1
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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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2
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Jurasz H, Pawłowski T, Perlejewski K. Contamination Issue in Viral Metagenomics: Problems, Solutions, and Clinical Perspectives. Front Microbiol 2021; 12:745076. [PMID: 34745046 PMCID: PMC8564396 DOI: 10.3389/fmicb.2021.745076] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
We describe the most common internal and external sources and types of contamination encountered in viral metagenomic studies and discuss their negative impact on sequencing results, particularly for low-biomass samples and clinical applications. We also propose some basic recommendations for reducing the background noise in viral shotgun metagenomic (SM) studies, which would limit the bias introduced by various classes of contaminants. Regardless of the specific viral SM protocol, contamination cannot be totally avoided; in particular, the issue of reagent contamination should always be addressed with high priority. There is an urgent need for the development and validation of standards for viral metagenomic studies especially if viral SM protocols will be more widely applied in diagnostics.
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Affiliation(s)
- Henryk Jurasz
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Pawłowski
- Division of Psychotherapy and Psychosomatic Medicine, Department of Psychiatry, Wrocław Medical University, Wrocław, Poland
| | - Karol Perlejewski
- Department of Immunopathology of Infectious and Parasitic Diseases, Medical University of Warsaw, Warsaw, Poland
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3
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Bajerski F, Nagel M, Overmann J. Microbial occurrence in liquid nitrogen storage tanks: a challenge for cryobanking? Appl Microbiol Biotechnol 2021; 105:7635-7650. [PMID: 34559283 PMCID: PMC8460408 DOI: 10.1007/s00253-021-11531-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
Abstract Modern biobanks maintain valuable living materials for medical diagnostics, reproduction medicine, and conservation purposes. To guarantee high quality during long-term storage and to avoid metabolic activities, cryostorage is often conducted in the N2 vapour phase or in liquid nitrogen (LN) at temperatures below − 150 °C. One potential risk of cryostorage is microbial cross contamination in the LN storage tanks. The current review summarises data on the occurrence of microorganisms that may compromise the safety and quality of biological materials during long-term storage. We assess the potential for the microbial contamination of LN in storage tanks holding different biological materials based on the detection by culture-based and molecular approaches. The samples themselves, the LN, the human microbiome, and the surrounding environment are possible routes of contamination and can cause cross contaminations via the LN phase. In general, the results showed that LN is typically not the source of major contaminations and only a few studies provided evidence for a risk of microbial cross contamination. So far, culture-based and culture-independent techniques detected only low amounts of microbial cells, indicating that cross contamination may occur at a very low frequency. To further minimise the potential risk of microbial cross contaminations, we recommend reducing the formation of ice crystals in cryotanks that can entrap environmental microorganisms and using sealed or second sample packing. A short survey demonstrated the awareness for microbial contaminations of storage containers among different culture collections. Although most participants consider the risk of cross contaminations in LN storage tanks as low, they prevent potential contaminations by using sealed devices and − 150 °C freezers. It is concluded that the overall risk for cross contaminations in biobanks is relatively low when following standard operating procedures (SOPs). We evaluated the potential sources in detail and summarised our results in a risk assessment spreadsheet which can be used for the quality management of biobanks. Key points • Identification of potential contaminants and their sources in LN storage tanks. • Recommendations to reduce this risk of LN storage tank contamination. • Development of a risk assessment spreadsheet to support quality management. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11531-4.
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Affiliation(s)
- Felizitas Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany.
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland OT Gatersleben, Germany
| | - Joerg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany.,Institute of Microbiology, Braunschweig University of Technology, 38106, Brunswick, Germany
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4
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Loiseau V, Cordaux R, Giraud I, Beby-Defaux A, Lévêque N, Gilbert C. Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B). Sci Rep 2020; 10:16046. [PMID: 32994520 PMCID: PMC7524804 DOI: 10.1038/s41598-020-73169-y] [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: 10/04/2019] [Accepted: 08/31/2020] [Indexed: 11/09/2022] Open
Abstract
The use of misidentified cell lines contaminated by other cell lines and/or microorganisms has generated much confusion in the scientific literature. Detailed characterization of such contaminations is therefore crucial to avoid misinterpretation and ensure robustness and reproducibility of research. Here we use DNA-seq data produced in our lab to first confirm that the Hep2 (clone 2B) cell line (Sigma-Aldrich catalog number: 85011412-1VL) is indistinguishable from the HeLa cell line by mapping integrations of the human papillomavirus 18 (HPV18) at their expected loci on chromosome 8. We then show that the cell line is also contaminated by a xenotropic murine leukemia virus (XMLV) that is nearly identical to the mouse Bxv1 provirus and we characterize one Bxv1 provirus, located in the second intron of the pseudouridylate synthase 1 (PUS1) gene. Using an RNA-seq dataset, we confirm the high expression of the E6 and E7 HPV18 oncogenes, show that the entire Bxv1 genome is moderately expressed, and retrieve a Bxv1 splicing event favouring expression of the env gene. Hep2 (clone 2B) is the fourth human cell line so far known to be contaminated by the Bxv1 XMLV. This contamination has to be taken into account when using the cell line in future experiments.
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Affiliation(s)
- Vincent Loiseau
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Richard Cordaux
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Isabelle Giraud
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Agnès Beby-Defaux
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
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5
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Mansour NM, Balas EA, Yang FM, Vernon MM. Prevalence and Prevention of Reproducibility Deficiencies in Life Sciences Research: Large-Scale Meta-Analyses. Med Sci Monit 2020; 26:e922016. [PMID: 32960878 PMCID: PMC7519945 DOI: 10.12659/msm.922016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 03/18/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Studies have found that many published life sciences research results are irreproducible. Our goal was to provide comprehensive risk estimates of familiar reproducibility deficiencies to support quality improvement in research. MATERIAL AND METHODS Reports included were peer-reviewed, published between 1980 and 2016, and presented frequency data of basic biomedical research deficiencies. Manual and electronic literature searches were performed in seven bibliographic databases. For deficiency concepts with at least four frequency studies and with a sample size of at least 15 units in each, a meta-analysis was performed. RESULTS Overall, 68 publications met our inclusion criteria. The study identified several major groups of research quality defects: study design, cell lines, statistical analysis, and reporting. In the study design group of 3 deficiencies, missing power calculation was the most frequent (82.3% [95% Confidence Interval (CI): 69.9-94.6]). Among the 6 cell line deficiencies, mixed contamination was the most frequent (22.4% [95% CI: 10.4-34.3]). Among the 3 statistical analysis deficiencies, the use of chi-square test when expected cells frequency was <5 was the most prevalent (15.7% [95% CI: -3.2-34.7]). In the reporting group of 12 deficiencies, failure to state the number of tails was the most frequent (65% [95% CI: 39.3-90.8]). CONCLUSIONS The results of this study could serve as a general reference when consistently measurable sources of deficiencies need to be identified in research quality improvement.
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Affiliation(s)
- Nadine M. Mansour
- Biomedical Research Innovation Laboratory, Augusta University, Augusta, GA, U.S.A
- Department of Public Health, Cairo University, Cairo, Egypt
| | - E. Andrew Balas
- Biomedical Research Innovation Laboratory, Augusta University, Augusta, GA, U.S.A
| | | | - Marlo M. Vernon
- Medical College of Georgia, Augusta University, Augusta, GA, U.S.A
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6
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Khan AS, Blümel J, Deforce D, Gruber MF, Jungbäck C, Knezevic I, Mallet L, Mackay D, Matthijnssens J, O'Leary M, Theuns S, Victoria J, Neels P. Report of the second international conference on next generation sequencing for adventitious virus detection in biologics for humans and animals. Biologicals 2020; 67:94-111. [PMID: 32660862 PMCID: PMC7351673 DOI: 10.1016/j.biologicals.2020.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 11/20/2022] Open
Abstract
The IABS-EU, in association with PROVAXS and Ghent University, hosted the "2nd Conference on Next Generation Sequencing (NGS) for Adventitious Virus Detection in Human and Veterinary Biologics" held on November 13th and 14th 2019, in Ghent, Belgium. The meeting brought together international experts from regulatory agencies, the biotherapeutics and biologics industries, contract research organizations, and academia, with the goal to develop a scientific consensus on the readiness of NGS for detecting adventitious viruses, and on the use of this technology to supplement or replace/substitute the currently used assays. Participants discussed the progress on the standardization and validation of the technical and bioinformatics steps in NGS for characterization and safety evaluation of biologics, including human and animal vaccines. It was concluded that NGS can be used for the detection of a broad range of viruses, including novel viruses, and therefore can complement, supplement or even replace some of the conventional adventitious virus detection assays. Furthermore, the development of reference viral standards, complete and correctly annotated viral databases, and protocols for the validation and follow-up investigations of NGS signals is necessary to enable broader use of NGS. An international collaborative effort, involving regulatory authorities, industry, academia, and other stakeholders is ongoing toward this goal.
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Affiliation(s)
- Arifa S Khan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | | | | | - Marion F Gruber
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Carmen Jungbäck
- International Association for Biological Standardization for Europe, Lyon, France
| | | | | | | | | | - Maureen O'Leary
- P95 Pharmacovigilance and Epidemiology Services, Leuven, Belgium
| | | | | | - Pieter Neels
- International Association for Biological Standardization for Europe, Lyon, France
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7
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Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. Virus expression detection reveals RNA-sequencing contamination in TCGA. BMC Genomics 2020; 21:79. [PMID: 31992194 PMCID: PMC6986043 DOI: 10.1186/s12864-020-6483-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023] Open
Abstract
Background Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa-derived human papillomavirus 18 (H-HPV18) in several of The Cancer Genome Atlas (TCGA) RNA-sequencing samples. This work motivated us to assess a greater number of samples and determine the origin of possible contaminations using viral sequences. To detect viruses with high specificity, we developed the publicly available workflow, VirDetect, that detects virus and laboratory vector sequences in RNA-seq samples. We applied VirDetect to 9143 RNA-seq samples sequenced at one TCGA sequencing center (28/33 cancer types) over 5 years. Results We confirmed that H-HPV18 was present in many samples and determined that viral transcripts from H-HPV18 significantly co-occurred with those from xenotropic mouse leukemia virus-related virus (XMRV). Using laboratory metadata and viral transcription, we determined that the likely contaminant was a pool of cell lines known as the “common reference”, which was sequenced alongside TCGA RNA-seq samples as a control to monitor quality across technology transitions (i.e. microarray to GAII to HiSeq), and to link RNA-seq to previous generation microarrays that standardly used the “common reference”. One of the cell lines in the pool was a laboratory isolate of MCF-7, which we discovered was infected with XMRV; another constituent of the pool was likely HeLa cells. Conclusions Altogether, this indicates a multi-step contamination process. First, MCF-7 was infected with an XMRV. Second, this infected cell line was added to a pool of cell lines, which contained HeLa. Finally, RNA from this pool of cell lines contaminated several TCGA tumor samples most-likely during library construction. Thus, these human tumors with H-HPV or XMRV reads were likely not infected with H-HPV 18 or XMRV.
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Affiliation(s)
- Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - David Marron
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Daniel Hollern
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Corbin Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Dirk P Dittmer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA. .,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.
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8
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Loyola L, Achuthan V, Gilroy K, Borland G, Kilbey A, Mackay N, Bell M, Hay J, Aiyer S, Fingerman D, Villanueva RA, Cameron E, Kozak CA, Engelman AN, Neil J, Roth MJ. Disrupting MLV integrase:BET protein interaction biases integration into quiescent chromatin and delays but does not eliminate tumor activation in a MYC/Runx2 mouse model. PLoS Pathog 2019; 15:e1008154. [PMID: 31815961 PMCID: PMC6974304 DOI: 10.1371/journal.ppat.1008154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 01/21/2020] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Murine leukemia virus (MLV) integrase (IN) lacking the C-terminal tail peptide (TP) loses its interaction with the host bromodomain and extraterminal (BET) proteins and displays decreased integration at promoter/enhancers and transcriptional start sites/CpG islands. MLV lacking the IN TP via an altered open reading frame was used to infect tumorigenesis mouse model (MYC/Runx2) animals to observe integration patterns and phenotypic effects, but viral passage resulted in the restoration of the IN TP through small deletions. Mice subsequently infected with an MLV IN lacking the TP coding sequence (TP-) showed an improved median survival by 15 days compared to wild type (WT) MLV infection. Recombination with polytropic endogenous retrovirus (ERV), Pmv20, was identified in seven mice displaying both fast and slow tumorigenesis, highlighting the strong selection within the mouse to maintain the full-length IN protein. Mapping the genomic locations of MLV in tumors from an infected mouse with no observed recombination with ERVs, TP-16, showed fewer integrations at TSS and CpG islands, compared to integrations observed in WT tumors. However, this mouse succumbed to the tumor in relatively rapid fashion (34 days). Analysis of the top copy number integrants in the TP-16 tumor revealed their proximity to known MLV common insertion site genes while maintaining the MLV IN TP- genotype. Furthermore, integration mapping in K562 cells revealed an insertion preference of MLV IN TP- within chromatin profile states associated with weakly transcribed heterochromatin with fewer integrations at histone marks associated with BET proteins (H3K4me1/2/3, and H3K27Ac). While MLV IN TP- showed a decreased overall rate of tumorigenesis compared to WT virus in the MYC/Runx2 model, MLV integration still occurred at regions associated with oncogenic driver genes independently from the influence of BET proteins, either stochastically or through trans-complementation by functional endogenous Gag-Pol protein. Many different retroviruses, including murine leukemia virus (MLV), are used as vectors for human gene therapy and cancer immunotherapies (CAR-T) because of their stable and efficient delivery of genetic material into the host DNA. However, this process can result in activation and/or disruption of cellular genes, which has resulted in the outgrowth of tumors in previous clinical trials. Of critical importance is the preferred location within the host genome at which the retrovirus integrates. Our study presents a modified MLV virus that has lost the ability to bind to the host BET proteins, the drivers of insertion at promoter/enhancer regions of highly activated genes. This is the first direct study within an animal model to examine whether infection with this type of modified MLV virus affects tumor progression. We found that the modified virus improved the survival of the well-characterized MYC/Runx2 mouse compared to infections with the wild-type MLV. Most modified viral integrants mapped into less active regions of the genome, but some integration events still occurred near cancer-related genes. Thus, while the modified MLV virus can be a safer vector than the wildtype virus, it still maintains the potential to activate oncogenes. This study provides new insights on how to improve the safety of MLV retroviral vectors.
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Affiliation(s)
- Lorenz Loyola
- Rutgers-Robert Wood Johnson Medical School, Dept of Pharmacology, Piscataway, New Jersey, United States of America
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Harvard Medical School, Department of Medicine, Boston, Massachusetts, United States of America
| | - Kathryn Gilroy
- Beatson Institute for Cancer Research, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gillian Borland
- MRC Univ. of Glasgow Centre for Virus Research, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna Kilbey
- MRC Univ. of Glasgow Centre for Virus Research, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nancy Mackay
- MRC Univ. of Glasgow Centre for Virus Research, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Margaret Bell
- Univ. of Glasgow School of Veterinary Medicine, Department of Veterinary Pathology Bearsden, United Kingdom
| | - Jodie Hay
- MRC Univ. of Glasgow Centre for Virus Research, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sriram Aiyer
- Rutgers-Robert Wood Johnson Medical School, Dept of Pharmacology, Piscataway, New Jersey, United States of America
| | - Dylan Fingerman
- Rutgers-Robert Wood Johnson Medical School, Dept of Pharmacology, Piscataway, New Jersey, United States of America
| | - Rodrigo A. Villanueva
- Rutgers-Robert Wood Johnson Medical School, Dept of Pharmacology, Piscataway, New Jersey, United States of America
| | - Ewan Cameron
- Univ. of Glasgow School of Veterinary Medicine, Department of Veterinary Pathology Bearsden, United Kingdom
| | | | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Harvard Medical School, Department of Medicine, Boston, Massachusetts, United States of America
| | - James Neil
- MRC Univ. of Glasgow Centre for Virus Research, College of Medicine, Veterinary Medicine and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Monica J. Roth
- Rutgers-Robert Wood Johnson Medical School, Dept of Pharmacology, Piscataway, New Jersey, United States of America
- * E-mail:
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9
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Bajerski F, Bürger A, Glasmacher B, Keller ERJ, Müller K, Mühldorfer K, Nagel M, Rüdel H, Müller T, Schenkel J, Overmann J. Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples. Appl Microbiol Biotechnol 2019; 104:131-144. [PMID: 31781817 PMCID: PMC6942587 DOI: 10.1007/s00253-019-10242-1] [Citation(s) in RCA: 10] [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: 08/19/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 01/19/2023]
Abstract
The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.
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Affiliation(s)
- F Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
| | - A Bürger
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, München, Germany
| | - B Glasmacher
- Institute for Multiphase Processes, Leibniz University Hannover, Hannover, Germany
| | - E R J Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - K Müller
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - K Mühldorfer
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - M Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - H Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | | | - J Schenkel
- German Cancer Research Centre, Heidelberg, Germany
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - J Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
- Microbiology, Braunschweig University of Technology, Braunschweig, Germany
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10
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Garcin EB, Gon S, Sullivan MR, Brunette GJ, Cian AD, Concordet JP, Giovannangeli C, Dirks WG, Eberth S, Bernstein KA, Prakash R, Jasin M, Modesti M. Differential Requirements for the RAD51 Paralogs in Genome Repair and Maintenance in Human Cells. PLoS Genet 2019; 15:e1008355. [PMID: 31584931 PMCID: PMC6795472 DOI: 10.1371/journal.pgen.1008355] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/16/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A cells. Underlining their importance for genomic stability, mutant cell lines display variable growth defects, impaired sister chromatid recombination, reduced levels of stable RAD51 nuclear foci, and hyper-sensitivity to mitomycin C and olaparib, with the weakest phenotypes observed in RAD51B-deficient cells. Altogether these observations underscore the contributions of RAD51 paralogs in diverse DNA repair processes, and demonstrate essential differences in different cell types. Finally, this study will provide useful reagents to analyze patient-derived mutations and to investigate mechanisms of chemotherapeutic resistance deployed by cancers.
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Affiliation(s)
- Edwige B. Garcin
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Stéphanie Gon
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
| | - Meghan R. Sullivan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Gregory J. Brunette
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Anne De Cian
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Jean-Paul Concordet
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Carine Giovannangeli
- Museum National d'Histoire Naturelle, Inserm U1154, CNRS UMR 7196, Sorbonne Universités, Paris, France
| | - Wilhelm G. Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sonja Eberth
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German, Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kara A. Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, United States of America
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Mauro Modesti
- Cancer Research Center of Marseille; CNRS; Inserm; Institut Paoli-Calmettes; Aix-Marseille Université, Marseille, France
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11
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Brussel A, Brack K, Muth E, Zirwes R, Cheval J, Hebert C, Charpin JM, Marinaci A, Flan B, Ruppach H, Beurdeley P, Eloit M. Use of a new RNA next generation sequencing approach for the specific detection of virus infection in cells. Biologicals 2019; 59:29-36. [PMID: 30992161 DOI: 10.1016/j.biologicals.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/15/2019] [Accepted: 03/31/2019] [Indexed: 01/22/2023] Open
Abstract
The utilization of the current combination of in vitro, in vivo and PCR assays for the identification of adventitious viruses in production cells has a limited range of detection. While Next Generation Sequencing (NGS) has a broader breadth of detection, it is unable to differentiate sequences from replicating viruses versus background inert sequences. In order to improve NGS specificity, we have designed a new NGS approach which targets subsets of viral RNAs only synthesized during cell infection. In order to evaluate the performance of this approach for detecting low levels of adventitious viruses, we selected two difficult virus/cell systems. This included B95-8 cells persistently infected by Human herpesvirus 4 (HHV-4) and serially diluted into HHV-4 negative Ramos cells and Madin-Darby bovine kidney cells with an early infection produced via a low dose of Bovine viral diarrhea virus. We demonstrated that the sensitivity of our RNA NGS approach was equivalent to targeted PCR with an increased specificity for the detection of viral infection. We were also able to identify a previously undetected Murine Leukemia Virus contaminant in Ramos cells. Based on these results, we conclude that this new RNA NGS approach is suitable for conducting viral safety evaluations of cells.
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Affiliation(s)
| | - Kerstin Brack
- Charles River Laboratories Germany GmbH, Erkrath, Germany
| | | | | | | | | | | | - Alice Marinaci
- Charles River Laboratories Germany GmbH, Erkrath, Germany
| | | | - Horst Ruppach
- Charles River Laboratories Germany GmbH, Erkrath, Germany
| | | | - Marc Eloit
- PathoQuest, Paris, France; National Veterinary School of Alfort, Paris-Est University, Maisons-Alfort, France; Pathogen Discovery Laboratory, Biology of Infection Unit, Institut Pasteur, Paris, France.
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12
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Feng N, Huang X, Jia Y. Mycoplasma contamination affects cell characteristics and decreases the sensitivity of BV2 microglia to LPS stimulation. Cytotechnology 2019; 71:623-634. [PMID: 30945036 DOI: 10.1007/s10616-019-00311-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 01/12/2023] Open
Abstract
Mycoplasma is the most common contaminant and greatly affects host cells. The influence of mycoplasma on microglia cells remains unknown. Here, we investigated the influence of mycoplasma contamination on BV2 cells (a microglia cell line). We found that mycoplasma contamination increased the phosphorylation of NF-kB and MAPK signal pathway and induced the activation of BV2 cells. These mycoplasma-contaminated BV2 cells exhibited a transition of cell morphology and slower proliferation, as well as increased gene expression and protein secretion of inflammatory factors. Furthermore, mycoplasma-contaminated BV2 cells had decreased sensitivity to lipopolysaccharide stimulation. These findings suggested that mycoplasma contamination greatly influenced the characteristics and function of microglia cells. It is important to prevent and exclude mycoplasma contamination in our research.
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Affiliation(s)
- Nianhua Feng
- Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, 8# Gongti South Street, Chaoyang District, Beijing, 100020, China.
| | - Xiaoxi Huang
- Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, 8# Gongti South Street, Chaoyang District, Beijing, 100020, China
| | - Yanjun Jia
- Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, 8# Gongti South Street, Chaoyang District, Beijing, 100020, China
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13
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Uphoff CC, Pommerenke C, Denkmann SA, Drexler HG. Screening human cell lines for viral infections applying RNA-Seq data analysis. PLoS One 2019; 14:e0210404. [PMID: 30629668 PMCID: PMC6328144 DOI: 10.1371/journal.pone.0210404] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/21/2018] [Indexed: 01/09/2023] Open
Abstract
Monitoring viral infections of cell cultures is largely neglected although the viruses may have an impact on the physiology of cells and may constitute a biohazard regarding laboratory safety and safety of bioactive agents produced by cell cultures. PCR, immunological assays, and enzyme activity tests represent common methods to detect virus infections. We have screened more than 300 Cancer Cell Line Encyclopedia RNA sequencing and 60 whole exome sequencing human cell lines data sets for specific viral sequences and general viral nucleotide and protein sequence assessment applying the Taxonomer bioinformatics tool developed by IDbyDNA. The results were compared with our previous findings from virus specific PCR analyses. Both, the results obtained from the direct alignment method and the Taxonomer alignment method revealed a complete concordance with the PCR results: twenty cell lines were found to be infected with five virus species. Taxonomer further uncovered a bovine polyomavirus infection in the breast cancer cell line SK-BR-3 most likely introduced by contaminated fetal bovine serum. RNA-Seq data sets were more sensitive for virus detection although a significant proportion of cell lines revealed low numbers of virus specific alignments attributable to low level nucleotide contamination during RNA preparation or sequencing procedure. Low quality reads leading to Taxonomer false positive results can be eliminated by trimming the sequence data before analysis. One further important result is that no viruses were detected that had never been shown to occur in cell cultures. The results prove that the currently applied testing of cell cultures is adequate for the detection of contamination and for the risk assessment of cell cultures. The results emphasize that next generation sequencing is an efficient tool to determine the viral infection status of human cells.
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Affiliation(s)
- Cord C. Uphoff
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine A. Denkmann
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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14
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Cesi G, Philippidou D, Kozar I, Kim YJ, Bernardin F, Van Niel G, Wienecke-Baldacchino A, Felten P, Letellier E, Dengler S, Nashan D, Haan C, Kreis S. A new ALK isoform transported by extracellular vesicles confers drug resistance to melanoma cells. Mol Cancer 2018; 17:145. [PMID: 30290811 PMCID: PMC6172729 DOI: 10.1186/s12943-018-0886-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Drug resistance remains an unsolved clinical issue in oncology. Despite promising initial responses obtained with BRAF and MEK kinase inhibitors, resistance to treatment develops within months in virtually all melanoma patients. Methods Microarray analyses were performed in BRAF inhibitor-sensitive and resistant cell lines to identify changes in the transcriptome that might play a role in resistance. siRNA approaches and kinase inhibitors were used to assess the involvement of the identified Anaplastic Lymphoma Kinase (ALK) in drug resistance. The capability of extracellular vesicles (EVs) to transfer drug resistant properties was investigated in co-culture assays. Results Here, we report a new mechanism of acquired drug resistance involving the activation of a novel truncated form of ALK. Knock down or inhibition of ALK re-sensitised resistant cells to BRAF inhibition and induced apoptosis. Interestingly, truncated ALK was also secreted into EVs and we show that EVs were the vehicle for transferring drug resistance. Conclusions To our knowledge, this is the first report demonstrating the functional involvement of EVs in melanoma drug resistance by transporting a truncated but functional form of ALK, able to activate the MAPK signalling pathway in target cells. Combined inhibition of ALK and BRAF dramatically reduced tumour growth in vivo. These findings make ALK a promising clinical target in melanoma patients. Electronic supplementary material The online version of this article (10.1186/s12943-018-0886-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giulia Cesi
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | | | - Ines Kozar
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | | | | | - Guillaume Van Niel
- Institute Curie, PSL Research University, CNRS UMR144, Paris, France.,Center for Psychiatry and Neuroscience, Hopital Saint-Anne, Université Descartes, INSERM U894, Paris, France
| | | | - Paul Felten
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | | | | | | | - Claude Haan
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg
| | - Stephanie Kreis
- Life Sciences Research Unit, University of Luxembourg, Belvaux, Luxembourg.
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15
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Shioda S, Kasai F, Watanabe K, Kawakami K, Ohtani A, Iemura M, Ozawa M, Arakawa A, Hirayama N, Kawaguchi E, Tano T, Miyata S, Satoh M, Shimizu N, Kohara A. Screening for 15 pathogenic viruses in human cell lines registered at the JCRB Cell Bank: characterization of in vitro human cells by viral infection. ROYAL SOCIETY OPEN SCIENCE 2018; 5:172472. [PMID: 29892436 PMCID: PMC5990783 DOI: 10.1098/rsos.172472] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 03/23/2018] [Indexed: 05/04/2023]
Abstract
Human cell lines have been used in a variety of research fields as an in vitro model. These cells are all derived from human tissue samples, thus there is a possibility of virus infection. Virus tests are routinely performed in clinical practice, but are limited in cell lines. In this study, we investigated 15 kinds of viruses in 844 human cell lines registered at the Japanese Collection of Research Bioresources (JCRB) Cell Bank. Our real-time PCR analysis revealed that six viruses, EBV, HTLV-1, HBV, B19V, HHV-6 and HHV-7, were detected in 43 cell lines. Of them, 20 cell lines were transformed by intentional infection in vitro with EBV or HTLV-1. Viruses in the other 23 cell lines and one EBV transformed cell line are derived from an in vivo infection, including five de novo identifications of EBV, B19V or HHV-7 carriers. Among them, 17 cell lines were established from patients diagnosed with virus-associated diseases. However, the other seven cell lines originated from in vivo cells unrelated to disease or cellular tropism. Our approach to screen for a set of 15 viruses in each cell line has worked efficiently to identify these rare cases. Virus tests in cell lines contribute not only to safety assessments but also to investigation of in vivo viral infection which can be a characteristic feature of cell lines.
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Affiliation(s)
- Setsuko Shioda
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Author for correspondence: Fumio Kasai e-mail:
| | - Ken Watanabe
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kohei Kawakami
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Azusa Ohtani
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Masashi Iemura
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Midori Ozawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Akemi Arakawa
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Noriko Hirayama
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Eiko Kawaguchi
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Tomoko Tano
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Sayaka Miyata
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Motonobu Satoh
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Norio Shimizu
- Department of Virology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Arihiro Kohara
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
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16
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Xenotropic Murine Leukemia Virus-Related Virus (XMRV) and the Safety of the Blood Supply. Clin Microbiol Rev 2017; 29:749-57. [PMID: 27358491 DOI: 10.1128/cmr.00086-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2006, a new virus, xenotropic murine leukemia virus-related virus (XMRV), was discovered in a cohort of U.S. men with prostate cancer. Soon after this initial finding, XMRV was also detected in samples from patients with chronic fatigue syndrome (CFS). The blood community, which is highly sensitive to the threat of emerging infectious diseases since the HIV/AIDS crisis, recommended indefinite deferral of all blood donors with a history of CFS. As XMRV research progressed, conflicting results emerged regarding the importance of this virus in the pathophysiology of prostate cancer and/or CFS. Molecular biologists traced the development of XMRV to a recombination event in a laboratory mouse that likely occurred circa 1993. The virus was propagated via cell lines derived from a tumor present in this mouse and spread through contamination of laboratory samples. Well-controlled experiments showed that detection of XMRV was due to contaminated samples and was not a marker of or a causal factor in prostate cancer or CFS. This paper traces the development of XMRV in the prostate and CFS scientific communities and explores the effect it had on the blood community.
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