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Persistent Nonviral Plasmid Vector in Nasal Tissues Causes False-Positive SARS-CoV-2 Diagnostic Nucleic Acid Tests. Microbiol Spectr 2022; 10:e0169522. [PMID: 36226962 PMCID: PMC9769617 DOI: 10.1128/spectrum.01695-22] [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] [Indexed: 01/05/2023] Open
Abstract
Biomedical personnel can become contaminated with nonhazardous reagents used in the laboratory. We describe molecular studies performed on nasal secretions collected longitudinally from asymptomatic laboratory coworkers to determine if they were infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) circulating in the community or with SARS-CoV-2 DNA from a plasmid vector. Participants enrolled in a prospective study of incident SARS-CoV-2 infection had nasal swabs collected aseptically by study staff at enrollment, followed by weekly self-collection of anterior nasal swabs. SARS-CoV-2 diagnosis was performed by a real-time PCR test targeting the nucleocapsid gene. PCR tests targeting SARS-CoV-2 nonstructural protein 10 (nsp10), nsp14, and envelope and three regions of the plasmid vector were performed to differentiate amplification of SARS-CoV-2 RNA from the plasmid vector's DNA. Nasal swabs from four asymptomatic coworkers with positive real-time PCR results for the SARS-CoV-2 nucleocapsid targets were negative when tested for SARS-CoV-2 nsp10, nsp14, and envelope protein. However, nucleic acids extracted from these nasal swabs amplified DNA regions of the plasmid vector used by the coworkers, including the ampicillin and neomycin/kanamycin resistance genes, the promoter-nucleocapsid junction, and unique codon-optimized regions. Nasal swabs from these individuals tested positive repeatedly, including during isolation. Longitudinal detection of plasmid DNA with SARS-CoV-2 nucleocapsid in nasal swabs suggests persistence in nasal tissues or colonizing bacteria. Nonviral plasmid vectors, while regarded as safe laboratory reagents, can interfere with molecular diagnostic tests. These reagents should be handled using proper personal protective equipment to prevent contamination of samples or laboratory personnel. IMPORTANCE Asymptomatic laboratory workers who tested positive for SARS-CoV-2 for days to months were found to harbor a laboratory plasmid vector containing SARS-CoV-2 DNA, which they had worked with in the past, in their nasal secretions. While prior studies have documented contamination of research personnel with PCR amplicons, our observation is novel, as these individuals shed the laboratory plasmid over days to months, including during isolation in their homes. This suggests that the plasmid was in their nasal tissues or that bacteria containing the plasmid had colonized their noses. While plasmids are generally safe, our detection of plasmid DNA in the nasal secretions of laboratory workers for weeks after they had stopped working with the plasmid shows the potential for these reagents to interfere with clinical tests and emphasizes that occupational exposures in the preceding months should be considered when interpreting diagnostic clinical tests.
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2
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Munawar MA. Smart PCR machines can reduce the risk of carryover contamination. Biotechniques 2022; 72:77-80. [PMID: 35293794 DOI: 10.2144/btn-2021-0064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Mustafa Ahmad Munawar
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
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3
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Abstract
Bats are infamous reservoirs of deadly human viruses. While retroviruses, such as the human immunodeficiency virus (HIV), are among the most significant of virus families that have jumped from animals into humans, whether bat retroviruses have the potential to infect and cause disease in humans remains unknown. Recent reports of retroviruses circulating in bat populations builds on two decades of research describing the fossil records of retroviral sequences in bat genomes and of viral metagenomes extracted from bat samples. The impact of the global COVID-19 pandemic demands that we pay closer attention to viruses hosted by bats and their potential as a zoonotic threat. Here we review current knowledge of bat retroviruses and explore the question of whether they represent a threat to humans.
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Affiliation(s)
- Joshua A. Hayward
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Gilda Tachedjian
- Health Security Program, Life Sciences Discipline, Burnet Institute, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
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4
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Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ. KRAS-retroviral fusion transcripts and gene amplification in arsenic-transformed, human prostate CAsE-PE cancer cells. Toxicol Appl Pharmacol 2020; 397:115017. [PMID: 32344290 PMCID: PMC7606314 DOI: 10.1016/j.taap.2020.115017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/03/2023]
Abstract
CAsE-PE cells are an arsenic-transformed, human prostate epithelial line containing oncogenic mutations in KRAS compared to immortalized, normal KRAS parent cells, RWPE-1. We previously reported increased copy number of mutated KRAS in CAsE-PE cells, suggesting gene amplification. Here, KRAS flanking genomic and transcriptomic regions were sequenced in CAsE-PE cells for insight into KRAS amplification. Comparison of DNA-Seq and RNA-Seq showed increased reads from background aligning to all KRAS exons in CAsE-PE cells, while a uniform DNA-Seq read distribution occurred in RWPE-1 cells with normal transcript expression. We searched for KRAS fusions in DNA and RNA sequencing data finding a portion of reads aligning to KRAS and viral sequence. After generation of cDNA from total RNA, short and long KRAS probes were generated to hybridize cDNA and KRAS enriched fragments were PacBio sequenced. More KRAS reads were captured from CAsE-PE cDNA versus RWPE-1 by each probe set. Only CAsE-PE cDNA showed KRAS viral fusion transcripts, primarily mapping to LTR and endogenous retrovirus sequences on either 5'- or 3'-ends of KRAS. Most KRAS viral fusion transcripts contained 4 to 6 exons but some PacBio sequences were in unusual orientations, suggesting viral insertions within the gene body. Additionally, conditioned media was extracted for potential retroviral particles. RNA-Seq of culture media isolates identified KRAS retroviral fusion transcripts in CAsE-PE media only. Truncated KRAS transcripts suggested multiple retroviral integration sites occurred within the KRAS gene producing KRAS retroviral fusions of various lengths. Findings suggest activation of endogenous retroviruses in arsenic carcinogenesis should be explored.
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Affiliation(s)
- B Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States.
| | - Dhiral P Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States
| | - Meredith A Bostrom
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Ruchir R Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States
| | - Garron M Wright
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Xinguo Wang
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Oksana Gordon
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Katherine E Pelch
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Scott S Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Richard S Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Michael J DeVito
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Michael P Waalkes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Erik J Tokar
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
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5
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Abstract
Retroviruses infect a broad range of vertebrate hosts that includes amphibians, reptiles, fish, birds and mammals. In addition, a typical vertebrate genome contains thousands of loci composed of ancient retroviral sequences known as endogenous retroviruses (ERVs). ERVs are molecular remnants of ancient retroviruses and proof that the ongoing relationship between retroviruses and their vertebrate hosts began hundreds of millions of years ago. The long-term impact of retroviruses on vertebrate evolution is twofold: first, as with other viruses, retroviruses act as agents of selection, driving the evolution of host genes that block viral infection or that mitigate pathogenesis, and second, through the phenomenon of endogenization, retroviruses contribute an abundance of genetic novelty to host genomes, including unique protein-coding genes and cis-acting regulatory elements. This Review describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus-host interactions on evolutionary timescales. It also describes some of the many examples of cellular functions, including protein-coding genes and regulatory elements, that have evolved from ERVs.
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6
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Ottina E, Levy P, Eksmond U, Merkenschlager J, Young GR, Roels J, Stoye JP, Tüting T, Calado DP, Kassiotis G. Restoration of Endogenous Retrovirus Infectivity Impacts Mouse Cancer Models. Cancer Immunol Res 2018; 6:1292-1300. [PMID: 30143537 PMCID: PMC6485373 DOI: 10.1158/2326-6066.cir-18-0038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022]
Abstract
Mouse models have been instrumental in establishing fundamental principles of cancer initiation and progression and continue to be invaluable in the discovery and further development of cancer therapies. Nevertheless, important aspects of human disease are imperfectly approximated in mouse models, notably the involvement of endogenous retroviruses (ERVs). Replication-defective ERVs, present in both humans and mice, may affect tumor development and antitumor immunity through mechanisms not involving infection. Here, we revealed an adverse effect of murine ERVs with restored infectivity on the behavior of mouse cancer models. In contrast to human cancer, where infectious ERVs have never been detected, we found that ERV infectivity was frequently restored in transplantable, as well as genetic, mouse cancer models. Such replication-competent, ERV-derived retroviruses were responsible for unusually high expression of retroviral nucleic acids and proteins in mouse cancers. Infectious ERV-derived retroviruses produced by mouse cancer cells could directly infect tumor-infiltrating host immune cells and fundamentally modified the host's immune defenses to cancer, as well as the outcome of immunotherapy. Therefore, infectious retroviruses, variably arising in mouse cancer models, but not in human cancer, have the potential to confound many immunologic studies and should be considered as a variable, if not altogether avoided. Cancer Immunol Res; 6(11); 1292-300. ©2018 AACR.
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MESH Headings
- Animals
- Cell Line, Tumor
- Endogenous Retroviruses/pathogenicity
- Female
- Leukemia Virus, Murine/genetics
- Leukemia Virus, Murine/pathogenicity
- Lymphocytes, Tumor-Infiltrating/pathology
- Male
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Mice, Transgenic
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/pathology
- Neoplasms, Experimental/virology
- Positive Regulatory Domain I-Binding Factor 1/genetics
- Proto-Oncogene Proteins B-raf/genetics
- Retroviridae Infections/virology
- Viral Tropism/physiology
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Affiliation(s)
- Eleonora Ottina
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Prisca Levy
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Urszula Eksmond
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | | | - George R Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, UK
| | - Juliette Roels
- Retroviral Immunology, The Francis Crick Institute, London, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions, The Francis Crick Institute, London, UK
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas Tüting
- Laboratory of Experimental Dermatology, Department of Dermatology, University of Magdeburg, Magdeburg, Germany
| | - Dinis P Calado
- Immunity and Cancer Laboratory, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK.
- Department of Medicine, Faculty of Medicine, Imperial College London, London, UK
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7
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Keshavarz M, Karbalaie Niya MH, Tameshkel FS, Mozaffari Nejad AS, Monavari SH, Keyvani H. A Survey on Human T-cell Lymphotropic Virus Type 1 (HTLV-1) and Xenotropic Murine Leukemia Virus-Related Virus (XMRV) Coinfection in Tehran, Iran. J Pharm Bioallied Sci 2018; 10:166-171. [PMID: 30237687 PMCID: PMC6142885 DOI: 10.4103/jpbs.jpbs_25_18] [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] [Indexed: 11/26/2022] Open
Abstract
Background: Xenotropic murine leukemia virus-related virus (XMRV) is a gamma retrovirus, which has been detected in patients with prostate cancer, chronic fatigue syndrome, and general population with a number of acquired infections such as infection with human T-cell lymphotropic virus (HTLV) and human immunodeficiency virus (HIV). The aim of this study was to determine the HTLV-1 and XMRV coinfection for the first time in Iranian patients who were admitted to the Tehran hospitals. Materials and Methods: Two hundred and ninety one patients suspected with HTLV-1 were referred to the hospitals affiliated to the Iran University of Medical Sciences, Tehran, Iran from April 2012 to October 2016. Genomic deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) from peripheral blood mononuclear cells/cerebrospinal fluids was extracted by High Pure Viral Nucleic Acid Kit (Roche, Germany). After complementary DNA synthesis, conventional reverse transcriptase polymerase chain reaction was used for the detection of HTLV-1 or XMRV-infected patients. Statistical Package for Social Sciences (SPSS) software, version 16 (SPSS, Chicago, IL, USA) was used for statistical analyses. Results: Of the 291 patients suspected of HTLV infection, 123 (42.3%) were male with a mean age of 38±15 years. HTLV-1 RNA was found in 93 (31.9%) specimens comprising 40 men (41.3%) and 53 women (56.9%). Of the 93 patients who were HTLV-1 positive, one sample (1%) was positive for XMRV env gene. Conclusion: These findings suggest that the lack of significant detection of XMRV in patients who were HTLV-1 positive could not be associated with complications of HTLV-1. Although this is a preliminary report from Iranian patients with HTLV-1, further studies are needed to show the actual prevalence of XMRV infection by geographical distribution and various populations.
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Affiliation(s)
- Mohsen Keshavarz
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fahimeh Safarnezhad Tameshkel
- Gastrointestinal and Liver Disease Research Center (GILDRC), Iran University of Medical Sciences, Tehran, Iran.,Student Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Sasan Mozaffari Nejad
- Molecular Research Center, Student Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Hossein Keyvani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Gastrointestinal and Liver Disease Research Center (GILDRC), Iran University of Medical Sciences, Tehran, Iran
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8
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Weng J, Li Y, Cai L, Li T, Peng G, Fu C, Han X, Li H, Jiang Z, Zhang Z, Du J, Peng Q, Gao Y. Elimination of Mycoplasma Contamination from Infected Human Hepatocyte C3A Cells by Intraperitoneal Injection in BALB/c Mice. Front Cell Infect Microbiol 2017; 7:440. [PMID: 29075618 PMCID: PMC5643414 DOI: 10.3389/fcimb.2017.00440] [Citation(s) in RCA: 7] [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: 03/26/2017] [Accepted: 09/26/2017] [Indexed: 02/05/2023] Open
Abstract
Background/Aims: The use of antibiotics to eliminate Mycoplasma contamination has some serious limitations. Mycoplasma contamination can be eliminated by intraperitoneal injection of BALB/c mice with contaminated cells combined with screening monoclonal cells. However, in vivo passage in mice after injection with contaminated cells requires a long duration (20-54 days). Furthermore, it is important to monitor for cross-contamination of mouse and human cells, xenotropic murine leukemia virus-related virus (XMRV) infection, and altered cell function after the in vivo treatment. The present study aimed to validate a reliable and simplified method to eliminate mycoplasma contamination from human hepatocytes. BALB/c mice were injected with paraffin oil prior to injection with cells, in order to shorten duration of intraperitoneal passage. Cross-contamination of mouse and human cells, XMRV infection and cell function-related genes and proteins were also evaluated. Methods: PCR and DNA sequencing were used to confirm Mycoplasma hyorhinis (M. hyorhinis) contamination in human hepatocyte C3A cells. Five BALB/c mice were intraperitoneally injected with 0.5 ml paraffin oil 1 week before injection of the cells. The mice were then intraperitoneally injected with C3A hepatocytes (5.0 × 106/ml) contaminated with M. hyorhinis (6.2 ± 2.2 × 108 CFU/ml). Ascites were collected for monoclonal cell screening on the 14th day after injection of contaminated cells. Elimination of mycoplasma from cells was determined by PCR and Transmission Electron Microscopy (TEM). Human-mouse cell and XMRV contamination were also detected by PCR. Quantitative reverse transcription PCR and western blotting were used to compare the expression of genes and proteins among treated cells, non-treated infected cells, and uninfected cells. Results: Fourteen days after injection with cells, 4 of the 5 mice had ascites. Hepatocyte colonies extracted from the ascites of four mice were all mycoplasma-free. There was no cell cross-contamination or XMRV infection in treated cell cultures. Elimination of Mycoplasma resulted in partial or complete recovery in the expression of ALB, TF, and CYP3A4 genes as well as proteins. Proliferation of the treated cells was not significantly affected by this management. Conclusion: The method of elimination of Mycoplasma contamination in this study was validated and reproducible. Success was achieved in four of five cases examined. Compared to the previous studies, the duration of intraperitoneal passage in this study was significantly shorter.
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Affiliation(s)
- Jun Weng
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Yang Li
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Lei Cai
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Ting Li
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Gongze Peng
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Chaoyi Fu
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Xu Han
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Haiyan Li
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Zesheng Jiang
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Zhi Zhang
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
| | - Jiang Du
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qing Peng
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Artificial Organs and Tissue Engineering Centre of Guangdong Province, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
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9
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Baig FA, Mirza T, Hamid A, Syed S, Jamal Q. Ductal variant of prostate adenocarcinoma harbor Xenotropic murine leukemia virus related virus (XMRV) infection: a novel finding in subtype of prostate cancer. Turk J Urol 2017; 43:268-272. [PMID: 28861296 DOI: 10.5152/tud.2017.85451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 02/21/2017] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Xenotropic murine leukemia virus related virus (XMRV), is the first gammaretrovirus identified a decade ago, in human tissue bearing adenocarcinoma of prostate, followed by several researches documenting little or no prevalence of XMRV in prostate cancer samples. However, the status of XMRV within subtype of prostate adenocarcinoma has not been investigated yet. In this study, we investigated the relationship between XMRV and broad spectrum morphological entities of prostate adenocarcinoma, including acinar, ductal and other rare subtypes. MATERIAL AND METHODS The prevalence of XMRV DNA in different histological subtypes of prostate adenocarcinoma was examined after characterizing the tumors into groups, using formalin-fixed, paraffin-embedded tissue samples from newly diagnosed prostate adenocarcinomas and archival prostate cancer tissue from our XMRV case control analysis. Broad-spectrum XMRV DNA amplification was performed by end-point polymerase chain reaction, using commercially available primer set. RESULTS The study included 100 patients with prostate cancer. XMRV DNA was detected in 4 of 8 (50%) ductal adenocarcinomas, exhibiting papillary and cribriform histological features. XMRV DNA was not detected in any other variant of adenocarcinoma including acinar (0/91) and mucinous carcinomas (0/1). Majority of XMRV positive cases were biologically aggressive and present cancer at an early age upon diagnosis. CONCLUSION Ductal adenocarcinomas demonstrate a significant association of XMRV DNA while other histological variants of prostate adenocarcinoma seem unrelated to XMRV infection.
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Affiliation(s)
- Faraz Ahmed Baig
- Department of Pathology, College of Medicine, Ziauddin University, Karachi, Pakistan
| | - Talat Mirza
- Department of Pathology, Dow International Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Amna Hamid
- Department of Nephrology, Kidney Center - Postgraduate Training Institute, Karachi, Pakistan
| | - Serajuddaula Syed
- Department of Pathology, College of Medicine, Ziauddin University, Karachi, Pakistan
| | - Qamar Jamal
- Department of Pathology, College of Medicine, Ziauddin University, Karachi, Pakistan
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10
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Panelli S, Lorusso L, Balestrieri A, Lupo G, Capelli E. XMRV and Public Health: The Retroviral Genome Is Not a Suitable Template for Diagnostic PCR, and Its Association with Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Appears Unreliable. Front Public Health 2017; 5:108. [PMID: 28589117 PMCID: PMC5439170 DOI: 10.3389/fpubh.2017.00108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 05/02/2017] [Indexed: 11/13/2022] Open
Abstract
A few years ago, a highly significant association between the xenotropic murine leukemia virus-related virus (XMRV) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), a complex debilitating disease of poorly understood etiology and no definite treatment, was reported in Science, raising concern for public welfare. Successively, the failure to reproduce these findings, and the suspect that the diagnostic PCR was vitiated by laboratory contaminations, led to the retraction of the paper. Notwithstanding, XMRV continued to be the subject of researches and public debates. Occasional positivity in humans was also detected recently, even if the data always appeared elusive and non-reproducible. In this study, we discuss the current status of this controversial association and propose that a major role in the unreliability of the results was played by the XMRV genomic composition in itself. In this regard, we present bioinformatic analyses that show: (i) aspecific, spurious annealings of the available primers in multiple homologous sites of the human genome; (ii) strict homologies between whole XMRV genome and interspersed repetitive elements widespread in mammalian genomes. To further detail this scenario, we screen several human and mammalian samples by using both published and newly designed primers. The experimental data confirm that available primers are far from being selective and specific. In conclusion, the occurrence of highly conserved, repeated DNA sequences in the XMRV genome deeply undermines the reliability of diagnostic PCRs by leading to artifactual and spurious amplifications. Together with all the other evidences, this makes the association between the XMRV retrovirus and CFS totally unreliable.
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Affiliation(s)
- Simona Panelli
- Department of Earth and Environmental Sciences, Section of Animal Biology, University of Pavia, Pavia, Italy.,Centre for Health Technologies (C.H.T.), University of Pavia, Pavia, Italy
| | - Lorenzo Lorusso
- Neurology Unit, A.S.S.T. Franciacorta, Chiari (Brescia), Italy
| | | | - Giuseppe Lupo
- Department of Earth and Environmental Sciences, Section of Animal Biology, University of Pavia, Pavia, Italy.,Centre for Health Technologies (C.H.T.), University of Pavia, Pavia, Italy
| | - Enrica Capelli
- Department of Earth and Environmental Sciences, Section of Animal Biology, University of Pavia, Pavia, Italy.,Centre for Health Technologies (C.H.T.), University of Pavia, Pavia, Italy
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11
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Moreira ASD, Raabis SM, Graham ME, Dreyfus JM, Sibley SD, Godhardt-Cooper JA, Toohey-Kurth KL, Goldberg TL, Peek SF. Identification by next-generation sequencing of Aichivirus B in a calf with enterocolitis and neurologic signs. J Vet Diagn Invest 2017; 29:208-211. [PMID: 28176615 DOI: 10.1177/1040638716685597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 11-d-old Holstein bull calf was presented to the Veterinary Medical Teaching Hospital at the University of Wisconsin-Madison because of a 4-d history of diarrhea and persistent low-grade fever. Initial diagnosis was enteritis caused by Cryptosporidium and rotavirus. During hospitalization, the calf became stuporous and was only responsive to noxious stimuli, with hypotonia of all 4 limbs, tail, head, and neck. A cerebrospinal fluid analysis revealed xanthochromia, with marked lymphocytic pleocytosis, which was suggestive of viral meningitis and/or encephalitis. Aichivirus B, which belongs to the Kobuvirus genus, was tentatively identified in spinal fluid by next-generation DNA sequencing. This virus can affect a multitude of species, including humans and cattle, and has been isolated from both healthy and diarrheic individuals. However, to date, a possible connection with neurologic disease has not been described, to our knowledge.
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Affiliation(s)
- Ana S D Moreira
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Sarah M Raabis
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Melissa E Graham
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer M Dreyfus
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Samuel D Sibley
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Jennifer A Godhardt-Cooper
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Kathy L Toohey-Kurth
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Tony L Goldberg
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
| | - Simon F Peek
- Departments of Medical Sciences (Moreira, Raabis, Peek), University of Wisconsin-Madison, Madison, WI.,Pathobiological Sciences (Graham, Dreyfus, Sibley, Toohey-Kurth, Goldberg), University of Wisconsin-Madison, Madison, WI.,Wisconsin Veterinary Diagnostic Laboratory (Toohey-Kurth), University of Wisconsin-Madison, Madison, WI
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12
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Dudley JP, Golovkina TV, Ross SR. Lessons Learned from Mouse Mammary Tumor Virus in Animal Models. ILAR J 2017; 57:12-23. [PMID: 27034391 DOI: 10.1093/ilar/ilv044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mouse mammary tumor virus (MMTV), which was discovered as a milk-transmitted, infectious, cancer-inducing agent in the 1930s, has been used as an animal model for the study of retroviral infection and transmission, antiviral immune responses, and breast cancer and lymphoma biology. The main target cells for MMTV infection in vivo are cells of the immune system and mammary epithelial cells. Although the host mounts an immune response to the virus, MMTV has evolved multiple means of evading this response. MMTV causes mammary tumors when the provirus integrates into the mammary epithelial and lymphoid cell genome during viral replication and thereby activates cellular oncogene expression. Thus, tumor induction is a by-product of the infection cycle. A number of important oncogenes have been discovered by carrying out MMTV integration site analysis, some of which may play a role in human breast cancer.
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Affiliation(s)
- Jaquelin P Dudley
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
| | - Tatyana V Golovkina
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
| | - Susan R Ross
- Jaquelin P. Dudley, PhD, is a professor in the Department of Molecular Biosciences, Center for Infectious Disease and Institute for Cellular and Molecular Biology at the University of Texas at Austin. Tatyana V. Golovkina, PhD, is a professor in the Department of Microbiology at the University of Chicago in Chicago, Illinois. Susan R. Ross, PhD, is a professor in the Department of Microbiology in the Perelman School of Medicine of the University of Pennsylvania in Philadelphia, Pennsylvania
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13
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A contaminant-free assessment of Endogenous Retroviral RNA in human plasma. Sci Rep 2016; 6:33598. [PMID: 27640347 PMCID: PMC5027517 DOI: 10.1038/srep33598] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/30/2016] [Indexed: 12/21/2022] Open
Abstract
Endogenous retroviruses (ERVs) comprise 6–8% of the human genome. HERVs are silenced in most normal tissues, up-regulated in stem cells and in placenta but also in cancer and HIV-1 infection. Crucially, there are conflicting reports on detecting HERV RNA in non-cellular clinical samples such as plasma that suggest the study of HERV RNA can be daunting. Indeed, we find that the use of real-time PCR in a quality assured clinical laboratory setting can be sensitive to low-level proviral contamination. We developed a mathematical model for low-level contamination that allowed us to design a laboratory protocol and standard operating procedures for robust measurement of HERV RNA. We focus on one family, HERV-K HML-2 (HK2) that has been most recently active even though they invaded our ancestral genomes almost 30 millions ago. We extensively validated our experimental design on a model cell culture system showing high sensitivity and specificity, totally eliminating the proviral contamination. We then tested 236 plasma samples from patients infected with HIV-1, HCV or HBV and found them to be negative. The study of HERV RNA for human translational studies should be performed with extensively validated protocols and standard operating procedures to control the widespread low-level human DNA contamination.
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14
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Buelow HN, Winter AS, Van Horn DJ, Barrett JE, Gooseff MN, Schwartz E, Takacs-Vesbach CD. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1040. [PMID: 27486436 PMCID: PMC4947590 DOI: 10.3389/fmicb.2016.01040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.
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Affiliation(s)
- Heather N Buelow
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Ara S Winter
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - David J Van Horn
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - John E Barrett
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Michael N Gooseff
- Department of Civil, Architectural, and Environmental Engineering, Institute of Arctic and Alpine Research, University of Colorado Boulder Boulder, CO, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University Flagstaff, AZ, USA
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15
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Searching for Common Mammalian Retroviruses in Pediatric Idiopathic Diseases. Viruses 2016; 8:86. [PMID: 27102168 PMCID: PMC4810276 DOI: 10.3390/v8030086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 11/17/2022] Open
Abstract
Mammalian retroviruses cause a variety of diseases in their hosts, including hematological and immunodeficiency disorders. Both human T-cell leukemia (HTLV) and human immunodeficiency (HIV) viruses originated from several independent zoonotic transmissions, indicating that cross-species transmissions from animal to humans may still occur. Thus, as the risk for retroviral transmissions from animals to humans increase, we investigated whether mammalian retroviruses are involved in selected pediatric idiopathic diseases whose symptoms evoke retroviral infections. Blood samples, sera, and synovial fluids, or bone marrow cells were collected from pediatric patients under 18 years of age with different autoimmune idiopathic diseases. Overall, we screened clinical samples from 110 children using sensitive nested and semi-nested PCR strategies targeting env genes, and a C-type retrovirus reverse transcriptase (RT) activity kit. All clinical samples were free of retroviral signatures, indicating the unlikelihood of an etiological role of the retroviruses we assessed in the pediatric diseases we tested.
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16
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Naseer A, Terry A, Gilroy K, Kilbey A, Watts C, Mackay N, Bell M, Mason S, Blyth K, Cameron E, Neil JC. Frequent infection of human cancer xenografts with murine endogenous retroviruses in vivo. Viruses 2015; 7:2014-29. [PMID: 25912714 PMCID: PMC4411688 DOI: 10.3390/v7042014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/03/2015] [Accepted: 04/13/2015] [Indexed: 01/23/2023] Open
Abstract
Infection of human cancer xenografts in mice with murine leukemia viruses (MLVs) is a long-standing observation, but the likelihood of infection in vivo and its biological consequences are poorly understood. We therefore conducted a prospective study in commonly used xenograft recipient strains. From BALB/c nude mice engrafted with MCF7 human mammary carcinoma cells, we isolated a virus that was virtually identical to Bxv1, a locus encoding replication-competent xenotropic MLV (XMLV). XMLV was detected in 9/17 (53%) independently isolated explants. XMLV was not found in primary leukemias or in THP1 leukemia cells grown in Bxv1-negative NSG (NOD/SCID/γCnull) mice, although MCF7 explants harbored replication-defective MLV proviruses. To assess the significance of infection for xenograft behavior in vivo, we examined changes in growth and global transcription in MCF7 and the highly susceptible Raji Burkitt lymphoma cell line chronically infected with XMLV. Raji cells showed a stronger transcriptional response that included up-regulation of chemokines and effectors of innate antiviral immunity. In conclusion, the risk of de novo XMLV infection of xenografts is high in Bxv1 positive mice, while infection can have positive or negative effects on xenograft growth potential with significant consequences for interpretation of many xenograft studies.
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Affiliation(s)
- Asif Naseer
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Anne Terry
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Kathryn Gilroy
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Anna Kilbey
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Ciorsdaidh Watts
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Nancy Mackay
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Margaret Bell
- School of Veterinary Medicine, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - Susan Mason
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, G61 1BD Glasgow, UK.
| | - Karen Blyth
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Bearsden, G61 1BD Glasgow, UK.
| | - Ewan Cameron
- School of Veterinary Medicine, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
| | - James C Neil
- Molecular Oncology Laboratory, MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Garscube Estate, Bearsden Road, G61 1QH Glasgow, UK.
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17
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Identification of a microRNA signature for the diagnosis of fibromyalgia. PLoS One 2015; 10:e0121903. [PMID: 25803872 PMCID: PMC4372601 DOI: 10.1371/journal.pone.0121903] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/05/2015] [Indexed: 12/11/2022] Open
Abstract
Background Diagnosis of fibromyalgia (FM), a chronic musculoskeletal pain syndrome characterized by generalized body pain, hyperalgesia and other functional and emotional comorbidities, is a challenging process hindered by symptom heterogeneity and clinical overlap with other disorders. No objective diagnostic method exists at present. The aim of this study was to identify changes in miRNA expression profiles (miRNome) of these patients for the development of a quantitative diagnostic method of FM. In addition, knowledge of FM patient miRNomes should lead to a deeper understanding of the etiology and/or symptom severity of this complex disease. Methods Genome-wide expression profiling of miRNAs was assessed in Peripheral Blood Mononuclear Cells (PBMCs) of FM patients (N=11) and population-age-matched controls (N=10) using human v16-miRbase 3D-Gene microarrays (Toray Industries, Japan). Selected miRNAs from the screen were further validated by RT-qPCR. Participating patients were long term sufferers (over 10 years) diagnosed by more than one specialist under 1990 American College of Rheumatology criteria. Results Microarray analysis of FM patient PBMCs evidenced a marked downregulation of hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p, hsa-miR145-5p and hsa-miR-21-5p (4-fold or more). All but the mildest inhibited miRNA, hsa-miR-21-5p, were validated by RT-qPCR. Globally, 20% of the miRNAs analyzed (233/1212) showed downregulation of at least 2-fold in patients. This might indicate a general de-regulation of the miRNA synthetic pathway in FM. No significant correlations between miRNA inhibition and FM cardinal symptoms could be identified. However, the patient with the lowest score for mental fatigue coincided with the mildest inhibition in four of the five miRNAs associated with the FM-group. Conclusions We propose a signature of five strikingly downregulated miRNAs (hsa-miR223-3p, hsa-miR451a, hsa-miR338-3p, hsa-miR143-3p and hsa-miR145-5p) to be used as biomarkers of FM. Validation in larger study groups is required before the results can be transferred to the clinic.
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18
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Phan TG, Desnues C, Switzer WM, Djoko CF, Schneider BS, Deng X, Delwart E. Absence of giant blood Marseille-like virus DNA detection by polymerase chain reaction in plasma from healthy US blood donors and serum from multiply transfused patients from Cameroon. Transfusion 2015; 55:1256-62. [PMID: 25645088 DOI: 10.1111/trf.12997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/10/2014] [Accepted: 11/28/2014] [Indexed: 01/19/2023]
Abstract
BACKGROUND A new Marseilleviridae virus family member, giant blood Marseille-like (GBM) virus, was recently reported in persons from France in the serum of an infant with adenitis, in the blood of 4% of healthy blood donors, and in 9% of multiply transfused thalassemia patients. These results suggested the presence of a nucleocytoplasmic large DNA virus potentially transmissible by blood product transfusion. STUDY DESIGN AND METHODS To investigate this possibility we tested the plasma from 113 US blood donors and 74 multiply transfused Cameroon patients for GBM viral DNA using highly sensitive polymerase chain reaction (PCR) assays. RESULTS GBM DNA was not detected by nested PCR in any of these 187 human specimens. CONCLUSIONS Further testing is required to confirm the occurrence of human GBM virus infections.
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Affiliation(s)
- Tung Gia Phan
- Blood Systems Research Institute.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Christelle Desnues
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Xutao Deng
- Blood Systems Research Institute.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
| | - Eric Delwart
- Blood Systems Research Institute.,Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California
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19
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Wang W, Indik S, Wasilenko ST, Faschinger A, Carpenter EJ, Tian Z, Zhang Y, Wong GKS, Mason AL. Frequent proviral integration of the human betaretrovirus in biliary epithelium of patients with autoimmune and idiopathic liver disease. Aliment Pharmacol Ther 2015; 41:393-405. [PMID: 25521721 PMCID: PMC4312917 DOI: 10.1111/apt.13054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 11/17/2014] [Accepted: 11/26/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND A human betaretrovirus (HBRV) has been linked with primary biliary cirrhosis (PBC) following the detection of viral particles in biliary epithelium by electron microscopy and cloning of the betaretrovirus genome from biliary epithelium and peri-hepatic lymph nodes. Evidence for viral infection was found in the majority of PBC patients' peri-hepatic lymph node samples. However, less than a third of the liver samples had detectable HBRV, whereas others were unable to detect betaretrovirus infection or noted the presence of virus in the liver of patients with other diagnoses. AIMS To address the hypothesis that the betaretrovirus may be below the limits of detection in the liver, biliary epithelial cells (BEC) were investigated for the evidence of infection. METHODS Ligation-mediated PCR and next generation sequencing were used to detect proviral integrations in liver, lymph nodes and BEC isolated from liver transplant recipients. Hybridisation-based assays were used to detect betaretroviral RNA in BEC. RESULTS Unique HBRV integrations and betaretrovirus RNA were detected in the majority of biliary epithelia derived from patients with PBC, autoimmune hepatitis and cryptogenic liver disease but rarely in other liver transplant recipients with primary sclerosing cholangitis and other hepatic disorders. HBRV integrations were commonly found in PBC patients' lymph nodes but rarely in whole liver samples. CONCLUSIONS Human betaretrovirus infection is frequently observed at the site of disease in patients with primary biliary cirrhosis and also in biliary epithelium of patients with autoimmune hepatitis and cryptogenic liver disease.
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Affiliation(s)
- W Wang
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of AlbertaEdmonton, AB, Canada
| | - S Indik
- Department of Virology, University of Veterinary MedicineVienna, Austria
| | - S T Wasilenko
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of AlbertaEdmonton, AB, Canada
| | - A Faschinger
- Department of Virology, University of Veterinary MedicineVienna, Austria
| | - E J Carpenter
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
| | - Z Tian
- BGI-Shenzhen, Bei Shan Industrial ZoneShenzhen, China
| | - Y Zhang
- BGI-Shenzhen, Bei Shan Industrial ZoneShenzhen, China
| | - G K-S Wong
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of AlbertaEdmonton, AB, Canada,Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada,BGI-Shenzhen, Bei Shan Industrial ZoneShenzhen, China,Li Ka Shing Institute of Virology, University of AlbertaEdmonton, AB, Canada,Prof. G. K.-S. Wong,, Department of Biological Sciences, University of Alberta, Edmonton AB, T6G 2E9, Canada.,
| | - A L Mason
- Center of Excellence for Gastrointestinal Inflammation and Immunity Research, University of AlbertaEdmonton, AB, Canada,Li Ka Shing Institute of Virology, University of AlbertaEdmonton, AB, Canada,Correspondence to:, Dr A. L. Mason, Division of Gastroenterology and Hepatology, 7-142 KGR, University of Alberta, Edmonton, AB, Canada T6G 2E1., E-mail:
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20
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Bhardwaj N, Coffin JM. Endogenous retroviruses and human cancer: is there anything to the rumors? Cell Host Microbe 2014; 15:255-9. [PMID: 24629332 DOI: 10.1016/j.chom.2014.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Xenotropic murine leukemia virus-related virus (XMRV) infection was incorrectly associated with prostate cancer and chronic fatigue syndrome (CFS) in recent years. In this forum, we discuss the story of XMRV and how we can apply lessons learned here to inform the debate surrounding cancers associated with human endogenous retroviruses (HERVs).
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Affiliation(s)
- Neeru Bhardwaj
- Department of Molecular Biology and Microbiology, Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA.
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21
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Chevillet JR, Lee I, Briggs HA, He Y, Wang K. Issues and prospects of microRNA-based biomarkers in blood and other body fluids. Molecules 2014; 19:6080-105. [PMID: 24830712 PMCID: PMC6271291 DOI: 10.3390/molecules19056080] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/07/2014] [Accepted: 05/12/2014] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating microRNAs (miRNAs) in the blood are good diagnostic biomarker candidates for various physiopathological conditions, including cancer, neurodegeneration, diabetes and other diseases. Since their discovery in 2008 as blood biomarkers, the field has expanded rapidly with a number of important findings. Despite the initial optimistic views of their potential for clinical application, there are currently no circulating miRNA-based diagnostics in use. In this article, we review the status of circulating miRNAs, examine different analytical approaches, and address some of the challenges and opportunities.
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Affiliation(s)
| | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Hilary A Briggs
- Laboratory of the Biology of Addictive Diseases, Rockefeller University, New York, NY 10065, USA
| | - Yuqing He
- Institute of Medical Systems Biology, Guangdong Medical College, Dongguan, Guangdong 523808, China.
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA.
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22
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Delbue S, Ferrante P, Provenzano M. Polyomavirus BK and prostate cancer: an unworthy scientific effort? Oncoscience 2014; 1:296-303. [PMID: 25594022 PMCID: PMC4278296 DOI: 10.18632/oncoscience.32] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/30/2014] [Indexed: 12/11/2022] Open
Abstract
The Polyomavirus BK (BKV) has been proposed to be one of the possible co-factors in the genesis of prostate cancer (PCa) but, so far, the only convincing suggestion is the hypothesis of a “hit and run” carcinogenic mechanism induced by the virus at early stages of this disease. To support this hypothesis we conducted an updated systematic review on previous studies regarding the association between BKV and PCa, in order to interpret the contrasting results and to explore whether there might be a significant virus-disease link. This updated analysis provides evidence for a significant link between BKV expression and PCa development, particularly between the BKV infection and the cancer risk. Forthcoming scientific efforts that take cue from this study might overcome the atavistic and fruitless debate regarding the BKV-PCa association.
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Affiliation(s)
- Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milano, Italy
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milano, Italy
| | - Maurizio Provenzano
- Oncology Unit, Division of Urology, University Hospital of Zurich, Switzerland
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23
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Kassiotis G. Endogenous retroviruses and the development of cancer. THE JOURNAL OF IMMUNOLOGY 2014; 192:1343-9. [PMID: 24511094 DOI: 10.4049/jimmunol.1302972] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mammalian genomes include a considerable number of endogenous retroviruses (ERVs), relics of ancestral infectious retroviruses, whose proviruses have invaded the germ-line. The documented ability of infectious retroviruses to cause cancer has greatly contributed to the discovery of ERVs. It also reinforced the concept that ERVs are causative agents of many cancers, a notion that historically has not always stood up to experimental scrutiny. The recent greater appreciation of the complexity of ERV biology and the identification of dedicated host mechanisms controlling ERV activity have revealed novel interactions between ERVs and their hosts, with the potential to cause or contribute to disease. In this review, the involvement of ERVs in cancer initiation and progression is discussed, as well as their contribution to our understanding of the process of transformation and to the invention of innovative preventive and therapeutic cancer treatments.
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Affiliation(s)
- George Kassiotis
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
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24
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Barbeau B, Hiscott J, Bazarbachi A, Carvalho E, Jones K, Martin F, Matsuoka M, Murphy EL, Ratner L, Switzer WM, Watanabe T. Conference highlights of the 16th International Conference on Human Retrovirology: HTLV and related retroviruses, 26-30 June 2013, Montreal, Canada. Retrovirology 2014; 11:19. [PMID: 24558960 PMCID: PMC3939404 DOI: 10.1186/1742-4690-11-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/10/2014] [Indexed: 01/19/2023] Open
Abstract
The 16th International Conference on Human Retrovirology: HTLV and Related Retroviruses was held in Montreal, Québec from June 26th to June 30th, 2013 and was therefore hosted by a Canadian city for the first time. The major topic of the meeting was human T-lymphotropic viruses (HTLVs) and was covered through distinct oral and poster presentation sessions: clinical research, animal models, immunology, molecular and cellular biology, human endogenous and emerging exogenous retroviruses and virology. In this review, highlights of the meeting are provided by different experts for each of these research areas.
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Affiliation(s)
- Benoit Barbeau
- Département des sciences biologiques and BioMed Research Center, Université du Québec à Montréal, Room SB-3335, 2080 St-Urbain, Montréal, Québec, Canada
| | - John Hiscott
- VGTI Florida, Port St., Lucie, FL, USA
- Lady Davis Insitute, Montreal, Canada
| | - Ali Bazarbachi
- Department of Internal Medicine, American University of Beirut, Beirut, Lebanon
| | - Edgar Carvalho
- Immunology Department, Universidade Federal da Bahia (UFBA), Salvador, Bahia, Brazil
| | - Kathryn Jones
- Basic Research Program, Cancer and Inflammation Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Fabiola Martin
- Centre for Immunology and Infection, Department of Biology, Hull and York Medical School, University of York, York, UK
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Edward L Murphy
- University of California San Francisco and Blood Systems Research Institute, San Francisco, CA, USA
| | - Lee Ratner
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Toshiki Watanabe
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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25
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Witwer KW, Hirschi KD. Transfer and functional consequences of dietary microRNAs in vertebrates: concepts in search of corroboration: negative results challenge the hypothesis that dietary xenomiRs cross the gut and regulate genes in ingesting vertebrates, but important questions persist. Bioessays 2014; 36:394-406. [PMID: 24436255 PMCID: PMC4109825 DOI: 10.1002/bies.201300150] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
If validated, diet-derived foreign microRNA absorption and function in consuming vertebrates would drastically alter our understanding of nutrition and ecology. RNA interference (RNAi) mechanisms of Caenorhabditis elegans are enhanced by uptake of environmental RNA and amplification and systemic distribution of RNAi effectors. Therapeutic exploitation of RNAi in treating human disease is difficult because these accessory processes are absent or diminished in most animals. A recent report challenged multiple paradigms, suggesting that ingested microRNAs (miRNAs) are transferred to blood, accumulate in tissues, and exert canonical regulation of endogenous transcripts. Independent replication of these findings has been elusive, and multiple disconfirmatory findings have been published. In the face of mounting negative results, any additional positive reports must provide the proverbial “extraordinary proof” to support such claims. In this article, we review the evidence for and against a significant role for dietary miRNAs in influencing gene expression, and make recommendations for future studies.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, Baltimore, MD, USA
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26
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Oltra E, García-Escudero M, Mena-Durán AV, Monsalve V, Cerdá-Olmedo G. Lack of evidence for retroviral infections formerly related to chronic fatigue in Spanish fibromyalgia patients. Virol J 2013; 10:332. [PMID: 24216038 PMCID: PMC4226024 DOI: 10.1186/1743-422x-10-332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 10/17/2013] [Indexed: 01/04/2023] Open
Abstract
Background The etiology of fibromyalgia and chronic fatigue syndrome (FM/CFS) is currently unknown. A recurrent viral infection is an attractive hypothesis repeatedly found in the literature since it would explain the persistent pain and tiredness these patients suffer from. The initial striking link of two distinct orphan retroviruses: the gamma retroviruses murine leukemia virus (MLV)-related virus and the delta retrovirus T-lymphotropic virus type 2 (HTLV-2) to chronic fatigue have not been confirmed to date. Results Genomic DNA (gDNA) from 75 fibromyalgia patients suffering from chronic fatigue and 79 age-matched local healthy controls were screened for the presence of MLV-related and HTLV-2 related proviral sequences. The XMRV env gene was amplified in 20% of samples tested (24% patients/15% healthy controls). Unexpectedly, no PCR amplifications from independent gDNA preparations of the same individuals were obtained. None of the positive samples showed presence of contaminating murine sequences previously reported by other investigators, neither contained additional regions of the virus making us conclude that the initial env amplification came from spurious air-driven amplicon contaminants. No specific HTLV-2 sequences were obtained at any time from any of the 154 quality-controlled gDNA preparations screened. Conclusions Previous associations between MLV-related or HTLV-2 retrovirus infection with chronic fatigue must be discarded. Thus, studies showing positive amplification of HTLV-2 sequences from chronic fatigue participants should be revised for possible undetected technical problems. To avoid false positives of viral infection, not only extreme precautions should be taken when nested-PCR reactions are prepared and exhaustive foreign DNA contamination controls performed, but also consistent amplification of diverse regions of the virus in independent preparations from the same individual must be demanded. The fact that our cohort of patients did not present evidence of any of the two types of retroviral infection formerly associated to chronic fatigue does not rule out the possibility that other viruses are involved in inciting or maintaining fibromyalgia and/or chronic fatigue conditions.
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Affiliation(s)
- Elisa Oltra
- Facultad de Medicina, C/Quevedo, 2, 46001 Valencia, Spain.
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27
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Generation of multiple replication-competent retroviruses through recombination between PreXMRV-1 and PreXMRV-2. J Virol 2013; 87:11525-37. [PMID: 23966380 DOI: 10.1128/jvi.01787-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We previously identified two novel endogenous murine leukemia virus proviruses, PreXMRV-1 and PreXMRV-2, and showed that they most likely recombined during xenograft passaging of a human prostate tumor in mice to generate xenotropic murine leukemia virus-related virus (XMRV). To determine the recombination potential of PreXMRV-1 and PreXMRV-2, we examined the generation of replication-competent retroviruses (RCRs) over time in a cell culture system. We observed that either virus alone was noninfectious and the RNA transcripts of the viruses were undetectable in the blood and spleen of nude mice that carry them. To determine their potential to generate RCRs through recombination, we transfected PreXMRV-1 and PreXMRV-2 into 293T cells and used the virus produced to infect fresh cells; the presence of reverse transcriptase activity at 10 days postinfection indicated the presence of RCRs. Population sequencing of proviral DNA indicated that all RCRs contained the gag and 5' half of pol from PreXMRV-2 and the long terminal repeat, 3' half of pol (including integrase), and env from PreXMRV-1. All crossovers were within sequences of at least 9 identical nucleotides, and crossovers within each of two selected recombination zones of 415 nucleotides (nt) in the 5' untranslated region and 982 nt in pol were required to generate RCRs. A recombinant with the same genotype as XMRV was not detected, and our analysis indicates that the probability of generating an identical RCR is vanishingly small. In addition, the studies indicate that the process of RCR formation is primarily driven by selection for viable cis and trans elements from the parental proviruses.
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28
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Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SFJ, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 2013; 41:3874-87. [PMID: 23382176 PMCID: PMC3616737 DOI: 10.1093/nar/gkt053] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 11/19/2022] Open
Abstract
A key step in proliferation of retroviruses is the conversion of their RNA genome to double-stranded DNA, a process catalysed by multifunctional reverse transcriptases (RTs). Dimeric and monomeric RTs have been described, the latter exemplified by the enzyme of Moloney murine leukaemia virus. However, structural information is lacking that describes the substrate binding mechanism for a monomeric RT. We report here the first crystal structure of a complex between an RNA/DNA hybrid substrate and polymerase-connection fragment of the single-subunit RT from xenotropic murine leukaemia virus-related virus, a close relative of Moloney murine leukaemia virus. A comparison with p66/p51 human immunodeficiency virus-1 RT shows that substrate binding around the polymerase active site is conserved but differs in the thumb and connection subdomains. Small-angle X-ray scattering was used to model full-length xenotropic murine leukaemia virus-related virus RT, demonstrating that its mobile RNase H domain becomes ordered in the presence of a substrate-a key difference between monomeric and dimeric RTs.
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Affiliation(s)
- Elżbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Wojciech Potrzebowski
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Petr V. Konarev
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Jason W. Rausch
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marion K. Bona
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Dmitri I. Svergun
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Janusz M. Bujnicki
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Stuart F. J. Le Grice
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109 Warsaw, Poland, European Molecular Biology Laboratory, Hamburg Outstation c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany, RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory, Frederick, MD 21702, USA and Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
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