/12/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is the most lethal tumor of the female genital tract. Despite extensive studies and the identification of some precursor lesions like serous tubal intraepithelial cancer (STIC) or the deviated mutational status of the patients (BRCA germinal mutation), the pathophysiology of HGSOC and the existence of particular risk factors is still a puzzle. Moreover, a lack of screening programs results in delayed diagnosis, which is accompanied by a secondary chemo-resistance of the tumor and usually results in a high recurrence rate after the primary therapy. Therefore, there is an urgent need to identify the substantial risk factors for both predisposed and low-risk populations of women, as well as to create an economically and clinically justified screening program. This paper reviews the classic and novel risk factors for HGSOC and methods of diagnosis and prediction, including serum biomarkers, the liquid biopsy of circulating tumor cells or circulating tumor DNA, epigenetic markers, exosomes, and genomic and proteomic biomarkers. The novel future complex approach to ovarian cancer diagnosis should be devised based on these findings, and the general outcome of such an approach is proposed and discussed in the paper.
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Affiliation(s)
- Jacek Wilczyński
- Department of Gynecological Surgery and Gynecological Oncology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland;
| | - Miłosz Wilczyński
- Department of Surgical, Endoscopic and Gynecological Oncology, Polish Mother’s Health Center—Research Institute, 281/289 Rzgowska Str., 93-338 Lodz, Poland;
- Department of Surgical and Endoscopic Gynecology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
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5
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Youssef ASED, Zekri ARN, Mohanad M, Loutfy SA, Abdel Fattah NF, Elberry MH, El Leithy AA, El-Touny A, Rabie AS, Shalaby M, Hanafy A, Lotfy MM, El-Sisi ER, El-Sayyad GS, Nassar A. Deleterious and ethnic-related BRCA1/2 mutations in tissue and blood of Egyptian colorectal cancer patients and its correlation with human papillomavirus. Clin Exp Med 2023; 23:5063-5088. [PMID: 37804357 PMCID: PMC10725364 DOI: 10.1007/s10238-023-01207-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: 07/21/2023] [Accepted: 09/22/2023] [Indexed: 10/09/2023]
Abstract
This study aimed to identify BRCA1/2 mutational patterns in the tissue and blood of Egyptian colorectal cancer (CRC) patients and to study the possible correlation of this mutational pattern with Human papillomavirus (HPV) infection. Eighty-two colonoscopic biopsies and forty-six blood samples were collected from Egyptian CRC patients, as well as blood samples of age and sex-matched healthy controls (n = 43) were enrolled. The libraries were performed using Qiaseq Human BRCA1 and BRCA2 targeted DNA panel and sequenced via Ion proton sequencer. Also, the CRC tissues were subjected to conventional PCR targeting the HPV Late 1 (L1) region. Our analysis revealed that the BRCA-DNA damage pathway had been altered in more than 65% of the CRC patients. Comparing tissue and blood samples from CRC patients, 25 somatic mutations were found exclusively in tissue, while 41 germline mutations were found exclusively in blood. Additionally, we identified 23 shared BRCA1/2 pathogenic (PVs) mutations in both blood and tissue samples, with a significantly higher frequency in blood samples compared to tissue samples. The most affected exon in BRCA1 was exon 10, while the most affected exons in BRCA2 were 11, 14, 18, 24, and 27 exons. Notably, we revealed an ethnic-related cluster of polymorphism variants in our population closely related to South Asian and African ethnicities. Novel PVs were identified and submitted to the ClinVar database. HPV was found in 23.8% of the CRC tissues, and 54% of HPV-positive cases had somatic BRCA1/2 PVs. The results of this research point to a possible connection between infection with HPV and BRCA1/2 mutations in the occurrence of colorectal cancer in the Egyptian population, which has a mixed ethnic background. Our data also indicate that liquid biopsy (blood samples) may be more representative than tissue samples for detecting BRCA1/2 mutations. These findings may have implications for cancer screening and the development of personalized, targeted therapies, such as PARP inhibitors, which can effectively target BRCA1/2 mutations.
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Affiliation(s)
- Amira Salah El-Din Youssef
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
| | - Abdel Rahman N Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa Mohanad
- Department of Biochemistry, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt
| | - Samah A Loutfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
- Nanotechnology Research Center (NTRC), The British University in Egypt (BUE), El-Shorouk City, Suez Desert Road, P. O. Box 43, Cairo, Egypt
| | - Nasra F Abdel Fattah
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mostafa H Elberry
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Asmaa A El Leithy
- Department of Medical Biotechnology, College of Biotechnology, Misr University for Science and Technology, Giza, Egypt
| | - Ahmed El-Touny
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ahmed Samy Rabie
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed Shalaby
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Ayman Hanafy
- Surgical Oncology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mai M Lotfy
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Enas R El-Sisi
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Gharieb S El-Sayyad
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Galala University, New Galala City, Suez, Egypt.
- Drug Microbiology Lab., Drug Radiation Research Department, National Center for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt.
| | - Auhood Nassar
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
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6
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Yang L, Wang J, Altreuter J, Jhaveri A, Wong CJ, Song L, Fu J, Taing L, Bodapati S, Sahu A, Tokheim C, Zhang Y, Zeng Z, Bai G, Tang M, Qiu X, Long HW, Michor F, Liu Y, Liu XS. Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc 2023; 18:2404-2414. [PMID: 37391666 DOI: 10.1038/s41596-023-00841-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2023] [Indexed: 07/02/2023]
Abstract
RNA-sequencing (RNA-seq) has become an increasingly cost-effective technique for molecular profiling and immune characterization of tumors. In the past decade, many computational tools have been developed to characterize tumor immunity from gene expression data. However, the analysis of large-scale RNA-seq data requires bioinformatics proficiency, large computational resources and cancer genomics and immunology knowledge. In this tutorial, we provide an overview of computational analysis of bulk RNA-seq data for immune characterization of tumors and introduce commonly used computational tools with relevance to cancer immunology and immunotherapy. These tools have diverse functions such as evaluation of expression signatures, estimation of immune infiltration, inference of the immune repertoire, prediction of immunotherapy response, neoantigen detection and microbiome quantification. We describe the RNA-seq IMmune Analysis (RIMA) pipeline integrating many of these tools to streamline RNA-seq analysis. We also developed a comprehensive and user-friendly guide in the form of a GitBook with text and video demos to assist users in analyzing bulk RNA-seq data for immune characterization at both individual sample and cohort levels by using RIMA.
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Affiliation(s)
- Lin Yang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jin Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cheryl J Wong
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- School of Life Science and Technology, Tongji University, Shanghai, China
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Len Taing
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sudheshna Bodapati
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Avinash Sahu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Collin Tokheim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Zexian Zeng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xintao Qiu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Henry W Long
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
- The Ludwig Center at Harvard, Boston, MA, USA
| | - Yang Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
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7
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Mukherjee AG, Ramesh Wanjari U, Valsala Gopalakrishnan A, Jayaraj R, Katturajan R, Kannampuzha S, Murali R, Namachivayam A, Evan Prince S, Vellingiri B, Dey A, Renu K. HPV-associated cancers: insights into the mechanistic scenario and latest updates. Med Oncol 2023; 40:212. [PMID: 37358816 DOI: 10.1007/s12032-023-02085-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023]
Abstract
Cancer and related diseases are the second leading cause of death worldwide. The human papillomavirus (HPV) is an infectious agent that can be spread mainly through sexual contact and has been linked to several malignancies in both sexes. HPV is linked to almost all cases of cervical cancer. It is also linked to many head and neck cancer (HNC) cases, especially oropharyngeal cancer. Also, some HPV-related cancers, like vaginal, vulvar, penile, and anal cancers, are related to the anogenital area. Over the past few decades, testing for and preventing cervical cancer has improved, but anogenital cancers are still harder to confirm. HPV16 and HPV18 have been extensively researched due to their significant carcinogenic potential. The products of two early viral genes, E6 and E7, have been identified as playing crucial roles in cellular transformation, as emphasized by biological investigations. The complete characterization of numerous mechanisms employed by E6 and E7 in undermining the regulation of essential cellular processes has significantly contributed to our comprehension of HPV-induced cancer progression. This review focuses on the various types of cancers caused by HPV infection and also sheds light on the signaling cascades involved in the same.
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Affiliation(s)
- Anirban Goutam Mukherjee
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Uddesh Ramesh Wanjari
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
| | - Rama Jayaraj
- Jindal Institute of Behavioral Sciences (JIBS), Jindal Global Institution of Eminence Deemed to Be University, 28, Sonipat, 131001, India
- Director of Clinical Sciences, Northern Territory Institute of Research and Training, Darwin, NT, 0909, Australia
| | - Ramkumar Katturajan
- Department of Biotechnology, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sandra Kannampuzha
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Reshma Murali
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Arunraj Namachivayam
- Department of Biomedical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sabina Evan Prince
- Department of Biotechnology, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab (CUPB), Bathinda, Punjab, 151401, India
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, 700073, India
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College & Hospitals, Saveetha University, Chennai, Tamil Nadu, 600077, India
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8
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Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N. A deep learning approach reveals unexplored landscape of viral expression in cancer. Nat Commun 2023; 14:785. [PMID: 36774364 PMCID: PMC9922274 DOI: 10.1038/s41467-023-36336-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/25/2023] [Indexed: 02/13/2023] Open
Abstract
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
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Affiliation(s)
| | - Ying Ye
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel E Schäffer
- The Wistar Institute, Philadelphia, PA, 19104, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Xue Hao
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | - Konstantinos Tsingas
- The Wistar Institute, Philadelphia, PA, 19104, USA.,University of Pennsylvania, Philadelphia, PA, USA
| | | | - Qi Long
- University of Pennsylvania, Philadelphia, PA, USA
| | - Quaid Morris
- Computational and Systems Biology, Sloan Kettering Institute, New York City, NY, 10065, USA
| | - Rugang Zhang
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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9
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Min Y, Wei X, Xia X, Wei Z, Li R, Jin J, Liu Z, Hu X, Peng X. Hepatitis B virus infection: An insight into the clinical connection and molecular interaction between hepatitis B virus and host extrahepatic cancer risk. Front Immunol 2023; 14:1141956. [PMID: 36936956 PMCID: PMC10014788 DOI: 10.3389/fimmu.2023.1141956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
The evidence for chronic hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence is well established. The hepatocyte epithelium carcinogenesis caused by HBV has been investigated and reviewed in depth. Nevertheless, recent findings from preclinical and observational studies suggested that chronic HBV infection is equally important in extrahepatic cancer occurrence and survival, specifically gastrointestinal system-derived cancers. Immune microenvironment changes (immune-suppressive cytokine infiltration), epigenetic modification (N6-methyladenosine), molecular signaling pathways (PI3K-Akt and Wnt), and serum biomarkers such as hepatitis B virus X (HBx) protein are potential underlying mechanisms in chronic HBV infection-induced extrahepatic cancers. This narrative review aimed to comprehensively summarize the most recent advances in evaluating the association between chronic HBV infection and extrahepatic cancer risk and explore the potential underlying molecular mechanisms in the carcinogenesis induction of extrahepatic cancers in chronic HBV conditions.
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Affiliation(s)
- Yu Min
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
| | - Xiaoyuan Wei
- Department of Head and Neck Oncology, Department of Radiation Oncology, Cancer Center, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan, China
| | - Xi Xia
- Research and Development Department Shanghai ETERN Biopharma Co., Ltd., Shanghai, China
| | - Zhigong Wei
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
| | - Ruidan Li
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
| | - Jing Jin
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
| | - Zheran Liu
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Sichuan, China
- *Correspondence: Xingchen Peng, ; Xiaolin Hu,
| | - Xingchen Peng
- Department of Biotherapy and National Clinical Research Center for Geriatrics, Cancer Center, West China Hospital, Sichuan University, Sichuan, China
- *Correspondence: Xingchen Peng, ; Xiaolin Hu,
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10
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Shahi V, Agarwal P, Qayoom S, Kumar V, Tewari S, Raghuvanshi S, Singh US, Goel MM. Detection of Epstein Barr Nuclear Antigen-1 (EBNA-1), Early Antigen 1F, 2R (EA-1F, EA- 2R) along with Epstein-Barr virus Latent Membrane Protein 1 (LMP1) in Breast Cancer of Northern India: An Interim Analysis. Asian Pac J Cancer Prev 2022; 23:3717-3723. [PMID: 36444584 PMCID: PMC9930963 DOI: 10.31557/apjcp.2022.23.11.3717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Worldwide, breast cancer (BC) is a prominent cause of death, with a disproportionately high incidence in developed countries. Epstein-Barr virus (EBV) infection has been reported in up to 90% of the world's population. Although the exact link of EBV infection and breast carcinoma is not yet determined. The present study was carried out to assess the pathological correlation of EBV infection and BC in women from Northern India. METHODOLOGY In this prospective observational study, 130 patients with histologically proven breast carcinoma were included. After detailed histology, the paraffin block with infiltrative tumor was selected for molecular analysis and further immunohistochemistry (IHC)- EBV PCR and Epstein-Barr virus latent membrane protein 1 (LMP1) IHC. RESULTS Most of the patients were diagnosed with Infiltrating Ductal Carcinoma not otherwise specified (IDC-NOS), followed by Infiltrating Ductal Carcinoma + Ductal Carcinoma in situ (IDC + DCIS). The total of 25 tissues of breast carcinoma had positive EBV PCR results (19.23%). The co-relation between the molecular and immunohistochemical results was significant in 11/25 cases that showed immunoexpression for LMP1 by IHC. Sensitivity of 44% and specificity of 100% were observed for LMP1 IHC, having a PPV value of 100% and an NPV of 88%. No significant correlation was observed between age, tumor subtype, grade, stage with respect to EBV infection; however, there was a significant association with nodal metastasis with extra nodal extension in tumors that had EBV infection. CONCLUSION The present study establishes an association between LMP1 and patients with EBV positive breast cancer. The authors suggest that additional multicentric studies be conducted to strengthen the reliability and generalizability of the observations of the current study.
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Affiliation(s)
| | - Preeti Agarwal
- Department of Pathology, KGMU, Lucknow, UP, India. ,For Correspondence:
| | | | - Vijay Kumar
- Department of Surgical Oncology, KGMU, Lucknow, UP, India.
| | - Shikha Tewari
- Department of Laboratory Medicine and Pathology, Medanta Hospital, Lucknow, UP, India.
| | | | | | - Madhu Mati Goel
- Department of Laboratory Medicine and Pathology, Medanta Hospital, Lucknow, UP, India.
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11
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Cook CJ, Miller AE, Barker TH, Di Y, Fogg KC. Characterizing the extracellular matrix transcriptome of cervical, endometrial, and uterine cancers. Matrix Biol Plus 2022; 15:100117. [PMID: 35898192 PMCID: PMC9309672 DOI: 10.1016/j.mbplus.2022.100117] [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: 04/28/2022] [Revised: 07/09/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
The matrisome plays a critical role in the progression of cancer, but the matrisomes of gynecological cancers have not been well characterized. We built an in silico analysis pipeline to analyze publicly available bulk RNA-seq datasets of cervical, endometrial, and uterine cancers. Using a machine learning approach, we identified genes and gene networks that held inferential significance for cancer stage and patient survival. Cervical, endometrial, and uterine cancers are highly distinct from one another and should be analyzed separately.
Increasingly, the matrisome, a set of proteins that form the core of the extracellular matrix (ECM) or are closely associated with it, has been demonstrated to play a key role in tumor progression. However, in the context of gynecological cancers, the matrisome has not been well characterized. A holistic, yet targeted, exploration of the tumor microenvironment is critical for better understanding the progression of gynecological cancers, identifying key biomarkers for cancer progression, establishing the role of gene expression in patient survival, and for assisting in the development of new targeted therapies. In this work, we explored the matrisome gene expression profiles of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), uterine corpus endometrial carcinoma (UCEC), and uterine carcinosarcoma (UCS) using publicly available RNA-seq data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) portal. We hypothesized that the matrisomal expression patterns of CESC, UCEC, and UCS would be highly distinct with respect to genes which are differentially expressed and hold inferential significance with respect to tumor progression, patient survival, or both. Through a combination of statistical and machine learning analysis techniques, we identified sets of genes and gene networks which characterized each of the gynecological cancer cohorts. Our findings demonstrate that the matrisome is critical for characterizing gynecological cancers and transcriptomic mechanisms of cancer progression and outcome. Furthermore, while the goal of pan-cancer transcriptional analyses is often to highlight the shared attributes of these cancer types, we demonstrate that they are highly distinct diseases which require separate analysis, modeling, and treatment approaches. In future studies, matrisome genes and gene ontology terms that were identified as holding inferential significance for cancer stage and patient survival can be evaluated as potential drug targets and incorporated into in vitro models of disease.
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Affiliation(s)
- Carson J Cook
- Department of Bioengineering, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew E Miller
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Thomas H Barker
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Yanming Di
- Department of Statistics, Oregon State University, Corvallis, OR 97331, USA
| | - Kaitlin C Fogg
- Department of Bioengineering, Oregon State University, Corvallis, OR 97331, USA.,Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR 97201, USA
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12
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Ahn J, Shin C, Kim YS, Park JS, Jeun SS, Ahn S. Cytomegalovirus-Specific Immunotherapy for Glioblastoma Treatments. Brain Tumor Res Treat 2022; 10:135-143. [PMID: 35929110 PMCID: PMC9353163 DOI: 10.14791/btrt.2022.0010] [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: 03/14/2022] [Revised: 05/25/2022] [Accepted: 06/15/2022] [Indexed: 11/20/2022] Open
Abstract
Over the last two decades, numerous studies have investigated the presence of human cytomegalovirus (CMV) within glioblastoma or gliomas; however, the results are severely conflicting. While a few researchers have suggested the potential benefits of cytotoxic T lymphocyte or dendritic cell-based vaccines for recurrent or newly diagnosed glioblastoma patients, several studies did not at all agree with the existence of CMV in glioblastoma cells. In this review, we summarized the conflicting results and issues about the detection of CMV in glioblastoma or glioma patients. We also provided the clinical data of published and unpublished clinical trials using CMV-specific immunotherapy for glioblastomas.
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Affiliation(s)
- Jaehyun Ahn
- College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Christopher Shin
- College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeo Song Kim
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jae-Sung Park
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sin-Soo Jeun
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Stephen Ahn
- Department of Neurosurgery, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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13
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Wei E, Reisinger A, Li J, French LE, Clanner-Engelshofen B, Reinholz M. Integration of scRNA-Seq and TCGA RNA-Seq to Analyze the Heterogeneity of HPV+ and HPV- Cervical Cancer Immune Cells and Establish Molecular Risk Models. Front Oncol 2022; 12:860900. [PMID: 35719936 PMCID: PMC9198569 DOI: 10.3389/fonc.2022.860900] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
Background Numerous studies support that Human papillomavirus (HPV) can cause cervical cancer. However, few studies have surveyed the heterogeneity of HPV infected or uninfected (HPV+ and HPV-) cervical cancer (CESC) patients. Integration of scRNA-seq and TCGA data to analyze the heterogeneity of HPV+ and HPV- cervical cancer patients on a single-cell level could improve understanding of the cellular mechanisms during HPV-induced cervical cancer. Methods CESC scRNA-seq data obtained from the Gene Expression Omnibus (GEO) database and the Seurat, Monocle3 package were used for scRNA-seq data analysis. The ESTIMATE package was used for single-sample gene immune score, CIBERSORT package was used to identify immune scores of cells, and the “WGCNA” package for the weighted correlation network analysis. Univariate Cox and LASSO regression were performed to establish survival and relapse signatures. KEGG and GO analyses were performed for the signature gene. Gene Expression Profiling Interactive Analysis was used for Pan-cancer analysis. Results In the HPV+ CESC group, CD8+ T cells and B cells were down-regulated, whereas T reg cells, CD4+ T cells, and epithelial cells were up-regulated according to scRNA-seq data. Survival analysis of TCGA-CESC revealed that increased expression of naive B cells or CD8+ T cells favors the survival probability of CESC patients. WGCNA, univariate Cox, and LASSO Cox regression established a 9-genes survival signature and a 7-gene relapse model. Pan-cancer analysis identified IKZF3, FOXP3, and JAK3 had a similar distribution and effects in HPV-associated HNSC. Conclusion Analysis of scRNA-seq and bulk RNA-seq of HPV+ and HPV- CESC samples revealed heterogeneity from transcriptional state to immune infiltration. Survival and relapse models were adjusted according to the heterogeneity of HPV+ and HPV- CESC immune cells to assess the prognostic risk accurately. Hub genes represent similar protection in HPV- associated HNSC while showing irrelevant to other potential HPV-related cancers.
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Affiliation(s)
- Erdong Wei
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany
| | - Amin Reisinger
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany
| | - Jiahua Li
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany
| | - Lars E French
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany.,Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery , Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Benjamin Clanner-Engelshofen
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany
| | - Markus Reinholz
- Department of Dermatology and Allergy, Ludwig-Maximilians-Universität München (LMU) Munich, University Hospital, Munich, Germany
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14
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Yogi N, Usui G, Matsusaka K, Fukuyo M, Fujiki R, Seki M, Takano S, Abe H, Morikawa T, Ushiku T, Ohtsuka M, Kaneda A. Association of tumors having Epstein-Barr virus in surrounding lymphocytes with poor prognosis. Cancer Med 2022; 12:1122-1136. [PMID: 35726701 PMCID: PMC9883551 DOI: 10.1002/cam4.4967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/12/2022] [Accepted: 06/10/2022] [Indexed: 02/02/2023] Open
Abstract
Infection with certain viruses is an important cause of cancer. The Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium recently analyzed the whole-genome sequencing (WGS) data from 2656 cases across 21 cancer types, and indicated that Epstein-Barr virus (EBV) is detected in many different cancer cases at a higher frequency than previously reported. However, whether EBV-positive cancer cases detected by WGS-based screening correspond to those detected by conventional histopathological techniques is still unclear. In this study, to elucidate the involvement of EBV in various cancers, we reanalyzed the WGS data of the PCAWG cohort combined with the analysis of clinical samples of gastric and pancreatic cancer in our cohort. Based on EBV copy number in each case, we classified tumors into three subgroups: EBV-High, EBV-Low, and EBV-Negative. The EBV-High subgroup was found to be EBV-positive in the cancer cells themselves, whereas the EBV-Low subgroup was EBV-positive in the surrounding lymphocytes. Further, the EBV-Low subgroup showed a significantly worse prognosis for both gastric cancer and across cancer types. In summary, we classified tumors based on EBV copy number and found a unique cancer subgroup, EBV-positive in the surrounding lymphocytes, which was associated with a poor prognosis.
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Affiliation(s)
- Norikazu Yogi
- Department of General Surgery, Graduate School of MedicineChiba UniversityJapan,Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan
| | - Genki Usui
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan,Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan,Department of Diagnostic PathologyNTT Medical Center TokyoTokyoJapan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan,Department of PathologyChiba University HospitalChibaJapan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan
| | - Ryoji Fujiki
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan,Cancer Genomics CenterChiba University HospitalChibaJapan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan,Cancer Genomics CenterChiba University HospitalChibaJapan
| | - Shigetsugu Takano
- Department of General Surgery, Graduate School of MedicineChiba UniversityJapan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Teppei Morikawa
- Department of Diagnostic PathologyNTT Medical Center TokyoTokyoJapan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Masayuki Ohtsuka
- Department of General Surgery, Graduate School of MedicineChiba UniversityJapan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityJapan
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15
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Teles F, Collman RG, Mominkhan D, Wang Y. Viruses, periodontitis, and comorbidities. Periodontol 2000 2022; 89:190-206. [PMID: 35244970 DOI: 10.1111/prd.12435] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Seminal studies published in the 1990s and 2000s explored connections between periodontal diseases and systemic conditions, revealing potential contributions of periodontal diseases in the initiation or worsening of systemic conditions. The resulting field of periodontal medicine led to the publication of studies indicating that periodontal diseases can influence the risk of systemic conditions, including adverse pregnancy outcomes, cardiovascular and respiratory diseases, as well as Alzheimer disease and cancers. In general, these studies hypothesized that the periodontal bacterial insult and/or the associated proinflammatory cascade could contribute to the pathogenesis of these systemic diseases. While investigations of the biological basis of the connections between periodontal diseases and systemic conditions generally emphasized the bacteriome, it is also biologically plausible, under an analogous hypothesis, that other types of organisms may have a similar role. Human viruses would be logical "suspects" in this role, given their ubiquity in the oral cavity, association with periodontal diseases, and ability to elicit strong inflammatory response, compromise immune responses, and synergize with bacteria in favor of a more pathogenic microbial consortium. In this review, the current knowledge of the role of viruses in connecting periodontal diseases and systemic conditions is examined. We will also delve into the mechanistic basis for such connections and highlight the importance of those relationships in the management and treatment of patients.
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Affiliation(s)
- Flavia Teles
- Department of Basic and Translational Sciences, School of Dental Medicine, Center for Innovation & Precision Dentistry, School of Dental Medicine & School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G Collman
- Pulmonary, Allergy and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Dana Mominkhan
- Department of Endodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yu Wang
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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16
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Bousali M, Karamitros T. Hepatitis B Virus Integration into Transcriptionally Active Loci and HBV-Associated Hepatocellular Carcinoma. Microorganisms 2022; 10:microorganisms10020253. [PMID: 35208708 PMCID: PMC8879149 DOI: 10.3390/microorganisms10020253] [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: 12/31/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B Virus (HBV) DNA integrations into the human genome are considered major causative factors to HBV-associated hepatocellular carcinoma development. In the present study, we investigated whether HBV preferentially integrates parts of its genome in specific genes and evaluated the contribution of the integrations in HCC development per gene. We applied dedicated in-house developed pipelines on all of the available HBV DNA integration data and performed a statistical analysis to identify genes that could be characterized as hotspots of integrations, along with the evaluation of their association with HBV-HCC. Our results suggest that 15 genes are recurrently affected by HBV integrations and they are significantly associated with HBV-HCC. Further studies that focus on HBV integrations disrupting these genes are mandatory in order to understand the role of HBV integrations in clonal advantage gain and oncogenesis promotion, as well as to determine whether inhibition of the HBV-disrupted genes can provide a therapy strategy for HBV-HCC.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
- Correspondence: ; Tel.: +30-210-6478871
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17
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Chakravorty S, Afzali B, Kazemian M. EBV-associated diseases: Current therapeutics and emerging technologies. Front Immunol 2022; 13:1059133. [PMID: 36389670 PMCID: PMC9647127 DOI: 10.3389/fimmu.2022.1059133] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
EBV is a prevalent virus, infecting >90% of the world's population. This is an oncogenic virus that causes ~200,000 cancer-related deaths annually. It is, in addition, a significant contributor to the burden of autoimmune diseases. Thus, EBV represents a significant public health burden. Upon infection, EBV remains dormant in host cells for long periods of time. However, the presence or episodic reactivation of the virus increases the risk of transforming healthy cells to malignant cells that routinely escape host immune surveillance or of producing pathogenic autoantibodies. Cancers caused by EBV display distinct molecular behaviors compared to those of the same tissue type that are not caused by EBV, presenting opportunities for targeted treatments. Despite some encouraging results from exploration of vaccines, antiviral agents and immune- and cell-based treatments, the efficacy and safety of most therapeutics remain unclear. Here, we provide an up-to-date review focusing on underlying immune and environmental mechanisms, current therapeutics and vaccines, animal models and emerging technologies to study EBV-associated diseases that may help provide insights for the development of novel effective treatments.
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Affiliation(s)
- Srishti Chakravorty
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Department of Computer Science, Purdue University, West Lafayette IN, United States
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18
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Broecker F, Moelling K. The Roles of the Virome in Cancer. Microorganisms 2021; 9:microorganisms9122538. [PMID: 34946139 PMCID: PMC8706120 DOI: 10.3390/microorganisms9122538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/22/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
Viral infections as well as changes in the composition of the intestinal microbiota and virome have been linked to cancer. Moreover, the success of cancer immunotherapy with checkpoint inhibitors has been correlated with the intestinal microbial composition of patients. The transfer of feces-which contain mainly bacteria and their viruses (phages)-from immunotherapy responders to non-responders, known as fecal microbiota transplantation (FMT), has been shown to be able to convert some non-responders to responders. Since phages may also increase the response to immunotherapy, for example by inducing T cells cross-reacting with cancer antigens, modulating phage populations may provide a new avenue to improve immunotherapy responsiveness. In this review, we summarize the current knowledge on the human virome and its links to cancer, and discuss the potential utility of bacteriophages in increasing the responder rate for cancer immunotherapy.
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Affiliation(s)
- Felix Broecker
- Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
- Correspondence: (F.B.); (K.M.)
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Gloriastr. 30, CH-8006 Zurich, Switzerland
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
- Correspondence: (F.B.); (K.M.)
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19
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Chen S, Lai H, Zhao J, Chen B, Li Y, Li Y, Li Q, Zheng Q, Huang S, Zhu X. The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy. BMC Cancer 2021; 21:1183. [PMID: 34740324 PMCID: PMC8571886 DOI: 10.1186/s12885-021-08871-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherapy of human cancers. However, the landscape of viral expressions and immune status in human cancers remains incompletely understood. METHODS We developed a next-generation sequencing (NGS)-based pipeline to detect viral sequences from the whole transcriptome and used machine learning algorithms to classify different TIME subtypes. RESULTS We revealed a pan-cancer landscape of viral expressions in human cancers where 9 types of viruses were detected in 744 tumors of 25 cancer types. Viral infections showed different tissue tendencies and expression levels. Multi-omics analyses further revealed their distinct impacts on genomic, transcriptomic and immune responses. Epstein-Barr virus (EBV)-infected stomach adenocarcinoma (STAD) and Human Papillomavirus (HPV)-infected head and neck squamous cell carcinoma (HNSC) showed decreased genomic variations, significantly altered gene expressions, and effectively triggered anti-viral immune responses. We identified three TIME subtypes, in which the "Immune-Stimulation" subtype might be the promising candidate for immunotherapy. EBV-infected STAD and HPV-infected HNSC showed a higher frequency of the "Immune-Stimulation" subtype. Finally, we constructed the eVIIS pipeline to simultaneously evaluate viral infection and immune status in external datasets. CONCLUSIONS Viral infections are prevalent in human cancers and have distinct influences on hosts. EBV and HPV infections combined with the TIME subtype could be promising biomarkers of immunotherapy in STAD and HNSC, respectively. The eVIIS pipeline could be a practical tool to facilitate clinical practice and relevant studies.
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Affiliation(s)
- Siyuan Chen
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongyan Lai
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
| | - Bing Chen
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yan Li
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
| | - Yuchen Li
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
| | - Qin Li
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
| | - Qiupeng Zheng
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China
| | - Shenglin Huang
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xiaodong Zhu
- Department of Medical Oncology, Shanghai Key Laboratory of Medical Epigenetics, Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Fudan University, 270 Dong An Rd, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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20
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Oleynikova NA, Danilova NV, Grimuta MO, Malkov PG. Epstein-Barr Virus in the Development of Colorectal Cancer (Review). Sovrem Tekhnologii Med 2021; 13:82-91. [PMID: 34603767 PMCID: PMC8482827 DOI: 10.17691/stm2021.13.4.09] [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: 12/04/2020] [Indexed: 12/03/2022] Open
Abstract
The study of the influence of the Epstein–Barr virus (EBV) on the development of colorectal cancer is of current interest, particularly in light of the active discussion of the participation of this virus in the carcinogenesis of stomach cancer. In this review, aimed at a fundamental understanding of the processes associated with the impact of EBV on the human body, attention is paid to the issues of the life cycle of the virus, its phases (latent and lytic), as well as proteins that may be detected in each of the phases. The papers reporting on the role of EBV in the development of colorectal cancer have been analyzed. A summary table indicating the population under study, the number of samples, the method, and the result obtained is provided. Given that the primary cells affected by EBV are lymphocytes, it is logical to assume the involvement of this virus in the development of inflammatory bowel diseases. The review cites studies which confirm the presence of virus DNA in tissues in the inflammatory diseases of the colon, including microscopic and ulcerative colitis. To confirm the direct impact of EBV on the development of colorectal cancer, large studies with applying various methods for detecting the virus and the mandatory description of its localization are required. Besides, it is necessary to correlate these data with the clinical and morphological characteristics of EBV.
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Affiliation(s)
- N A Oleynikova
- Researcher, Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
| | - N V Danilova
- Senior Researcher, Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
| | - M O Grimuta
- Student; I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya St., Moscow, 119991, Russia
| | - P G Malkov
- Head of the Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
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21
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Bousali M, Papatheodoridis G, Paraskevis D, Karamitros T. Hepatitis B Virus DNA Integration, Chronic Infections and Hepatocellular Carcinoma. Microorganisms 2021; 9:1787. [PMID: 34442866 PMCID: PMC8398950 DOI: 10.3390/microorganisms9081787] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B Virus (HBV) is an Old World virus with a high mutation rate, which puts its origins in Africa alongside the origins of Homo sapiens, and is a member of the Hepadnaviridae family that is characterized by a unique viral replication cycle. It targets human hepatocytes and can lead to chronic HBV infection either after acute infection via horizontal transmission usually during infancy or childhood or via maternal-fetal transmission. HBV has been found in ~85% of HBV-related Hepatocellular Carcinomas (HCC), and it can integrate the whole or part of its genome into the host genomic DNA. The molecular mechanisms involved in the HBV DNA integration is not yet clear; thus, multiple models have been described with respect to either the relaxed-circular DNA (rcDNA) or the double-stranded linear DNA (dslDNA) of HBV. Various genes have been found to be affected by HBV DNA integration, including cell-proliferation-related genes, oncogenes and long non-coding RNA genes (lincRNAs). The present review summarizes the advances in the research of HBV DNA integration, focusing on the evolutionary and molecular side of the integration events along with the arising clinical aspects in the light of WHO's commitment to eliminate HBV and viral hepatitis by 2030.
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Affiliation(s)
- Maria Bousali
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - George Papatheodoridis
- Department of Gastroenterology, “Laiko” General Hospital of Athens, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Dimitrios Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece
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22
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Hatano Y, Ideta T, Hirata A, Hatano K, Tomita H, Okada H, Shimizu M, Tanaka T, Hara A. Virus-Driven Carcinogenesis. Cancers (Basel) 2021; 13:2625. [PMID: 34071792 PMCID: PMC8198641 DOI: 10.3390/cancers13112625] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer arises from the accumulation of genetic and epigenetic alterations. Even in the era of precision oncology, carcinogens contributing to neoplastic process are still an important focus of research. Comprehensive genomic analyses have revealed various combinations of base substitutions, referred to as the mutational signatures, in cancer. Each mutational signature is believed to arise from specific DNA damage and repair processes, including carcinogens. However, as a type of carcinogen, tumor viruses increase the cancer risk by alternative mechanisms, including insertional mutagenesis, viral oncogenes, and immunosuppression. In this review, we summarize virus-driven carcinogenesis to provide a framework for the control of malignant cell proliferation. We first provide a brief overview of oncogenic viruses and describe their implication in virus-related tumors. Next, we describe tumor viruses (HPV, Human papilloma virus; HBV, Hepatitis B virus; HCV, Hepatitis C virus; EBV, Epstein-Barr virus; Kaposi sarcoma herpesvirus; MCV, Merkel cell polyoma virus; HTLV-1, Human T-cell lymphotropic virus, type-1) and tumor virus-related cancers. Lastly, we introduce emerging tumor virus candidates, human cytomegalovirus (CMV), human herpesvirus-6 (HHV-6) and adeno-associated virus-2 (AAV-2). We expect this review to be a hub in a complex network of data for virus-associated carcinogenesis.
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Affiliation(s)
- Yuichiro Hatano
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
| | - Takayasu Ideta
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (T.I.); (M.S.)
- Department of Laboratory Medicine, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan
| | - Akihiro Hirata
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1194, Japan;
| | - Kayoko Hatano
- Department of Obstetrics and Gynecology, Gifu University Hospital, Gifu 501-1194, Japan;
| | - Hiroyuki Tomita
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
| | - Hideshi Okada
- Department of Emergency and Disaster Medicine, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan;
| | - Masahito Shimizu
- Department of Gastroenterology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (T.I.); (M.S.)
| | - Takuji Tanaka
- Department of Diagnostic Pathology (DDP) and Research Center of Diagnostic Pathology (RC-DiP), Gifu Municipal Hospital, Gifu 500-8513, Japan;
| | - Akira Hara
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu 501-1194, Japan; (H.T.); (A.H.)
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23
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Soheili M, Keyvani H, Soheili M, Nasseri S. Human papilloma virus: A review study of epidemiology, carcinogenesis, diagnostic methods, and treatment of all HPV-related cancers. Med J Islam Repub Iran 2021; 35:65. [PMID: 34277502 PMCID: PMC8278030 DOI: 10.47176/mjiri.35.65] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Human papillomavirus (HPV) infection is considered as the most common viral sexually transmitted infection worldwide. This poses an increasingly interdisciplinary medical challenge. Since there is vast scattered information in databases about HPV and the correlated diseases, we decided to collect useful data so that the experts can get a more comprehensive view of HPV. Methods: In this article, HPV-associated diseases, prevalence, prevention, and new treatments are discussed. The retrieved articles reporting the latest data about the required information for our review were selected through searching in Web of Science, Scopus, Medline (PubMed), EMBASE, Cochrane Library, Ovid, and CINHAL with language limitations of English and German. Results: There are 2 groups of HPVs: (1) low-risk HPV types that can lead to genital warts, and (2) high-risk HPV types that are involved in HPV-associated oncogenesis. About 70% of all sexually active women are infected and most of these infections heal within many weeks or months. In the case of HPV-persistence, a risk of preneoplasia or carcinoma exists. These types of viruses are responsible for the existence of genitoanal, gastrointestinal, urinary tract, and head and neck tumors. There is still no definite successful treatment. The detection of HPV-related condylomata occurs macroscopically in women and men, and the diagnosis of the precursors of cervical carcinoma in women is possible by Pap smear. Conclusion: For extragenital manifestations, there is no structured early detection program. Meanwhile, studies on HPV vaccines confirm that they should be used for the primary prevention of HPV-dependent diseases. However, we need more research to find out the real advantages and disadvantages of vaccines.
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Affiliation(s)
- Maryam Soheili
- School of Kinesiology and Health Science, York University, Toronto, Canada
| | - Hossein Keyvani
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Gastrointestinal and Liver Disease Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Marzieh Soheili
- Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Human Revivification Society of Congress 60, Tehran, Iran
| | - Sherko Nasseri
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
- Department of Molecular Medicine and Medical Genetics, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
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24
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Cameron DL, Jacobs N, Roepman P, Priestley P, Cuppen E, Papenfuss AT. VIRUSBreakend: Viral Integration Recognition Using Single Breakends. Bioinformatics 2021; 37:3115-3119. [PMID: 33973999 PMCID: PMC8504616 DOI: 10.1093/bioinformatics/btab343] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/25/2021] [Accepted: 05/03/2021] [Indexed: 12/17/2022] Open
Abstract
Motivation Integration of viruses into infected host cell DNA can cause DNA damage and disrupt genes. Recent cost reductions and growth of whole genome sequencing has produced a wealth of data in which viral presence and integration detection is possible. While key research and clinically relevant insights can be uncovered, existing software has not achieved widespread adoption, limited in part due to high computational costs, the inability to detect a wide range of viruses, as well as precision and sensitivity. Results Here, we describe VIRUSBreakend, a high-speed tool that identifies viral DNA presence and genomic integration. It utilizes single breakends, breakpoints in which only one side can be unambiguously placed, in a novel virus-centric variant calling and assembly approach to identify viral integrations with high sensitivity and a near-zero false discovery rate. VIRUSBreakend detects viral integrations anywhere in the host genome including regions such as centromeres and telomeres unable to be called by existing tools. Applying VIRUSBreakend to a large metastatic cancer cohort, we demonstrate that it can reliably detect clinically relevant viral presence and integration including HPV, HBV, MCPyV, EBV and HHV-8. Availability and implementation VIRUSBreakend is part of the Genomic Rearrangement IDentification Software Suite (GRIDSS). It is available under a GPLv3 license from https://github.com/PapenfussLab/VIRUSBreakend. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel L Cameron
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Australia.,Hartwig Medical Foundation Australia, Sydney, Australia
| | - Nina Jacobs
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, The Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Australia.,Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Australia
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25
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Egan KM, Kim Y, Bender N, Hodge JM, Coghill AE, Smith-Warner SA, Rollison DE, Teras LR, Grimsrud TK, Waterboer T. Prospective investigation of polyomavirus infection and the risk of adult glioma. Sci Rep 2021; 11:9642. [PMID: 33953301 PMCID: PMC8100283 DOI: 10.1038/s41598-021-89133-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/16/2021] [Indexed: 12/23/2022] Open
Abstract
Glioma is an aggressive primary tumor of the brain with a poorly understood etiology. We studied the association of 4 human polyomaviruses (HPyV)—JC virus (JCV), BK virus (BKV), human polyomavirus 6 (HPyV6), and Merkel cell polyomavirus (MCPyV) with glioma risk within the Cancer Prevention Study II in the US (CPS-II) and the Janus Serum Bank in Norway. Cohort participants subsequently diagnosed with glioma from the CPS-II (n = 37) and Janus Serum Bank (n = 323), a median of 6.9 and 15.4 years after blood collection, respectively, were matched to individual controls on age, sex, and date of blood draw. Serum antibodies to the major viral capsid protein (VP1) were used to establish infection history for each polyomavirus. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using conditional logistic regression. In the Janus Serum Bank, MCPyV infection was associated with a higher risk of glioma overall (OR: 1.56; 95% CI 1.10, 2.19). A modest, nonsignificant positive association with MCPyV infection was also observed in CPS-II (OR: 1.29; 95% CI 0.54, 3.08). In both cohorts, glioma risk was not significantly related to infection with JCV, BKV or HPyV6. The present study suggests that MCPyV infection may increase glioma risk.
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Affiliation(s)
- Kathleen M Egan
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Youngchul Kim
- Department of Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Noemi Bender
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), 69120, Heidelberg, Germany
| | - James M Hodge
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Anna E Coghill
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Stephanie A Smith-Warner
- Departments of Nutrition and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Dana E Rollison
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Tom K Grimsrud
- Department of Research, Cancer Registry of Norway, 0379, Oslo, Norway
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), 69120, Heidelberg, Germany
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26
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Borchmann S. An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer. MICROBIOME 2021; 9:94. [PMID: 33888160 PMCID: PMC8063312 DOI: 10.1186/s40168-021-01039-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/18/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Host tissue infections by bacteria and viruses can cause cancer. Known viral carcinogenic mechanisms are disruption of the host genome via genomic integration and expression of oncogenic viral proteins. An important bacterial carcinogenic mechanism is chronic inflammation. Massively parallel sequencing now routinely generates datasets large enough to contain detectable traces of bacterial and viral nucleic acids of taxa that colonize the examined tissue or are integrated into the host genome. However, this hidden resource has not been comprehensively studied in large patient cohorts. METHODS In the present study, 3025 whole genome sequencing datasets and, where available, corresponding RNA-seq datasets are leveraged to gain insight into novel links between viruses, bacteria, and cancer. Datasets were obtained from multiple International Cancer Genome Consortium studies, with additional controls added from the 1000 genome project. A customized pipeline based on KRAKEN was developed and validated to identify bacterial and viral sequences in the datasets. Raw results were stringently filtered to reduce false positives and remove likely contaminants. RESULTS The resulting map confirms known links and expands current knowledge by identifying novel associations. Moreover, the detection of certain bacteria or viruses is associated with profound differences in patient and tumor phenotypes, such as patient age, tumor stage, survival, and somatic mutations in cancer genes or gene expression profiles. CONCLUSIONS Overall, these results provide a detailed, unprecedented map of links between viruses, bacteria, and cancer that can serve as a reference for future studies and further experimental validation. Video Abstract.
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Affiliation(s)
- Sven Borchmann
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, University of Cologne, Cologne, Germany.
- Cancer Center Cologne Essen - Partner Site Cologne, CIO Cologne, University of Cologne, Cologne, Germany.
- German Hodgkin Study Group, Cologne, Germany.
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27
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Pathogenic Role of Immune Evasion and Integration of Human Papillomavirus in Oropharyngeal Cancer. Microorganisms 2021; 9:microorganisms9050891. [PMID: 33919460 PMCID: PMC8143538 DOI: 10.3390/microorganisms9050891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023] Open
Abstract
The incidence of oropharyngeal cancer (OPC) is increasing remarkably among all head and neck cancers, mainly due to its association with the human papillomavirus (HPV). Most HPVs are eliminated by the host’s immune system; however, because HPV has developed an effective immune evasion mechanism to complete its replication cycle, a small number of HPVs are not eliminated, leading to persistent infection. Moreover, during the oncogenic process, the extrachromosomal HPV genome often becomes integrated into the host genome. Integration involves the induction and high expression of E6 and E7, leading to cell cycle activation and increased genomic instability in the host. Therefore, integration is an important event in oncogenesis, although the associated mechanism remains unclear, especially in HPV-OPC. In this review, we summarize the current knowledge on HPV-mediated carcinogenesis, with special emphasis on immune evasion and integration mechanisms, which are crucial for oncogenesis.
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28
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Li YJ, Wu HH, Chen CH, Wang HH, Chiang YJ, Hsu HH, Pang ST, Wang RYL, Tian YC. High Incidence and Early Onset of Urinary Tract Cancers in Patients with BK Polyomavirus Associated Nephropathy. Viruses 2021; 13:v13030476. [PMID: 33799453 PMCID: PMC8001968 DOI: 10.3390/v13030476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
Over-immunosuppressed kidney transplant recipients are susceptible to malignancies and BK polyomavirus (BKPyV)-associated nephropathy (BKPyVAN). This study aimed to verify the association between BKPyV infection and urinary tract cancers (UTC). A total of 244 kidney transplant recipients were enrolled at Chang Gung Memorial Hospital from June 2000 to February 2020. Biopsy-proven BKPyVAN patients (n = 17) had worse kidney function (eGFR: 26 ± 13.7 vs. 47.8 ± 31.0 mL/min/1.73 m2). The 5-year allograft survival rates for patients with and without BKPyVAN were 67% and 93%, respectively (p = 0.0002), while the 10-year patient survival was not different between the two groups. BKPyVAN patients had a significantly higher incidence of UTC compared to the non-BKPyVAN group (29.4% vs. 6.6%). Kaplan-Meier analysis showed that the UTC-free survival rate was significantly lower in BKPyVAN patients, and the onset of UTC was significantly shorter in BKPyVAN patients (53.4 vs. 108.9 months). The multivariate logistic regression analysis demonstrated that age (RR = 1.062) and BKVAN (RR = 6.459) were the most significant risk factors for the development of UTC. Our study demonstrates that BKPyVAN patients have greater allograft losses, higher incidence, a lower cancer-free survival rate, and an earlier onset with a higher relative risk of developing UTC compared to non-BKPyVAN patients.
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Affiliation(s)
- Yi-Jung Li
- Kidney Research Center and Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (Y.-J.L.); (H.-H.W.); (H.-H.H.)
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
| | - Hsin-Hsu Wu
- Kidney Research Center and Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (Y.-J.L.); (H.-H.W.); (H.-H.H.)
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
| | - Cheng-Hsu Chen
- Division of Nephrology, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 407, Taiwan;
| | - Hsu-Han Wang
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
- Department of Urology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
| | - Yang-Jen Chiang
- Department of Urology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
| | - Hsiang-Hao Hsu
- Kidney Research Center and Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (Y.-J.L.); (H.-H.W.); (H.-H.H.)
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
| | - See-Tong Pang
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
- Department of Urology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan;
| | - Robert Y. L. Wang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Ya-Chung Tian
- Kidney Research Center and Department of Nephrology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan; (Y.-J.L.); (H.-H.W.); (H.-H.H.)
- Department of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-H.W.); (S.-T.P.)
- Correspondence: ; Tel.: +886-328-1200 (ext. 8181); Fax: +886-328-2173
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29
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The Association of Human Herpesviruses with Malignant Brain Tumor Pathology and Therapy: Two Sides of a Coin. Int J Mol Sci 2021; 22:ijms22052250. [PMID: 33668202 PMCID: PMC7956256 DOI: 10.3390/ijms22052250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/13/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
The role of certain viruses in malignant brain tumor development remains controversial. Experimental data demonstrate that human herpesviruses (HHVs), particularly cytomegalovirus (CMV), Epstein–Barr virus (EBV) and human herpes virus 6 (HHV-6), are implicated in brain tumor pathology, although their direct role has not yet been proven. CMV is present in most gliomas and medulloblastomas and is known to facilitate oncomodulation and/or immunomodulation, thus promoting cancer cell proliferation, invasion, apoptosis, angiogenesis, and immunosuppression. EBV and HHV-6 have also been detected in brain tumors and high-grade gliomas, showing high rates of expression and an inflammatory potential. On the other hand, due to the neurotropic nature of HHVs, novel studies have highlighted the engagement of such viruses in the development of new immunotherapeutic approaches in the context of oncolytic viral treatment and vaccine-based strategies against brain tumors. This review provides a comprehensive evaluation of recent scientific data concerning the emerging dual role of HHVs in malignant brain pathology, either as potential causative agents or as immunotherapeutic tools in the fight against these devastating diseases.
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30
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Karimzadeh M, Tabibzadeh A, Moghoofei M, Abbasi S, Sadri Nahand J, Sadeghii F, Karbalaie Niya MH, Keyvani H, Bokharaei-Salim F, Esghaei M, Esghaei M. As Evidence-Based Tumorigenic Role of Epstein-Barr Virus miR-BART1-3p in Neurological Tumors. Asian Pac J Cancer Prev 2021; 22:257-266. [PMID: 33507707 PMCID: PMC8184183 DOI: 10.31557/apjcp.2021.22.1.257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Central nervous system tumors are a diverse group of tumors that account for 2% of all adult cancers and 17% of childhood malignancies. Several internal and external risk factors are involved in the development of this cancer such as viral infections. The aim of this study was to the determination of the EBV infection frequency and the expression level of miR-122 and miR-BART in CNS tumors samples. METHODS One hundred and thirty-eight fresh tissue sample (106 case and 32 control) was collected from CNS specimens. The presence of Epstein-Barr virus (EBV) DNA was examined by PCR assay and the expression level of miR-122 and miR-BART were evaluated by using real-time PCR assay in CNS tissue samples. RESULTS EBV DNA was detected in 17% (18 of 106) of tumors tissue samples and 6.4% (2 of 32) of control samples. according to results, there was a significant relationship between the presence of EBV-DNA with CNS tumors. Additionally, the expression level of miR-122 was significantly downregulated in the EBV-positive sample compared to that of the EBV-negative sample. Also, the level of EBV-BART1-3p expression was significantly higher in EBV-positive tumors samples than EBV-positive normal samples. CONCLUSION The results of this study suggest that the EBV could change the condition of cancer cells by altering the expression of miR-122 and EBV-BART1-3p and maybe contribute to the development of cancer cells. However, the role of viral infections in CNS cancer requires further studies. <br />.
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Affiliation(s)
- Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabibzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeedeh Abbasi
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farzin Sadeghii
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Hossin Keyvani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Laboratory of National Center, Vice Chancellor for Health, Iran University of Medical Sciences, Tehran, Iran
| | - Moein Esghaei
- Cognitive Neuroscience Laboratory, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany
| | - Maryam Esghaei
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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31
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Bartlett PC, Ruggiero VJ, Hutchinson HC, Droscha CJ, Norby B, Sporer KRB, Taxis TM. Current Developments in the Epidemiology and Control of Enzootic Bovine Leukosis as Caused by Bovine Leukemia Virus. Pathogens 2020; 9:E1058. [PMID: 33352855 PMCID: PMC7766781 DOI: 10.3390/pathogens9121058] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 01/29/2023] Open
Abstract
Enzootic Bovine Leukosis (EBL) caused by the bovine leukemia virus (BLV) has been eradicated in over 20 countries. In contrast, the U.S. and many other nations are experiencing increasing prevalence in the absence of efforts to control transmission. Recent studies have shown that BLV infection in dairy cattle has a greater impact beyond the long-recognized lymphoma development that occurs in <5% of infected cattle. Like other retroviruses, BLV appears to cause multiple immune system disruptions, affecting both cellular and humoral immunity, which are likely responsible for increasingly documented associations with decreased dairy production and decreased productive lifespan. Realization of these economic losses has increased interest in controlling BLV using technology that was unavailable decades ago, when many nations eradicated BLV via traditional antibody testing and slaughter methods. This traditional control is not economically feasible for many nations where the average herd antibody prevalence is rapidly approaching 50%. The ELISA screening of cattle with follow-up testing via qPCR for proviral load helps prioritize the most infectious cattle for segregation or culling. The efficacy of this approach has been demonstrated in at least four herds. Breeding cattle for resistance to BLV disease progression also appears to hold promise, and several laboratories are working on BLV vaccines. There are many research priorities for a wide variety of disciplines, especially including the need to investigate the reports linking BLV and human breast cancer.
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Affiliation(s)
- Paul C. Bartlett
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (V.J.R.); (B.N.)
| | - Vickie J. Ruggiero
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (V.J.R.); (B.N.)
| | | | - Casey J. Droscha
- CentralStar Cooperative, East Lansing, MI 48910, USA; (C.J.D.); (K.R.B.S.)
| | - Bo Norby
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA; (V.J.R.); (B.N.)
| | - Kelly R. B. Sporer
- CentralStar Cooperative, East Lansing, MI 48910, USA; (C.J.D.); (K.R.B.S.)
| | - Tasia M. Taxis
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA;
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Massimino L, Lovisa S, Antonio Lamparelli L, Danese S, Ungaro F. Gut eukaryotic virome in colorectal carcinogenesis: Is that a trigger? Comput Struct Biotechnol J 2020; 19:16-28. [PMID: 33363706 PMCID: PMC7750180 DOI: 10.1016/j.csbj.2020.11.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is composed of bacteria and viruses that might be associated with colorectal cancer (CRC) onset and progression. Indeed, although viral infections have been reported to be the primary trigger in many diseases, the role of eukaryotic viruses populating the gut mucosa during early colorectal carcinogenesis is underinvestigated. Human eukaryotic viruses in the gut were found to induce alterations of the immune homeostasis so that some viral-dependent mechanisms likely able to induce DNA alterations in the bowel wall have been proposed, although no demonstration is available yet. However, thanks to the latest advancements in computational biology and the implementation of the bioinformatic pipelines, the option of establishing a direct causative link between intestinal virome and CRC will be possible soon, hopefully paving the way to innovative therapeutic strategies blocking or reverting the CRC pathogenesis.
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Affiliation(s)
- Luca Massimino
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
| | - Sara Lovisa
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | | | - Silvio Danese
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Federica Ungaro
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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Yuan Z, Ye X, Zhu L, Zhang N, An Z, Zheng WJ. Virome assembly and annotation in brain tissue based on next-generation sequencing. Cancer Med 2020; 9:6776-6790. [PMID: 32738030 PMCID: PMC7520322 DOI: 10.1002/cam4.3325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/20/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022] Open
Abstract
The glioblastoma multiforme (GBM) is one of the deadliest tumors. It has been speculated that virus plays a role in GBM but the evidences are controversy. Published researches are mainly limited to studies on the presence of human cytomegalovirus (HCMV) in GBM. No comprehensive assessment of the brain virome, the collection of viral material in the brain, based on recently sequenced data has been performed. Here, we characterized the virome from 111 GBM samples and 57 normal brain samples from eight projects in the SRA database by a tested and comprehensive assembly approach. The annotation of the assembled contigs showed that most viral sequences in the brain belong to the viral family Retroviridae. In some GBM samples, we also detected full genome sequence of a novel picornavirus recently discovered in invertebrates. Unlike previous reports, our study did not detect herpes virus such as HCMV in GBM from the data we used. However, some contigs that cannot be annotated with any known genes exhibited antibody epitopes in their sequences. These findings provide several avenues for potential cancer therapy: the newly discovered picornavirus could be a starting point to engineer novel oncolytic virus; and the exhibited antibody epitopes could be a source to explore potential drug targets for immune cancer therapy. By characterizing the virosphere in GBM and normal brain at a global level, the results from this study strengthen the link between GBM and viral infection which warrants the further investigation.
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Affiliation(s)
- Zihao Yuan
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Xiaohua Ye
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Lisha Zhu
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Ningyan Zhang
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - Zhiqiang An
- Texas Therapeutics InstituteInstitute of Molecular MedicineMcGovern Medical SchoolUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - W. Jim Zheng
- School of Biomedical InformaticsUniversity of Texas Health Science Center at HoustonHoustonTXUSA
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in der Stroth L, Tharehalli U, Günes C, Lechel A. Telomeres and Telomerase in the Development of Liver Cancer. Cancers (Basel) 2020; 12:E2048. [PMID: 32722302 PMCID: PMC7464754 DOI: 10.3390/cancers12082048] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is one of the most common cancer types worldwide and the fourth leading cause of cancer-related death. Liver carcinoma is distinguished by a high heterogeneity in pathogenesis, histopathology and biological behavior. Dysregulated signaling pathways and various gene mutations are frequent in hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which represent the two most common types of liver tumors. Both tumor types are characterized by telomere shortening and reactivation of telomerase during carcinogenesis. Continuous cell proliferation, e.g., by oncogenic mutations, can cause extensive telomere shortening in the absence of sufficient telomerase activity, leading to dysfunctional telomeres and genome instability by breakage-fusion-bridge cycles, which induce senescence or apoptosis as a tumor suppressor mechanism. Telomerase reactivation is required to stabilize telomere functionality and for tumor cell survival, representing a genetic risk factor for the development of liver cirrhosis and liver carcinoma. Therefore, telomeres and telomerase could be useful targets in hepatocarcinogenesis. Here, we review similarities and differences between HCC and iCCA in telomere biology.
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Affiliation(s)
- Lena in der Stroth
- Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany; (L.i.d.S.); (U.T.)
| | - Umesh Tharehalli
- Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany; (L.i.d.S.); (U.T.)
| | - Cagatay Günes
- Department of Urology, University Hospital Ulm, 89081 Ulm, Germany;
| | - André Lechel
- Department of Internal Medicine I, University Hospital Ulm, 89081 Ulm, Germany; (L.i.d.S.); (U.T.)
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35
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Cao C, Hong P, Huang X, Lin D, Cao G, Wang L, Feng B, Wu P, Shen H, Xu Q, Ren C, Meng Y, Zhi W, Yu R, Wei J, Ding W, Tian X, Zhang Q, Li W, Gao Q, Chen G, Li K, Sung WK, Hu Z, Wang H, Li G, Wu P. HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. J Genet Genomics 2020; 47:437-450. [PMID: 33023834 DOI: 10.1016/j.jgg.2020.05.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
Integration of human papillomavirus (HPV) DNA into the human genome is a reputed key driver of cervical cancer. However, the effects of HPV integration on chromatin structural organization and gene expression are largely unknown. We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19. We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome, RNA, chromatin immunoprecipitation and high-throughput chromosome conformation capture (Hi-C) sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis. Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities, with correlation found between three-dimensional (3D) structural change and gene expression. Importantly, HPV integration divided one topologically associated domain (TAD) into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106, with a decrease in PEG3 expression and an increase in CCDC106 expression. This expression dysregulation was further confirmed using 10 samples from our cohort, which exhibited the same HPV-CCDC106 integration. In summary, we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling. Thus, this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.
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Affiliation(s)
- Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ping Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xingyu Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Da Lin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; Bio-Medical Center, Huazhong Agricultural University, Wuhan, 430070, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liming Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bei Feng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ping Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hui Shen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ci Ren
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yifan Meng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenhua Zhi
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ruidi Yu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Juncheng Wei
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Key Laboratory for Molecular Diagnosis of Hubei Province, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430010, China
| | - Wei Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qinglei Gao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Chen
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Kezhen Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China; Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Zheng Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Department of Gynecological Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui Wang
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China; Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Peng Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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36
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Identification of Specific Tumor Markers in Vulvar Carcinoma Through Extensive Human Papillomavirus DNA Characterization Using Next Generation Sequencing Method. J Low Genit Tract Dis 2020; 24:53-60. [PMID: 31860576 DOI: 10.1097/lgt.0000000000000498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES A subset of vulvar carcinomas (VC) are associated with human papillomavirus (HPV) DNA. This trait can be used to identify tumor markers for patient's follow-up. A large diversity of HPV prevalence in VC has been reported, but no data are available concerning the insertional HPV status in this tumor type. Therefore, we have used an innovative next generation sequencing (NGS)-based CaptHPV method able to provide an extensive characterization of HPV DNA in tumors. MATERIAL AND METHODS Tumor tissue specimens from 55 patients with VC were analyzed using p16 immunohistochemistry, in situ hybridization, polymerase chain reaction, and CaptHPV-NGS assays. RESULTS Our analyses showed that 8 (14.5%) of 55 cases were associated with HPV 16 DNA. No other HPV genotypes were identified. The HPV genome was in a free episomal state only in one case and both episomal and integrated into the tumor cell genome in 7. There was a single insertion in 5 cases and multiple sites, scattered at different chromosomal loci in two. ISH data suggest that some of these might reflect tumor heterogeneity. Viral integration targeted cellular genes among which were TP63, CCDC148, LOC100133091, PKP1, and POLA2. Viral integration at the PKP1 locus was associated with partial gene deletion, and no PKP1 protein was detected in tumor tissue. CONCLUSIONS Using the NGS-based innovative capture-HPV approach, we established a cartography of HPV 16 DNA in 8 VC cases and identified novel genes targeted by integration that may be used as specific tumor markers. In addition, we established a rationale strategy for optimal characterization of HPV status in VC.
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37
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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38
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Foy JP, Bertolus C, Boutolleau D, Agut H, Gessain A, Herceg Z, Saintigny P. Arguments to Support a Viral Origin of Oral Squamous Cell Carcinoma in Non-Smoker and Non-Drinker Patients. Front Oncol 2020; 10:822. [PMID: 32528893 PMCID: PMC7253757 DOI: 10.3389/fonc.2020.00822] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 04/28/2020] [Indexed: 12/18/2022] Open
Abstract
In some western countries, an increasing incidence of oral squamous cell carcinoma (OSCC) has been observed in non-smoker non-drinker patients (NSND), mostly in women with HPV-negative OSCC. In the context of the unknown etiology and mechanisms of tumorigenesis of OSCC in NSND, we discuss data supporting the hypothesis of a viral origin not related to HPV. OSCC from NSND are characterized by an antiviral DNA methylation and gene expression signature. Based on the similar increasing incidence of oral tongue SCC (OTSCC) and oropharyngeal SCC (OPSCC) in young women and men respectively, we hypothesize that changes in sexual behaviors may lead to an increasing incidence of herpesvirus in the oral cavity, especially HSV-2, similarly to what has already been described in HPV-positive OPSCC. Because viral genome integration has not been detected in OSCC from NSND, a "hit and run" viral mechanism involving epigenome deregulation could therefore play a key role at early steps of oral carcinogenesis in this population of patients. In conclusion, epidemiological, clinical and molecular data supports a "hit and run" viral origin of OSCC from NSND.
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Affiliation(s)
- Jean-Philippe Foy
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
- Sorbonne Université, AP-HP, Groupe Hospitalier Pitié-Salpêtrière Charles Foix, Department of Oral and Maxillo-Facial Surgery, Paris, France
| | - Chloé Bertolus
- Sorbonne Université, AP-HP, Groupe Hospitalier Pitié-Salpêtrière Charles Foix, Department of Oral and Maxillo-Facial Surgery, Paris, France
| | - David Boutolleau
- Sorbonne Université, AP-HP, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Centre National de Référence Herpèsvirus, Department of Virology, Paris, France
- Sorbonne Université, CR7, Centre d'Immunologie et de Maladies Infectieuses (CIMI-Paris), INSERM U1135, Paris, France
| | - Henri Agut
- Sorbonne Université, AP-HP, Groupe Hospitalier Pitié-Salpêtrière-Charles Foix, Centre National de Référence Herpèsvirus, Department of Virology, Paris, France
- Sorbonne Université, CR7, Centre d'Immunologie et de Maladies Infectieuses (CIMI-Paris), INSERM U1135, Paris, France
| | - Antoine Gessain
- Department of Virology, Institut Pasteur, CNRS, UMR 3569, Paris, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
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39
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Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J 2020; 18:631-641. [PMID: 32257046 PMCID: PMC7109368 DOI: 10.1016/j.csbj.2020.03.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/26/2022] Open
Abstract
Identification of microbial composition directly from tumor tissue permits studying the relationship between microbial changes and cancer pathogenesis. We interrogated bacterial presence in tumor and adjacent normal tissue strictly in pairs utilizing human whole exome sequencing to generate microbial profiles. Profiles were generated for 813 cases from stomach, liver, colon, rectal, lung, head & neck, cervical and bladder TCGA cohorts. Core microbiota examination revealed twelve taxa to be common across the nine cancer types at all classification levels. Paired analyses demonstrated significant differences in bacterial shifts between tumor and adjacent normal tissue across stomach, colon, lung squamous cell, and head & neck cohorts, whereas little or no differences were evident in liver, rectal, lung adenocarcinoma, cervical and bladder cancer cohorts in adjusted models. Helicobacter pylori in stomach and Bacteroides vulgatus in colon were found to be significantly higher in adjacent normal compared to tumor tissue after false discovery rate correction. Computational results were validated with tissue from an independent population by species-specific qPCR showing similar patterns of co-occurrence among Fusobacterium nucleatum and Selenomonas sputigena in gastric samples. This study demonstrates the ability to identify bacteria differential composition derived from human tissue whole exome sequences. Taken together our results suggest the microbial profiles shift with advanced disease and that the microbial composition of the adjacent tissue can be indicative of cancer stage disease progression.
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Key Words
- BLCA, bladder carcinoma
- CESC, cervical & endocervical squamous cell carcinomas
- COAD, colon adenocarcinoma
- COREAD, colon and rectal adenocarcinoma TCGA cohorts
- Cancer microbiome
- Exome sequencing
- HNSC, head & neck squamous cell carcinoma
- L2FC, log 2 fold change
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Microbial landscape
- READ, rectal adenocarcinoma
- STAD, stomach adenocarcinoma
- TCGA
- TCGA, The Cancer Genome Atlas
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Affiliation(s)
- Rebecca M. Rodriguez
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Brenda Y. Hernandez
- Epidemiology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Mark Menor
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
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40
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Trabert B, Waterboer T, Idahl A, Brenner N, Brinton LA, Butt J, Coburn SB, Hartge P, Hufnagel K, Inturrisi F, Lissowska J, Mentzer A, Peplonska B, Sherman ME, Wills GS, Woodhall SC, Pawlita M, Wentzensen N. Antibodies Against Chlamydia trachomatis and Ovarian Cancer Risk in Two Independent Populations. J Natl Cancer Inst 2020; 111:129-136. [PMID: 29790947 DOI: 10.1093/jnci/djy084] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/20/2018] [Accepted: 04/03/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Pelvic inflammatory disease (PID) has been associated with ovarian cancer risk. To clarify the role of Chlamydia trachomatis and other infectious agents in the development of ovarian cancer, we evaluated the association of serologic markers with incident ovarian cancer using a staged approach in two independent populations. METHODS Studies included: 1) a case-control study in Poland (244 ovarian cancers/556 control subjects) and 2) a prospective nested case-control study in the PLCO Cancer Screening Trial (160 ovarian cancers/159 control subjects). Associations of serologic marker levels with ovarian cancer risk at diagnostic as well as higher thresholds, identified in Poland and independently evaluated in PLCO, were estimated using multivariable adjusted logistic regression. RESULTS In the Polish study, antibodies (based on laboratory cut-point) against the chlamydia plasmid-encoded Pgp3 protein (serological gold standard) were associated with increased ovarian cancer risk (adjusted odds ratio [OR] = 1.63, 95% confidence interval [CI] = 1.20 to 2.22); when a positive result was redefined at higher levels, ovarian cancer risk was increased (cut-point 2: OR = 2.00, 95% CI = 1.38 to 2.89; cut-point 3 [max OR]: OR = 2.19, 95% CI = 1.29 to 3.73). In the prospective PLCO study, Pgp3 antibodies were associated with elevated risk at the laboratory cut-point (OR = 1.43, 95% CI = 0.78 to 2.63) and more stringent cut-points (cut-point 2: OR = 2.25, 95% CI = 1.07 to 4.71); cut-point 3: OR = 2.53, 95% CI = 0.63 to 10.08). In both studies, antibodies against other infectious agents measured were not associated with risk. CONCLUSIONS In two independent populations, antibodies against prior/current C. trachomatis (Pgp3) were associated with a doubling in ovarian cancer risk, whereas markers of other infectious agents were unrelated. These findings lend support for an association between PID and ovarian cancer.
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Affiliation(s)
- Britton Trabert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annika Idahl
- Department of Clinical Science, Obstetrics and Gynecology, Umeå University, Umeå, Sweden
| | - Nicole Brenner
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Louise A Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Julia Butt
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sally B Coburn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Katrin Hufnagel
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Federica Inturrisi
- Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jolanta Lissowska
- Department of Epidemiology and Cancer Prevention, Cancer Center and M. Sklodowska-Curie Institute of Oncology, Warsaw, Poland
| | | | - Beata Peplonska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Mark E Sherman
- Department of Pulmonary Medicine, Mayo Clinic, Jacksonville, FL
| | - Gillian S Wills
- Jefferiss Research Trust Laboratories, Imperial College London, St Mary's Campus, London, UK
| | - Sarah C Woodhall
- National Infection Service, Public Health England, London, UK.,Research Department of Infection and Population Health, UCL, London, UK.,Gloucestershire Hospitals NHS Foundation Trust, Cheltenham, UK
| | - Michael Pawlita
- Molecular Diagnostics of Oncogenic Infections Division, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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41
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Sadato D, Ogawa M, Hirama C, Hishima T, Horiguchi S, Harada Y, Shimoyama T, Itokawa M, Ohashi K, Oboki K. Potential prognostic impact of EBV RNA-seq reads in gastric cancer: a reanalysis of The Cancer Genome Atlas cohort. FEBS Open Bio 2020; 10:455-467. [PMID: 31991047 PMCID: PMC7050242 DOI: 10.1002/2211-5463.12803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 01/18/2023] Open
Abstract
Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC), whose prognosis remains controversial, is diagnosed by in situ hybridization of EBV-derived EBER1/2 small RNAs. In The Cancer Genome Atlas (TCGA) Stomach Adenocarcinoma (STAD) project, the EBV molecular subtype was determined through a combination of multiple next-generation sequencing methods, but not by the gold standard in situ hybridization method. This leaves unanswered questions regarding the discordance of EBV positivity detected by different approaches and the threshold of sequencing reads. Therefore, we reanalyzed the TCGA-STAD RNA sequencing (RNA-seq) dataset including 375 tumor and 32 normal samples, using our analysis pipeline. We defined a reliable threshold for EBV-derived next-generation sequencing reads by mapping them to the EBV genome with three different random arbitrary alignments. We analyzed the prognostic impact of EBV status on the histopathological subtypes of gastric cancer. EBV-positive cases identified by reanalysis comprised nearly half of the cases (49.6%) independent from infiltrating lymphocyte signatures, and showed significantly longer overall survival for adenocarcinomas of the 'not-otherwise-specified' type [P = 0.016 (log-rank test); hazard ratios (HR): 0.476; 95% CI: 0.260-0.870, P = 0.016 (Cox univariate analysis)], but shorter overall survival for the tubular adenocarcinoma type [P = 0.005 (log-rank test); HR: 3.329; 95% CI: 1.406-7.885, P = 0.006 (Cox univariate analysis)]. These results demonstrate that the EBV positivity rates were higher when determined by RNA-seq than when determined by EBER1/2 in situ hybridization. The RNA-seq-based EBV positivity demonstrated distinct results for gastric cancer prognosis depending on the histopathological subtype, suggesting its potential to be used in clinical prognoses.
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Affiliation(s)
- Daichi Sadato
- Division of HematologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
- Center for Medical Research CooperationTokyo Metropolitan Institute of Medical ScienceSetagaya‐kuJapan
- Divisions of Clinical Research SupportTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo-kuJapan
| | - Mina Ogawa
- Center for Medical Research CooperationTokyo Metropolitan Institute of Medical ScienceSetagaya‐kuJapan
- Divisions of Clinical Research SupportTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo-kuJapan
- Department of Medical OncologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
| | - Chizuko Hirama
- Division of HematologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
- Center for Medical Research CooperationTokyo Metropolitan Institute of Medical ScienceSetagaya‐kuJapan
- Divisions of Clinical Research SupportTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo-kuJapan
| | - Tsunekazu Hishima
- Department of PathologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
| | - Shin‐Ichiro Horiguchi
- Department of PathologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
| | - Yuka Harada
- Divisions of Clinical Research SupportTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo-kuJapan
| | - Tatsu Shimoyama
- Department of Medical OncologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
| | - Masanari Itokawa
- Center for Medical Research CooperationTokyo Metropolitan Institute of Medical ScienceSetagaya‐kuJapan
| | - Kazuteru Ohashi
- Division of HematologyTokyo Metropolitan Cancer and Infectious Diseases Center Komagome HospitalBunkyo‐kuJapan
| | - Keisuke Oboki
- Center for Medical Research CooperationTokyo Metropolitan Institute of Medical ScienceSetagaya‐kuJapan
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42
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Pathak S, Wilczyński JR, Paradowska E. Factors in Oncogenesis: Viral Infections in Ovarian Cancer. Cancers (Basel) 2020; 12:E561. [PMID: 32121320 PMCID: PMC7139377 DOI: 10.3390/cancers12030561] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/16/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancer (OC) is one of the leading causes of cancer death in women, with high-grade serous ovarian cancer (HGSOC) being the most lethal gynecologic malignancy among women. This high fatality rate is the result of diagnosis of a high number of new cases when cancer implants have already spread. The poor prognosis is due to our inadequate understanding of the molecular mechanisms preceding ovarian malignancy. Knowledge about the site of origination has been improved recently by the discovery of tube intraepithelial cancer (TIC), but the potential risk factors are still obscure. Due to high tumoral heterogeneity in OC, the establishment of early stage biomarkers is still underway. Microbial infection may induce or result in chronic inflammatory infection and in the pathogenesis of cancers. Microbiome research has shed light on the relationships between the host and microbiota, as well as the direct roles of host pathogens in cancer development, progression, and drug efficacy. While controversial, the detection of viruses within ovarian malignancies and fallopian tube tissues suggests that these pathogens may play a role in the development of OC. Genomic and proteomic approaches have enhanced the methods for identifying candidates in early screening. This article summarizes the existing knowledge related to the molecular mechanisms that lead to tumorigenesis in the ovary, as well as the viruses detected in OC cases and how they may elevate this process.
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Affiliation(s)
- Sudipta Pathak
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 93-232 Lodz, Poland;
| | - Jacek R. Wilczyński
- Department of Surgical and Oncological Gynecology, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 93-232 Lodz, Poland;
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43
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Reina J, Reina N. Cáncer de mama y virus, sí pero no. CLINICA E INVESTIGACION EN GINECOLOGIA Y OBSTETRICIA 2020. [DOI: 10.1016/j.gine.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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44
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Qiu Q, Li Y, Fan Z, Yao F, Shen W, Sun J, Yuan Y, Chen J, Cai L, Xie Y, Liu K, Chen X, Jiao X. Gene Expression Analysis of Human Papillomavirus-Associated Colorectal Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5201587. [PMID: 32258125 PMCID: PMC7103040 DOI: 10.1155/2020/5201587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 02/05/2023]
Abstract
PURPOSE Human papillomavirus (HPV) antigens had been found in colorectal cancer (CRC) tissue, but little evidence demonstrates the association of HPV with oncogene mutations in CRC. We aim to elucidate the mutated genes that link HPV infection and CRC carcinogenesis. METHODS Cancerous and adjacent noncancerous tissues were obtained from CRC patients. HPV antigen was measured by using the immunohistochemical (IHC) technique. The differentially expressed genes (DEGs) in HPV-positive and HPV-negative tumor tissues were measured by using TaqMan Array Plates. The target genes were validated with the qPCR method. RESULTS 15 (31.9%) cases of CRC patients were observed to be HPV positive, in which HPV antigen was expressed in most tumor tissues rather than in adjacent noncancerous tissues. With TaqMan Array Plates analyses, we found that 39 differentially expressed genes (DEGs) were upregulated, while 17 DEGs were downregulated in HPV-positive CRC tissues compared with HPV-negative tissues. Four DEGs (MMP-7, MYC, WNT-5A, and AXIN2) were upregulated in tumor vs. normal tissues, or adenoma vs. normal tissue in TCGA, which was overlapped with our data. In the confirmation test, MMP-7, MYC, WNT-5A, and AXIN2 were upregulated in cancerous tissue compared with adjacent noncancerous tissue. MYC, WNT-5A, and AXIN2 were shown to be upregulated in HPV-positive CRC tissues when compared to HPV-negative tissues. CONCLUSION HPV-encoding genome may integrate into the tumor genomes that involved in multiple signaling pathways. Further genomic and proteomic investigation is necessary for obtaining a more comprehensive knowledge of signaling pathways associated with the CRC carcinogenesis.
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Affiliation(s)
- Qiancheng Qiu
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yazhen Li
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
- Jiangmen Central Hosptial (Affiliated Jiangmen Hospital of Sun Yat-Sen University), Guangdong 529000, China
| | - Zhiqiang Fan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wenjun Shen
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jinghong Chen
- Center for Disease Control and Prevention of Shantou, Guangdong 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yanxuan Xie
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Kaixi Liu
- Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Xiang Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
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45
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Ramqvist T, Ortiz-Villalon C, Brandén E, Koyi H, de Petris L, Wagenius G, Brodin O, Reuterswärd C, Dalianis T, Jönsson M, Staaf J, Lewensohn R, Planck M. Analysis of human papillomaviruses and human polyomaviruses in lung cancer from Swedish never-smokers. Acta Oncol 2020; 59:28-32. [PMID: 31460811 DOI: 10.1080/0284186x.2019.1657588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Torbjörn Ramqvist
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Christian Ortiz-Villalon
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Eva Brandén
- Centre for Research and Development, Uppsala University, Gävle, Sweden
| | - Hirsh Koyi
- Centre for Research and Development, Uppsala University, Gävle, Sweden
| | - Luigi de Petris
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Gunnar Wagenius
- National Lung Cancer Registry, Regional Cancer Centre Uppsala Örebro, Uppsala University Hospital, Uppsala, Sweden
| | - Ola Brodin
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Christel Reuterswärd
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Tina Dalianis
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Mats Jönsson
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
| | - Rolf Lewensohn
- Department of Oncology-Pathology, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Maria Planck
- Department of Clinical Sciences Lund, Division of Oncology, Lund University, Lund, Sweden
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46
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Paradowska E, Jabłońska A, Studzińska M, Wilczyński M, Wilczyński JR. Detection and genotyping of CMV and HPV in tumors and fallopian tubes from epithelial ovarian cancer patients. Sci Rep 2019; 9:19935. [PMID: 31882737 PMCID: PMC6934444 DOI: 10.1038/s41598-019-56448-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/11/2019] [Indexed: 01/02/2023] Open
Abstract
Viral and bacterial infections are detected in epithelial ovarian cancer (EOC) tissues. Since the fallopian tubes are often affected by pelvic inflammatory disease (PID) and the majority of serous EOCs appear to originate from dysplastic lesions in the distal tube, it is relevant to consider the potential role that infectious agents may play in ovarian carcinogenesis. We sought to analyze the prevalence of human papillomavirus (HPV) and cytomegalovirus (CMV) in EOC tissue and fallopian tube specimens obtained at tumor resection. Ovarian cancer and fallopian tube tissue samples obtained from patients with EOC were analyzed by both qualitative and quantitative PCR to detect and quantify viral DNA. The presence of CMV and HPV DNA was detected in 70% and 74% cancerous ovarian tissues, respectively, and was significantly higher in EOC than in benign tumor cases (P ≤ 0.01). CMV or HPV infection was observed also in the fallopian tube samples. Infection with HPV16 was determined in 70% of EOC cases. Almost two thirds of EOC patients demonstrated coinfection with CMV and HPV in the pathological samples. The results revealed that the presence of CMV and HPV in EOC samples is common. CMV and HPV infections can be potential risks for EOC development.
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Affiliation(s)
- Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland.
| | - Agnieszka Jabłońska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Mirosława Studzińska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, Lodz, Poland
| | - Miłosz Wilczyński
- Department of Surgical, Endoscopic and Oncological Gynecology, Polish Mother's Health Center Research Institute, Lodz, Poland
| | - Jacek R Wilczyński
- Department of Surgical and Oncological Gynecology, Medical University of Lodz, Lodz, Poland
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Limam S, Missaoui N, Mestiri S, Yacoubi M, Krifa H, Selmi B, Mokni M. Epstein-Barr virus infection in gliomas. Curr Res Transl Med 2019; 67:129-133. [DOI: 10.1016/j.retram.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/07/2019] [Accepted: 06/30/2019] [Indexed: 12/23/2022]
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48
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Chakravorty S, Yan B, Wang C, Wang L, Quaid JT, Lin CF, Briggs SD, Majumder J, Canaria DA, Chauss D, Chopra G, Olson MR, Zhao B, Afzali B, Kazemian M. Integrated Pan-Cancer Map of EBV-Associated Neoplasms Reveals Functional Host-Virus Interactions. Cancer Res 2019; 79:6010-6023. [PMID: 31481499 DOI: 10.1158/0008-5472.can-19-0615] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/24/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]
Abstract
Epstein-Barr virus (EBV) is a complex oncogenic symbiont. The molecular mechanisms governing EBV carcinogenesis remain elusive and the functional interactions between virus and host cells are incompletely defined. Here we present a comprehensive map of the host cell-pathogen interactome in EBV-associated cancers. We systematically analyzed RNA sequencing from >1,000 patients with 15 different cancer types, comparing virus and host factors of EBV+ to EBV- tissues. EBV preferentially integrated at highly accessible regions of the cancer genome, with significant enrichment in super-enhancer architecture. Twelve EBV transcripts, including LMP1 and LMP2, correlated inversely with EBV reactivation signature. Overexpression of these genes significantly suppressed viral reactivation, consistent with a "virostatic" function. In cancer samples, hundreds of novel frequent missense and nonsense variations in virostatic genes were identified, and variant genes failed to regulate their viral and cellular targets in cancer. For example, one-third of patients with EBV+ NK/T-cell lymphoma carried two novel nonsense variants (Q322X, G342X) of LMP1 and both variant proteins failed to restrict viral reactivation, confirming loss of virostatic function. Host cell transcriptional changes in response to EBV infection classified tumors into two molecular subtypes based on patterns of IFN signature genes and immune checkpoint markers, such as PD-L1 and IDO1. Overall, these findings uncover novel points of interaction between a common oncovirus and the human genome and identify novel regulatory nodes and druggable targets for individualized EBV and cancer-specific therapies. SIGNIFICANCE: This study provides a comprehensive map of the host cell-pathogen interactome in EBV+ malignancies.See related commentary by Mbulaiteye and Prokunina-Olsson, p. 5917.
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Affiliation(s)
| | - Bingyu Yan
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Chong Wang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Luopin Wang
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | | | - Chin Fang Lin
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana
| | - Scott D Briggs
- Department of Biochemistry, Purdue University, West Lafayette, Indiana
| | - Joydeb Majumder
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - D Alejandro Canaria
- Department of Biological Science, Purdue University, West Lafayette, Indiana
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Gaurav Chopra
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Matthew R Olson
- Department of Biological Science, Purdue University, West Lafayette, Indiana
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, Indiana. .,Department of Computer Science, Purdue University, West Lafayette, Indiana
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Del Valle L, Piña-Oviedo S. Human Polyomavirus JCPyV and Its Role in Progressive Multifocal Leukoencephalopathy and Oncogenesis. Front Oncol 2019; 9:711. [PMID: 31440465 PMCID: PMC6694743 DOI: 10.3389/fonc.2019.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
The human neurotropic virus JCPyV, a member of the Polyomaviridiae family, is the opportunistic infectious agent of Progressive Multifocal Leukoencephalopathy (PML), a fatal disease seen in severe immunosuppressive conditions and, during the last decade, in patients undergoing immunotherapy. JCPyV is a ubiquitous pathogen with up to 85% of the adult population word-wide exhibiting antibodies against it. Early experiments demonstrated that direct inoculation of JCPyV into the brain of different species resulted in the development of brain tumors and other neuroectodermal-derived neoplasias. Later, several reports showed the detection of viral sequences in medulloblastomas and glial tumors, as well as expression of the viral protein T-Antigen. Few oncogenic viruses, however, have caused so much controversy regarding their role in the pathogenesis of brain tumors, but the discovery of new Polyomaviruses that cause Merkel cell carcinomas in humans and brain tumors in racoons, in addition to the role of JCPyV in colon cancer and multiple mechanistic studies have shed much needed light on the role of JCPyV in cancer. The pathways affected by the viral protein T-Antigen include cell cycle regulators, like p53 and pRb, and transcription factors that activate pro-proliferative genes, like c-Myc. In addition, infection with JCPyV causes chromosomal damage and T-Antigen inhibits homologous recombination, and activates anti-apoptotic proteins, such as Survivin. Here we review the different aspects of the biology and physiopathology of JCPyV.
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Affiliation(s)
- Luis Del Valle
- Department of Pathology and Stanley S. Scott Cancer Center, Louisiana State University Health, New Orleans, LA, United States
| | - Sergio Piña-Oviedo
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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Stern J, Miller G, Li X, Saxena D. Virome and bacteriome: two sides of the same coin. Curr Opin Virol 2019; 37:37-43. [PMID: 31177014 PMCID: PMC6768692 DOI: 10.1016/j.coviro.2019.05.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022]
Abstract
Although bacterial dysbiosis has been previously associated with carcinogenesis and HIV infection, the impact of the virome and these disease states has been less well studied. In this review, we will summarize what is known about the interplay between both the bacterial and the viral components of the microbiome on cancer and HIV pathogenesis. Bacterial dysbiosis has been associated with carcinogenesis such as colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer, breast cancer, and gastric cancer. The dysbiotic pathogenesis may be species-based or community-based and can have varying mechanisms of carcinogenesis. The human virome was also associated with certain cancers. Viruses, such as cytomegalovirus (CMV), Human herpesvirus 8 (HHV-8), human papilloma virus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV), and Epstein-Barr virus (EBV), all had associations with cancers. It was also reported that an altered bacteriophage community may lead to carcinogenesis by allowing opportunistic, oncogenic bacteria to proliferate in a gastrointestinal biofilm. This mechanism shows the importance of analyzing the bacteriome and the virome concurrently as their interactions can provide insight into new mechanisms in the pathogenesis of not only cancer, but other diseases as well. The enteric bacteriome was shown to be distinctly altered in immunocompromised HIV-infected individuals, and highly active antiretroviral therapy (HAART) was shown to at least partially reverse the alterations that HIV causes in the bacteriome. Studies have shown that the progression to HIV is associated with changes in the plasma concentration of commensal viruses. HIV also acts synergistically with multiple other viruses, such as HPV, EBV, varicella zoster virus (VZV), and HHV-8. Although it has been shown that HIV infection leads to enteric virome expansion in humans, most of the research on HIV's effect on the virome was conducted in non-human primates, and there is a lack of research on the effect of HAART on the virome. Virome-wide analysis is necessary for identifying novel viral etiologies. There is currently a wealth of information on the bacteriome and its associations with cancer and HIV, but more research should be conducted on the virome's associations and reaction to HAART as well as the bacteriome-virome interactions that may play a major role in pathogenesis and recovery.
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Affiliation(s)
- Jonathan Stern
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, United States
| | - George Miller
- S. Arthur Localio Laboratory, Departments of Surgery, New York University, School of Medicine, New York, NY 10016, United States
| | - Xin Li
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, United States
| | - Deepak Saxena
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, United States; S. Arthur Localio Laboratory, Departments of Surgery, New York University, School of Medicine, New York, NY 10016, United States.
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