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Driedonks TAP, Nyberg LH, Conte A, Ma Z, Pekosz A, Duban E, Tonevitsky A, Sültmann H, Turchinovich A, Witwer KW. Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs. Heliyon 2024; 10:e24570. [PMID: 38314306 PMCID: PMC10837498 DOI: 10.1016/j.heliyon.2024.e24570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024] Open
Abstract
RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs generated from SARS-CoV-1 and SARS-CoV-2 genomic RNAs remained largely unexplored, possibly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA sequencing datasets, we observed that human Calu-3 cells infected by SARS-CoV-1 or SARS-CoV-2 accumulate multiple previously unreported short viral RNAs. In addition, we verified the presence of the five most abundant SARS-CoV-2 short viral RNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by quantitative PCR. Interestingly, the copy number of the observed SARS-CoV-2 short viral RNAs dramatically exceeded the expression of previously reported viral microRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 short viral RNAs could serve as biomarkers for early infection stages due to their high abundance. Furthermore, unlike SARS-CoV-1, the SARS-CoV-2 infection induced significant (Benjamini-Hochberg-corrected p-value <0.05) deregulation of Y-RNA, transfer RNA, vault RNA, as well as more than 300 endogenous short RNAs that aligned predominantly to human protein-coding and long noncoding RNA transcripts. In particular, more than 20-fold upregulation of reads derived from Y-RNA (and several transfer RNAs) have been documented in RNA-seq datasets from SARS-CoV-2 infected cells. Finally, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various human genome (hg38) sequences, suggesting opportunities to investigate regulatory roles of short viral RNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.
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Affiliation(s)
- Tom A P Driedonks
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lyle H Nyberg
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zexu Ma
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Heidelberg Biolabs GmbH, Heidelberg, Germany
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Heidelberg University, Heidelberg/Mannheim, Germany
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Ağın F, Doğan İS. Voltammetric Methods Used in the Determination of Nucleoside Reverse Transcriptase Inhibitors. CURR PHARM ANAL 2021. [DOI: 10.2174/1573412916999200519141257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background:
The Human Immunodeficiency Virus (HIV) has now been established as the
causative agent of the Acquired Immunodeficiency Syndrome (AIDS) and exactly 25 antiretroviral
drugs have been formally approved for clinical use in the treatment of AIDS. The life quality and duration
of HIV-positive patients have increased with the usage of antiretroviral drugs in the treatment of
AIDS. Nucleoside Reverse Transcriptase Inhibitors (NRTIs) are one of the subgroups of antiretroviral.
Objective:
The quantification of drugs is important, as they make positive contributions to dose adjustments
in practice. Voltammetric methods are very powerful analytical methods used in the pharmaceutical
industry because of the determination of therapeutic agents and/or their metabolites in clinical
samples at extremely low concentrations (10-50 ng/ml).
Methods:
This review mainly includes the pharmacological properties and recent determination studies
by voltammetric methods from pharmaceutical dosage forms and biological samples of eight NRTIs
group antiretroviral drugs (zidovudine, abacavir, adefovir, entecavir, zalcitabine, didanosine, emtricitabine,
lamivudine) that are used in the clinic and show electroactive properties, were performed.
Conclusion:
Due to the variety of working electrodes in voltammetric methods, it is possible to choose
the electrode that best responds. In this way, the analysis of NRTIs was possible at lower concentrations
in pharmaceuticals and biological samples with voltammetric methods in these studies without
the necessity for the sample pre-treatment or time-consuming extraction steps. The voltammetric methods
provide good stability, repeatability, reproducibility and high recovery for the analysis of the analyte.
They could be used for the pharmacokinetic studies as well as for quality control laboratory studies.
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Affiliation(s)
- Fatma Ağın
- Department of Analytical Chemistry, Faculty of Pharmacy, Karadeniz Technical University, Trabzon,Turkey
| | - İnci Selin Doğan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Karadeniz Technical University, Trabzon,Turkey
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Panova V, Attig J, Young GR, Stoye JP, Kassiotis G. Antibody-induced internalisation of retroviral envelope glycoproteins is a signal initiation event. PLoS Pathog 2020; 16:e1008605. [PMID: 32453763 PMCID: PMC7274472 DOI: 10.1371/journal.ppat.1008605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/05/2020] [Accepted: 05/05/2020] [Indexed: 12/31/2022] Open
Abstract
As obligate parasites, viruses highjack, modify and repurpose the cellular machinery for their own replication. Viral proteins have, therefore, evolved biological functions, such as signalling potential, that alter host cell physiology in ways that are still incompletely understood. Retroviral envelope glycoproteins interact with several host proteins, extracellularly with their cellular receptor and anti-envelope antibodies, and intracellularly with proteins of the cytoskeleton or sorting, endocytosis and recirculation pathways. Here, we examined the impact of endogenous retroviral envelope glycoprotein expression and interaction with host proteins, particularly antibodies, on the cell, independently of retroviral infection. We found that in the commonly used C57BL/6 substrains of mice, where murine leukaemia virus (MLV) envelope glycoproteins are expressed by several endogenous MLV proviruses, the highest expressed MLV envelope glycoprotein is under the control of an immune-responsive cellular promoter, thus linking MLV envelope glycoprotein expression with immune activation. We further showed that antibody ligation induces extensive internalisation from the plasma membrane into endocytic compartments of MLV envelope glycoproteins, which are not normally subject to constitutive endocytosis. Importantly, antibody binding and internalisation of MLV envelope glycoproteins initiates signalling cascades in envelope-expressing murine lymphocytic cell lines, leading to cellular activation. Similar effects were observed by MLV envelope glycoprotein ligation by its cellular receptor mCAT-1, and by overexpression in human lymphocytic cells, where it required an intact tyrosine-based YXXΦ motif in the envelope glycoprotein cytoplasmic tail. Together, these results suggest that signalling potential is a general property of retroviral envelope glycoproteins and, therefore, a target for intervention. The outcome of viral infection depends on the balance between host immunity and the ability of the virus to avoid, evade or subvert it. The envelope glycoproteins of diverse viruses, including retroviruses, are displayed on the surface of virions and of infected cells and thus constitute the major target of the host antibody response. Antibody responses are elicited not only against infectious viruses we acquire during our life-history, but also against the numerous retroviral envelopes encoded by our genome and acquired during our species’ life-history. In turn, viruses have evolved ways to reduce exposure of their envelope glycoproteins to the host immune system, including constitutive endocytosis or antibody-induced internalisation. Using murine leukaemia viruses as models of infectious and endogenous retroviruses, we show that antibody binding to retroviral envelopes induces extensive internalisation of the envelope-antibody complex and initiates signalling cascades, ultimately leading to transcriptional activation of envelope glycoprotein-expressing lymphocytes. We further show that expression of endogenous retroviral envelopes is coupled to physiological lymphocyte activation, integrating them with the immune response. These findings reveal an unexpected layer of interaction between the host antibody response and retroviral envelope glycoproteins, which could be considered immune receptors.
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Affiliation(s)
- Veera Panova
- Retroviral Immunology, The Francis Crick Institute, United Kingdom
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, United Kingdom
| | - George R. Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom
- Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, United Kingdom
- Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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Talotta R, Atzeni F, Laska MJ. The contribution of HERV-E clone 4-1 and other HERV-E members to the pathogenesis of rheumatic autoimmune diseases. APMIS 2020; 128:367-377. [PMID: 32202683 DOI: 10.1111/apm.13039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/26/2020] [Indexed: 12/16/2022]
Abstract
Human endogenous retroviruses (HERV)-E consist of a family of more than 1300 elements, stably integrated in the human genome. Some of them are full-length proviruses able to synthesize the viral proteins gag, pol and env. The reactivation of HERV-E elements has been associated to placentation, cancer and autoimmunity. In this narrative review, we aimed to report the status of the art concerning the involvement of HERV-E in rheumatic autoimmune diseases. Following a research on PubMed database, a total of 87 articles were selected. The highest amount of evidence derives from studies on systemic lupus erythematosus (SLE), whereas a few to no data are available on other immune-mediated diseases. In SLE, the hyper-expression of HERV-E clone 4-1 in peripheral blood mononuclear cells or differentiated lymphocytes has been associated with disease activity and autoantibody production. It is likely that HERV-E take part to the pathogenesis of rheumatic autoimmune diseases but additional research is needed.
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Affiliation(s)
- Rossella Talotta
- Department of Clinical and Experimental Medicine, Rheumatology Unit, University of Messina, Azienda Ospedaliera "Gaetano Martino", Messina, Italy
| | - Fabiola Atzeni
- Department of Clinical and Experimental Medicine, Rheumatology Unit, University of Messina, Azienda Ospedaliera "Gaetano Martino", Messina, Italy
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Duroy PO, Bosshard S, Schmid-Siegert E, Neuenschwander S, Arib G, Lemercier P, Masternak J, Roesch L, Buron F, Girod PA, Xenarios I, Mermod N. Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. Biotechnol Bioeng 2019; 117:466-485. [PMID: 31631325 PMCID: PMC7003738 DOI: 10.1002/bit.27200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/10/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022]
Abstract
The Chinese hamster ovary (CHO) cells used to produce biopharmaceutical proteins are known to contain type‐C endogenous retrovirus (ERV) sequences in their genome and to release retroviral‐like particles. Although evidence for their infectivity is missing, this has raised safety concerns. As the genomic origin of these particles remained unclear, we characterized type‐C ERV elements at the genome, transcriptome, and viral particle RNA levels. We identified 173 type‐C ERV sequences clustering into three functionally conserved groups. Transcripts from one type‐C ERV group were full‐length, with intact open reading frames, and cognate viral genome RNA was loaded into retroviral‐like particles, suggesting that this ERV group may produce functional viruses. CRISPR‐Cas9 genome editing was used to disrupt the gag gene of the expressed type‐C ERV group. Comparison of CRISPR‐derived mutations at the DNA and RNA level led to the identification of a single ERV as the main source of the release of RNA‐loaded viral particles. Clones bearing a Gag loss‐of‐function mutation in this ERV showed a reduction of RNA‐containing viral particle release down to detection limits, without compromising cell growth or therapeutic protein production. Overall, our study provides a strategy to mitigate potential viral particle contaminations resulting from ERVs during biopharmaceutical manufacturing.
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Affiliation(s)
- Pierre-Olivier Duroy
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Present address: Selexis SA, Plan-les-Ouates, Switzerland
| | - Sandra Bosshard
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Present address: Lonza AG, Visp, Switzerland
| | | | | | | | - Philippe Lemercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Jacqueline Masternak
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Lucien Roesch
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Flavien Buron
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Ioannis Xenarios
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Present address: Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology and Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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6
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Chan SM, Sapir T, Park SS, Rual JF, Contreras-Galindo R, Reiner O, Markovitz DM. The HERV-K accessory protein Np9 controls viability and migration of teratocarcinoma cells. PLoS One 2019; 14:e0212970. [PMID: 30818388 PMCID: PMC6394991 DOI: 10.1371/journal.pone.0212970] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/12/2019] [Indexed: 11/19/2022] Open
Abstract
Human endogenous retroviruses are remnants of ancient germline infections that make up approximately 8% of the modern human genome. The HERV-K (HML-2) family is one of the most recent entrants into the human germline, these viruses appear to be transcriptionally active, and HERV-K viral like particles (VLPs) are found in cell lines from a number of human malignancies. HERV-K VLPs were first found to be produced in teratocarcinoma cell lines, and since then teratocarcinoma has been thought of as the classical model for HERV-Ks, with the NCCIT teratocarcinoma cell line particularly known to produce VLPs. Treatment for teratocarcinoma has progressed since its discovery, with improved prognosis for patients. Since the introduction of platinum based therapy, first year survival has greatly improved even with disseminated disease; however, it is estimated that 20% to 30% of patients present with metastatic germ cell tumor relapse following initial treatments. Also, the toxicity associated with the use of chemotherapeutic agents used to treat germ cell tumors is still a major concern. In this study, we show that the depletion of the HERV-K accessory protein Np9 increases the sensitivity of NCCIT teratocarcinoma cells to bleomycin and cisplatin. While decreasing the expression of Np9 had only a modest effect on the baseline viability of the cells, the reduced expression of Np9 increased the sensitivity of the teratocarcinoma cells to environmental (serum starvation) and chemical (chemotherapeutic) stresses. Np9 is also essential to the migration of NCCIT teratocarcinoma cells: in a wound closure assay, reduced expression of Np9 resulted in cells migrating into the wound at a slower rate, whereas reintroduction of Np9 resulted in NCCIT cells migrating back into the wound in a manner similar to the control. These findings support the implication that the HERV-K accessory protein Np9 has oncogenic potential.
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Affiliation(s)
- Susana M. Chan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sung-Soo Park
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jean-François Rual
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Rafael Contreras-Galindo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - David M. Markovitz
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- Cancer Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
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7
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Zare M, Mostafaei S, Ahmadi A, Azimzadeh Jamalkandi S, Abedini A, Esfahani-Monfared Z, Dorostkar R, Saadati M. Human endogenous retrovirus env genes: Potential blood biomarkers in lung cancer. Microb Pathog 2018; 115:189-193. [DOI: 10.1016/j.micpath.2017.12.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 02/07/2023]
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Absence of Replication-Competent Lentivirus in the Clinic: Analysis of Infused T Cell Products. Mol Ther 2017; 26:280-288. [PMID: 28970045 DOI: 10.1016/j.ymthe.2017.09.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 11/23/2022] Open
Abstract
Exposure to replication-competent lentivirus (RCL) is a theoretical safety concern for individuals treated with lentiviral gene therapy. For certain ex vivo gene therapy applications, including cancer immunotherapy trials, RCL detection assays are used to screen the vector product as well as the vector-transduced cells. In this study, we reviewed T cell products screened for RCL using methodology developed in the National Gene Vector Biorepository. All trials utilized third-generation lentiviral vectors produced by transient transfection. Samples from 26 clinical trials totaling 460 transduced cell products from 375 subjects were evaluated. All cell products were negative for RCL. A total of 296 of the clinical trial participants were screened for RCL at least 1 month after infusion of the cell product. No research subject has shown evidence of RCL infection. These findings provide further evidence attesting to the safety of third-generation lentiviral vectors and that testing T cell products for RCL does not provide added value to screening the lentiviral vector product.
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Bergallo M, Montanari P, Mareschi K, Merlino C, Berger M, Bini I, Daprà V, Galliano I, Fagioli F. Expression of the pol gene of human endogenous retroviruses HERV-K and -W in leukemia patients. Arch Virol 2017; 162:3639-3644. [DOI: 10.1007/s00705-017-3526-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/16/2017] [Indexed: 11/30/2022]
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Human endogenous retroviruses and chosen disease parameters in morphea. Postepy Dermatol Alergol 2017; 34:47-51. [PMID: 28261031 PMCID: PMC5329106 DOI: 10.5114/ada.2017.65621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/10/2016] [Indexed: 11/30/2022] Open
Abstract
Introduction Morphea (localized scleroderma) is a relatively rare disease characterized by excessive skin fibrosis. Human endogenous retroviruses (HERV) are largely distributed within the human genome with hundreds of thousands of elements. The HERV have been widely studied in autoimmune disorders, yet hardly ever assessed in diseases with a good prognosis such as morphea. Aim In this study we focus on the possible relations between the expression of chosen HERV and factors influencing the pathomechanism of the disease, such as age, sex, titres of anti-nuclear antibodies, as well as duration, activity, and severity of the disease (LoSSI index). Material and methods Real-time polymerase chain reaction (PCR) targeting six HERV sequences of interest were performed on samples derived from peripheral blood mononuclear cells (PBMC) and skin biopsies. Results In PBMC we found a statistically significant negative correlation between HERV-W env expression and LoSSI index (p = 0.01). Additionally, HERV-W env was downregulated in patients with the active form of morphea. In all other cases we found no correlation whatsoever nor statistically significant differences below the p = 0.05 threshold. Conclusions Morphea seems to be an autoimmune disease where the impact of HERV is not so apparent. It seems that probing many patients for the expression of just a few sequences is not as effective as previously expected. For initial studies of HERV in other diseases we recommend high throughput techniques such as HERV-dedicated DNA microarrays or massive parallel sequencing.
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Kowalczyk MJ, Teresiak-Mikołajczak E, Dańczak-Pazdrowska A, Żaba R, Adamski Z, Osmola-Mańkowska A. Effects of UVA1 Phototherapy on Expression of Human Endogenous Retroviral Sequence (HERV)-K10 gag in Morphea: A Preliminary Study. Med Sci Monit 2017; 23:505-512. [PMID: 28130554 PMCID: PMC5292988 DOI: 10.12659/msm.897985] [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] [Indexed: 11/23/2022] Open
Abstract
Background Morphea, also known as localized scleroderma, is a rare autoimmune connective tissue disease characterized by skin fibrosis. UVA1 phototherapy is an important asset in the reduction of clinical manifestations in morphea. There are studies claiming that UV light modulates the expression of some human endogenous retroviral sequences. The aim of this study was to determine if the expression of HERV-K10 gag element is lowered by UVA1 phototherapy in morphea, a disease in which such irradiation has a soothing effect. Material/Methods The expression levels of the HERV-K10 gag were assessed by real-time PCR (polymerase chain reaction) in peripheral blood mononuclear cells (PBMC) and skin-punch biopsies of healthy volunteers and 9 morphea patients before and after phototherapy. Additionally, correlations between the HERV-K10 gag expression and age, disease duration, the Localized Scleroderma Skin Severity Index (LoSSI), and antinuclear antibody (ANA) titers were assessed. Results In PBMC, HERV-K10 gag mRNA was significantly elevated after UVA1 phototherapy compared to healthy controls. Most of the patients responded with an increased expression level of this sequence. However, we found no statistical evidence at this point that phototherapy indeed has an effect on the HERV-K10 gag expression (there were no statistical differences in PBMC of morphea patients before and after phototherapy). Similarly, there was no statistically relevant effect of the UVA1 on the expression of HERV-K10 gag in skin. Conclusions At this point, the effect of UVA1 phototherapy on the expression of HERV-K10 gag cannot be statistically confirmed.
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Affiliation(s)
- Michał Jacek Kowalczyk
- Department of Dermatology and Venereology, Psoriasis and Novel Therapies in Dermatology Unit, Poznań University of Medical Sciences, Poznań, Poland
| | | | | | - Ryszard Żaba
- Department of Dermatology and Venereology, Psoriasis and Novel Therapies in Dermatology Unit, Poznań University of Medical Sciences, Poznań, Poland
| | - Zygmunt Adamski
- Department of Dermatology, Poznań University of Medical Sciences, Poznań, Poland
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She Z, Topping K, Dong B, Shamsi MH, Kraatz HB. An unexpected use of ferrocene. A scanning electrochemical microscopy study of a toll-like receptor array and its interaction with E. coli. Chem Commun (Camb) 2017; 53:2946-2949. [DOI: 10.1039/c7cc00863e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Toll-like receptor microarrays were investigated by scanning electrochemical microscopy with enhanced contrast from using ferrocene derivatives.
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Affiliation(s)
- Zhe She
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto
- Canada
- Department of Chemistry and Chemical Engineering
| | - Kristin Topping
- Department of Chemistry and Chemical Engineering
- Royal Military College of Canada
- Kingston
- Canada
| | - Bin Dong
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto
- Canada
- Department of Chemistry and Chemical Engineering
| | - Mohtashim H. Shamsi
- Department of Chemistry
- Toronto
- Canada
- Department of Chemistry and Biochemistry
- Southern Illinois University Carbondale Neckers
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences
- University of Toronto Scarborough
- Toronto
- Canada
- Department of Chemistry and Chemical Engineering
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Hsu K, Lee YK, Chew A, Chiu S, Lim D, Greenhalgh DG, Cho K. Inherently variable responses to glucocorticoid stress among endogenous retroviruses isolated from 23 mouse strains. Biochim Biophys Acta Mol Basis Dis 2016; 1863:2594-2600. [PMID: 27816520 DOI: 10.1016/j.bbadis.2016.10.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/28/2016] [Accepted: 10/27/2016] [Indexed: 10/20/2022]
Abstract
Active participation of endogenous retroviruses (ERVs) in disease processes has been exemplified by the finding that the HERV (human ERV)-W envelope protein is involved in the pathogenesis of multiple sclerosis, an autoimmune disease. We also demonstrated that injury-elicited stressors alter the expression of murine ERVs (MuERVs), both murine leukemia virus-type and mouse mammary tumor virus (MMTV)-type (MMTV-MuERV). In this study, to evaluate MMTV-MuERVs' responses to stress (e.g., injury, infection)-elicited systemic glucocorticoid (GC) levels, we examined the GC-stress response of 64 MMTV-MuERV promoters isolated from the genomes of 23 mouse strains. All 64 promoters responded to treatment with a synthetic GC, dexamethasone (DEX), at a wide range from a 0.6- to 85.7-fold increase in reporter activity compared to no treatment. An analysis of the 10 lowest and 10 highest DEX responders revealed specific promoter elements exclusively present in either the three lowest or the two highest responders. Each promoter had a unique profile of transcription regulatory elements and the glucocorticoid response element (GRE) was identified in all promoters with the number of GREs ranging from 2 to 7. The three lowest DEX responders were the only promoters with two GREs. The findings from this study suggest that certain MMTV-MuERVs are more responsive to stress-elicited systemic GC elevation compared to the others. The mouse strain-specific genomic MMTV-MuERV profiles and individual MMTV-MuERVs' differential responses to GC-stress might explain, at least in part, the variable inflammatory responses to injury and/or infection, often observed among different mouse strains. This article is part of a Special Issue entitled: Immune and Metabolic Alterations in Trauma and Sepsis edited by Dr. Raghavan Raju.
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Affiliation(s)
- Karen Hsu
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Young-Kwan Lee
- Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Alex Chew
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Sophia Chiu
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA
| | - Debora Lim
- Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - David G Greenhalgh
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA
| | - Kiho Cho
- Burn Research, Shriners Hospitals for Children Northern California, Davis, Sacramento, CA 95817, USA; Department of Surgery, University of California, Davis, Sacramento, CA 95817, USA.
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Schütz E, Wehrhahn C, Wanjek M, Bortfeld R, Wemheuer WE, Beck J, Brenig B. The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TBF1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB. PLoS One 2016; 11:e0154602. [PMID: 27128314 PMCID: PMC4851415 DOI: 10.1371/journal.pone.0154602] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 04/17/2016] [Indexed: 12/17/2022] Open
Abstract
Background With the availability of massive SNP data for several economically important cattle breeds, haplotype tests have been performed to identify unknown recessive disorders. A number of so-called lethal haplotypes, have been uncovered in Holstein Friesian cattle and, for at least seven of these, the causative mutations have been identified in candidate genes. However, several lethal haplotypes still remain elusive. Here we report the molecular genetic causes of lethal haplotype 5 (HH5) and cholesterol deficiency (CDH). A targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used to interrogate for causative mutations in a case/control approach. Methods Targeted enrichment for the known genomic regions, followed by massive parallel sequencing was used in a case/control approach. PCRs for the causing mutations were developed and compared to routine imputing in 2,100 (HH5) and 3,100 (CDH) cattle. Results HH5 is caused by a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event. TFB1M di-methylates adenine residues in the hairpin loop at the 3’-end of mitochondrial 12S rRNA, being essential for synthesis and function of the small ribosomal subunit of mitochondria. Homozygous TFB1M-/- mice reportedly exhibit embryonal lethality with developmental defects. A 2.8% allelic frequency was determined for the German HF population. CDH results from a 1.3kbp insertion of an endogenous retrovirus (ERV2-1-LTR_BT) into exon 5 of the APOB gene at BTA11:77,959kb. The insertion is flanked by 6bp target site duplications as described for insertions mediated by retroviral integrases. A premature stop codon in the open reading frame of APOB is generated, resulting in a truncation of the protein to a length of only <140 amino acids. Such early truncations have been shown to cause an inability of chylomicron excretion from intestinal cells, resulting in malabsorption of cholesterol. The allelic frequency of this mutation in the German HF population was 6.7%, which is substantially higher than reported so far. Compared to PCR assays inferring the genetic variants directly, the routine imputing used so far showed a diagnostic sensitivity of as low as 91% (HH5) and 88% (CDH), with a high specificity for both (≥99.7%). Conclusion With the availability of direct genetic tests it will now be possible to more effectively reduce the carrier frequency and ultimately eliminate the disorders from the HF populations. Beside this, the fact that repetitive genomic elements (RE) are involved in both diseases, underline the evolutionary importance of RE, which can be detrimental as here, but also advantageous over generations.
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Affiliation(s)
- Ekkehard Schütz
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Göttingen, Germany
- Chronix Biomedical GmbH, Göttingen, Germany
- * E-mail:
| | - Christin Wehrhahn
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Göttingen, Germany
| | - Marius Wanjek
- Institute for Livestock Reproduction GmbH, Schönow, Germany
| | - Ralf Bortfeld
- Institute for Livestock Reproduction GmbH, Schönow, Germany
| | - Wilhelm E. Wemheuer
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Göttingen, Germany
| | - Julia Beck
- Chronix Biomedical GmbH, Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, Georg-August-University Göttingen, Göttingen, Germany
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Kong W, Li Y, Cheng S, Yan C, An S, Dong Z, Yan L, Yuan Y. Luminex xMAP combined with Western blot improves HIV diagnostic sensitivity. J Virol Methods 2015; 227:1-5. [PMID: 26500038 DOI: 10.1016/j.jviromet.2015.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 11/28/2022]
Abstract
Currently, Western blot is used to confirm the initial serodiagnosis of HIV infection by antibody detection. However, a major deficiency of the Western blot relates to a lack of sufficient sensitivity in detecting HIV antibodies. This report describes a simple, sensitive and inexpensive bead-based assay for detection of early HIV infection. A panel of 138 positive specimens including 105 blood donors and 33 MSM with known Western blot results were evaluated using Luminex xMAP at Tianjin Centers for Disease Control and Prevention (CDC). We demonstrate a superior sensitivity of Luminex xMAP compared with Western blot. Of the 87 confirmed HIV positive blood donors, Western blot only confirmed 65 cases with 74.7% (65/87) sensitivity while Luminex xMAP identified 72 cases with 82.8% (72/87) sensitivity (p<0.05). Western blot and Luminex xMAP verified 13 and 19 of 33 MSM specimens, respectively. The sensitivity was 39.4% (13/33) for Western blot and 57.6% (19/33) for Luminex xMAP (p<0.1). Luminex xMAP combined with Western blot improves the diagnostic sensitivity of HIV infection at an early stage, and reduces the chances of missed diagnosis.
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Affiliation(s)
- Weiwei Kong
- School of Basic Medicine Sciences, Tianjin Medical University, Tianjin 300000, China
| | - Yan Li
- Tianjin Blood Center, Tianjin 300000, China
| | - Shaohui Cheng
- Tianjin Center for AIDS/STD Control and Prevention, Tianjin Centers For Disease Control and Prevention, Tianjin 300000, China
| | - Chen Yan
- School of Basic Medicine Sciences, Tianjin Medical University, Tianjin 300000, China
| | - Shiping An
- Tianjin Blood Center, Tianjin 300000, China
| | - Zheng Dong
- Tianjin Blood Center, Tianjin 300000, China
| | - Lina Yan
- Tianjin Blood Center, Tianjin 300000, China
| | - Yuhua Yuan
- Clinical Laboratory Diagnostics, General Hospital of Tianjin Medical University, Tianjin 30000, China.
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Abstract
Inflammatory responses are essential for the clearance of pathogens and the repair of injured tissues; however, if these responses are not properly controlled chronic inflammation can occur. Chronic inflammation is now recognized as a contributing factor to many age-associated diseases including metabolic disorders, arthritis, neurodegeneration, and cardiovascular disease. Due to the connection between chronic inflammation and these diseases, it is essential to understand underlying mechanisms behind this process. In this review, factors that contribute to chronic inflammation are discussed. Further, we emphasize the emerging roles of microRNAs (miRNAs) and other noncoding RNAs (ncRNA) in regulating chronic inflammatory states, making them important future diagnostic markers and therapeutic targets.
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Affiliation(s)
- Margaret Alexander
- Department of Pathology, Division of Microbiology and ImmunologyUniversity of UtahSalt Lake CityUTUSA
| | - Ryan M. O'Connell
- Department of Pathology, Division of Microbiology and ImmunologyUniversity of UtahSalt Lake CityUTUSA
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17
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Gim JA, Han K, Kim HS. Identification and expression analysis of human endogenous retrovirus Y (HERV-Y) in various human tissues. Arch Virol 2015; 160:2161-8. [PMID: 26088444 DOI: 10.1007/s00705-015-2486-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 06/07/2015] [Indexed: 11/29/2022]
Abstract
Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome. To date, several HERV families have been identified in the human genome, with some being valid biomarkers for specific disease states. In this study, we have identified three HERV-Y elements in the human genome and characterized their structure and expression in various human tissues. New HERV-Y elements (HERV-Y101, HERV-Y102, and HERV-Y103) were detected on human chromosomes 8 and 13. In a pol-based phylogenetic tree, HERV-Y elements were closely grouped with HERV-I, -T, -E, and -R. The HERV-Y pol gene was expressed ubiquitously in all examined tissues, and it was dominantly expressed in the pons among the 12 different brain regions investigated. These results will allow future studies to elucidate the potential functional roles of HERVs in the brain and other tissues.
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Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 609-735, Republic of Korea
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The placental protein syncytin-1 impairs antiviral responses and exaggerates inflammatory responses to influenza. PLoS One 2015; 10:e0118629. [PMID: 25831059 PMCID: PMC4382184 DOI: 10.1371/journal.pone.0118629] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/21/2015] [Indexed: 12/22/2022] Open
Abstract
Background Pregnancy increases susceptibility to influenza. The placenta releases an immunosuppressive endogenous retroviral protein syncytin-1. We hypothesised that exposure of peripheral monocytes (PBMCs) to syncytin-1 would impair responses to H1N1pdm09 influenza. Methods and Findings Recombinant syncytin-1 was produced. PBMCs from non-pregnant women (n=10) were exposed to H1N1pdm09 in the presence and absence of syncytin-1 and compared to responses of PBMCs from pregnant women (n=12). PBMCs were characterised using flow cytometry, release of interferon (IFN)-α, IFN-λ, IFN-γ, IL-10, IL-2, IL-6 and IL-1β were measured by cytometric bead array or ELISA. Exposure of PBMCs to H1N1pdm09 resulted in the release of IFN-α, (14,787 pg/mL, 95% CI 7311-22,264 pg/mL) IFN-λ (1486 pg/mL, 95% CI 756-2216 pg/mL) and IFN-γ (852 pg/mL, 95% CI 193-1511 pg/mL) after 48 hours. This was significantly impaired in pregnant women (IFN-α; p<0.0001 and IFN-λ; p<0.001). Furthermore, in the presence of syncytin-1, PBMCs demonstrated marked reductions in IFN-α and IFN-λ, while enhanced release of IL-10 as well as IL-6 and IL-1β. Conclusions Our data indicates that a placental derived protein, syncytin-1 may be responsible for the heightened vulnerability of pregnant women to influenza.
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Downey RF, Sullivan FJ, Wang-Johanning F, Ambs S, Giles FJ, Glynn SA. Human endogenous retrovirus K and cancer: Innocent bystander or tumorigenic accomplice? Int J Cancer 2014; 137:1249-57. [PMID: 24890612 PMCID: PMC6264888 DOI: 10.1002/ijc.29003] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 05/02/2014] [Accepted: 05/09/2014] [Indexed: 12/20/2022]
Abstract
Harbored as relics of ancient germline infections, human endogenous retroviruses (HERVs) now constitute up to 8% of our genome. A proportion of this sequence has been co-opted for molecular and cellular processes, beneficial to human physiology, such as the fusogenic activity of the envelope protein, a vital component of placentogenesis. However, the discovery of high levels of HERV-K mRNA and protein and even virions in a wide array of cancers has revealed that HERV-K may be playing a more sinister role–a role as an etiological agent in cancer itself. Whether the presence of this retroviral material is simply an epiphenomenon, or an actual causative factor, is a hotly debated topic. This review will summarize the current state of knowledge regarding HERV-K and cancer and attempt to outline the potential mechanisms by which HERV-K could be involved in the onset and promotion of carcinogenesis.
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Affiliation(s)
- Ronan F Downey
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland
| | - Francis J Sullivan
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland.,Department of Radiation Oncology, Galway University Hospitals, Galway, Ireland
| | | | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD
| | - Francis J Giles
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland.,HRB Clinical Research Facilities Galway & Dublin, National University of Ireland Galway and Trinity College Dublin, Galway, Ireland
| | - Sharon A Glynn
- Prostate Cancer Institute, National University of Ireland Galway, Galway, Ireland
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Burns G, Brooks K, Wildung M, Navakanitworakul R, Christenson LK, Spencer TE. Extracellular vesicles in luminal fluid of the ovine uterus. PLoS One 2014; 9:e90913. [PMID: 24614226 PMCID: PMC3948691 DOI: 10.1371/journal.pone.0090913] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 02/05/2014] [Indexed: 01/15/2023] Open
Abstract
Microvesicles and exosomes are nanoparticles released from cells and can contain small RNAs, mRNA and proteins that affect cells at distant sites. In sheep, endogenous beta retroviruses (enJSRVs) are expressed in the endometrial epithelia of the uterus and can be transferred to the conceptus trophectoderm. One potential mechanism of enJSRVs transfer from the uterus to the conceptus is via exosomes/microvesicles. Therefore, studies were conducted to evaluate exosomes in the uterine luminal fluid (ULF) of sheep. Exosomes/microvesicles (hereafter referred to as extracellular vesicles) were isolated from the ULF of day 14 cyclic and pregnant ewes using ExoQuick-TC. Transmission electron microscopy and nanoparticle tracking analysis found the isolates contained vesicles that ranged from 50 to 200 nm in diameter. The isolated extracellular vesicles were positive for two common markers of exosomes (CD63 and HSP70) by Western blot analysis. Proteins in the extracellular vesicles were determined by mass spectrometry and Western blot analysis. Extracellular vesicle RNA was analyzed for small RNAs by sequencing and enJSRVs RNA by RT-PCR. The ULF extracellular vesicles contained a large number of small RNAs and miRNAs including 81 conserved mature miRNAs. Cyclic and pregnant ULF extracellular vesicles contained enJSRVs env and gag RNAs that could be delivered to heterologous cells in vitro. These studies support the hypothesis that ULF extracellular vesicles can deliver enJSRVs RNA to the conceptus, which is important as enJSRVs regulate conceptus trophectoderm development. Importantly, these studies support the idea that extracellular vesicles containing select miRNAs, RNAs and proteins are present in the ULF and likely have a biological role in conceptus-endometrial interactions important for the establishment and maintenance of pregnancy.
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Affiliation(s)
- Gregory Burns
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kelsey Brooks
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
| | - Mark Wildung
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Raphatphorn Navakanitworakul
- Department of Molecular and Integrative Physiology, University of Kansas Medical School, Kansas City, Kansas, United States of America
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, University of Kansas Medical School, Kansas City, Kansas, United States of America
| | - Thomas E Spencer
- Department of Animal Sciences, Washington State University, Pullman, Washington, United States of America
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22
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Chudak C, Beimforde N, George M, Zimmermann A, Lausch V, Hanke K, Bannert N. Identification of late assembly domains of the human endogenous retrovirus-K(HML-2). Retrovirology 2013; 10:140. [PMID: 24252269 PMCID: PMC3874623 DOI: 10.1186/1742-4690-10-140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 11/11/2013] [Indexed: 11/10/2022] Open
Abstract
Background Late assembly (L)-domains are protein interaction motifs, whose dysfunction causes characteristic budding defects in enveloped viruses. Three different amino acid motifs, namely PT/SAP, PPXY and YPXnL have been shown to play a major role in the release of exogenous retroviruses. Although the L-domains of exogenous retroviruses have been studied comprehensively, little is known about these motifs in endogenous human retroviruses. Results Using a molecular clone of the human endogenous retrovirus K113 that had been engineered to reverse the presumed non-synonymous postinsertional mutations in the major genes, we identified three functional L-domains of the virus, all located in the Gag p15 protein. A consensus PTAP tetrapeptide serves as the core of a main L-domain for the virus and its inactivation reduces virus release in HEK 293T cells by over 80%. Electron microscopy of cells expressing the PTAP mutant revealed predominantly late budding structures and budding chains at the plasma membrane. The fact that this motif determines subcellular colocalization with Tsg101, an ESCRT-I complex protein known to bind to the core tetrapeptide, supports its role as an L-domain. Moreover, two YPXnL motifs providing additional L-domain function were identified in the p15 protein. One is adjacent to the PTAP sequence and the other is in the p15 N-terminus. Mutations in either motif diminishes virus release and induces an L-domain phenotype while inactivation of all three L-domains results in a complete loss of particle release in HEK 293T cells. The flexibility of the virus in the use of L-domains for gaining access to the ESCRT machinery is demonstrated by overexpression of Tsg101 which rescues the release of the YPXnL mutants. Similarly, overexpression of Alix not only enhances release of the PTAP mutant by a factor of four but also the release of a triple mutant, indicating that additional cryptic YPXnL domains with a low affinity for Alix may be present. No L-domain activity is provided by the proline-rich peptides at the Gag C-terminus. Conclusions Our data demonstrate that HERV-K(HML-2) release is predominantly mediated through a consensus PTAP motif and two auxiliary YPXnL motifs in the p15 protein of the Gag precursor.
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Affiliation(s)
| | | | | | | | | | | | - Norbert Bannert
- Department for HIV and other Retroviruses, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
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23
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do Olival GS, Faria TS, Nali LHS, de Oliveira ACP, Casseb J, Vidal JE, Cavenaghi VB, Tilbery CP, Moraes L, Fink MCS, Sumita LM, Perron H, Romano CM. Genomic analysis of ERVWE2 locus in patients with multiple sclerosis: absence of genetic association but potential role of human endogenous retrovirus type W elements in molecular mimicry with myelin antigen. Front Microbiol 2013; 4:172. [PMID: 23805135 PMCID: PMC3693062 DOI: 10.3389/fmicb.2013.00172] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/05/2013] [Indexed: 12/11/2022] Open
Abstract
Human endogenous retroviruses (HERVs) arise from ancient infections of the host germline cells by exogenous retroviruses, constituting 8% of the human genome. Elevated level of envelope transcripts from HERVs-W has been detected in CSF, plasma and brain tissues from patients with Multiple Sclerosis (MS), most of them from Xq22.3, 15q21.3, and 6q21 chromosomes. However, since the locus Xq22.3 (ERVWE2) lack the 5' LTR promoter and the putative protein should be truncated due to a stop codon, we investigated the ERVWE2 genomic loci from 84 individuals, including MS patients with active HERV-W expression detected in PBMC. In addition, an automated search for promoter sequences in 20 kb nearby region of ERVWE2 reference sequence was performed. Several putative binding sites for cellular cofactors and enhancers were found, suggesting that transcription may occur via alternative promoters. However, ERVWE2 DNA sequencing of MS and healthy individuals revealed that all of them harbor a stop codon at site 39, undermining the expression of a full-length protein. Finally, since plaque formation in central nervous system (CNS) of MS patients is attributed to immunological mechanisms triggered by autoimmune attack against myelin, we also investigated the level of similarity between envelope protein and myelin oligodendrocyte glycoprotein (MOG). Comparison of the MOG to the envelope identified five retroviral regions similar to the Ig-like domain of MOG. Interestingly, one of them includes T and B cell epitopes, capable to induce T effector functions and circulating Abs in rats. In sum, although no DNA substitutions that would link ERVWE2 to the MS pathogeny was found, the similarity between the envelope protein to MOG extends the idea that ERVEW2 may be involved on the immunopathogenesis of MS, maybe facilitating the MOG recognizing by the immune system. Although awaiting experimental evidences, the data presented here may expand the scope of the endogenous retroviruses involvement on MS pathogenesis.
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Affiliation(s)
- Guilherme S. do Olival
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Thiago S. Faria
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Luiz H. S. Nali
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | | | - Jorge Casseb
- Departamento de Neurologia, Instituto de Infectologia Emilio RibasSão Paulo, Brazil
- Laboratório de Imunodeficiências e Dermatologia, Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Jose E. Vidal
- Departamento de Neurologia, Instituto de Infectologia Emilio RibasSão Paulo, Brazil
| | - Vitor B. Cavenaghi
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Charles P. Tilbery
- Departamento de Neurologia, Irmandade da Santa Casa de Misericórdia de São PauloSão Paulo, Brazil
| | - Lenira Moraes
- Departamento de Neurologia, Hospital das Clínicas da Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Maria C. S. Fink
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | - Laura M. Sumita
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
| | | | - Camila M. Romano
- Departamento de Moléstias Infecciosas e Parasitárias – (LIMHC), Instituto de Medicina Tropical de São Paulo e Faculdade de Medicina, Universidade de São PauloSão Paulo, Brazil
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Retroviruses and amyotrophic lateral sclerosis. Antiviral Res 2013; 99:180-7. [PMID: 23707220 DOI: 10.1016/j.antiviral.2013.05.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 11/20/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, invariably fatal neurologic disorder resulting from upper and lower motor neuron degeneration, which typically develops during the sixth or seventh decade of life, and is diagnosed based on standard clinical criteria. Its underlying cause remains undetermined. The disease may occur with increased frequency within certain families, often in association with specific genomic mutations, while some sporadic cases have been linked to environmental toxins or trauma. Another possibility, first proposed in the 1970s, is that retroviruses play a role in pathogenesis. In this paper, we review the published literature for evidence that ALS is associated either with infection by an exogenous retrovirus or with the expression of human endogenous retroviral (HERV) sequences in cells of the central nervous system. A small percentage of persons infected with the human immunodeficiency virus-1 (HIV-1) or human T cell leukemia virus-1 (HTLV-1) develop ALS-like syndromes. While HTLV-1 associated ALS-like syndrome has several features that may distinguish it from classical ALS, HIV-infected patients may develop neurological manifestations that resemble classical ALS although it occurs at a younger age and they may show a dramatic improvement following the initiation of antiretroviral therapy. However, most patients with probable or definite ALS show no evidence of HIV-1 or HTLV-1 infection. In contrast, recent reports have shown a stronger association with HERV, as analysis of serum samples, and postmortem brain tissue from a number of patients with a classical ALS has revealed significantly increased expression of HERV-K, compared to controls. These findings suggest that endogenous retroviral elements are involved in the pathophysiology of ALS, but there is no evidence that they are the primary cause of the syndrome.
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Manghera M, Douville RN. Endogenous retrovirus-K promoter: a landing strip for inflammatory transcription factors? Retrovirology 2013; 10:16. [PMID: 23394165 PMCID: PMC3598470 DOI: 10.1186/1742-4690-10-16] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 02/01/2013] [Indexed: 12/24/2022] Open
Abstract
Humans are symbiotic organisms; our genome is populated with a substantial number of endogenous retroviruses (ERVs), some remarkably intact, while others are remnants of their former selves. Current research indicates that not all ERVs remain silent passengers within our genomes; re-activation of ERVs is often associated with inflammatory diseases. ERVK is the most recently endogenized and transcriptionally active ERV in humans, and as such may potentially contribute to the pathology of inflammatory disease. Here, we showcase the transcriptional regulation of ERVK. Expression of ERVs is regulated in part by epigenetic mechanisms, but also depends on transcriptional regulatory elements present within retroviral long terminal repeats (LTRs). These LTRs are responsive to both viral and cellular transcription factors; and we are just beginning to appreciate the full complexity of transcription factor interaction with the viral promoter. In this review, an exploration into the inflammatory transcription factor sites within the ERVK LTR will highlight the possible mechanisms by which ERVK is induced in inflammatory diseases.
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Affiliation(s)
- Mamneet Manghera
- Department of Biology, The University of Winnipeg, Winnipeg, MB, Canada
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Pačes J, Huang YT, Pačes V, Rídl J, Chang CM. New insight into transcription of human endogenous retroviral elements. N Biotechnol 2012. [PMID: 23201072 DOI: 10.1016/j.nbt.2012.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
It is generally assumed that human endogenous retroviral elements (HERVs) belong to the class of genomic repetitive nucleotide sequences often called 'junk DNA'. These elements were categorized to families, and members of some of these families (e.g. HERV-H, HERV-W and HERV-K) were shown to be transcribed. These transcriptions were associated with several severe diseases such as mental disorders, AIDS, autoimmune diseases and cancer. In this review we discuss several bioinformatics strategies for genome-wide scan of HERVs transcription using high-throughput RNA sequencing on several platforms. We show that many more HERVs than previously described are transcribed to various levels and we discuss possible implications of these transcriptions.
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Affiliation(s)
- Jan Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, CZ-14220 Prague, Czech Republic.
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Kowalczyk MJ, Dańczak-Pazdrowska A, Szramka-Pawlak B, Zaba R, Silny W, Osmola-Mańkowska A. Expression of selected human endogenous retroviral sequences in skin and peripheral blood mononuclear cells in morphea. Arch Med Sci 2012. [PMID: 23185190 PMCID: PMC3506226 DOI: 10.5114/aoms.2012.30954] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Morphea or localized scleroderma is a relatively rare disease whose main symptom is excessive skin fibrosis. Here we focus on the involvement of human endogenous retroviruses (HERVs) in morphea. The HERVs are a vast and intensely growing field in genomics. HERVs are of special interest as far as autoimmune disorders are concerned, yet little effort has been made until now to assess the possible changes of their expression in morphea. MATERIAL AND METHODS Six sequences of particular interest were chosen for this study. Real-time polymerase chain reaction was performed on samples derived from peripheral blood mononuclear cells (PBMCs) and skin biopsies. The results were normalized to the level of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) transcription. RESULTS In PBMCs we found a statistically significant decrease of transcription of HERV-E pol, while HERV-K env, HERV-R pol-env, and HERV-W env were found to be up-regulated. In skin biopsies HERV-K env was strongly up-regulated. On the other hand, we noted a decrease of transcription of HERV-H env 62, HERV-K10 gag, HERV-R pol-env, and HERV-W env. In PBMCs we found a statistically significant decrease of transcription of HERV-E pol (-81.8%, p < 0.001), while HERV-K env (+94.1%, p = 0.010), HERV-R pol-env (+140.0%, p < 0.001), and HERV-W env (+97.7%, p < 0.001) were found to be up-regulated. In skin biopsies HERV-K env was strongly up-regulated (+713.0%, p = 0.003). On the other hand, we noted a decrease of transcription of HERV-H env 62 (-83.5%, p < 0.001, HERV-K10 gag (-33.7%, p = 0.044), HERV-R pol-env (-71.3%, p < 0.001), and HERV-W env (-59.3%, p = 0.029). CONCLUSIONS The studied HERV sequences generally show an increase of transcription in PBMCs of morphea patients, while being down-regulated in their skin, with some exceptions for both types of tissue.
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Affiliation(s)
- Michał J Kowalczyk
- Department of Dermatology, Poznan University of Medical Sciences, Poland
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Tolosa J, Schjenken J, Clifton V, Vargas A, Barbeau B, Lowry P, Maiti K, Smith R. The endogenous retroviral envelope protein syncytin-1 inhibits LPS/PHA-stimulated cytokine responses in human blood and is sorted into placental exosomes. Placenta 2012; 33:933-41. [DOI: 10.1016/j.placenta.2012.08.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 08/09/2012] [Accepted: 08/27/2012] [Indexed: 12/25/2022]
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Kao D, Hsu K, Chiu S, Tu V, Chew A, Lee KH, Lee YK, Kwon DN, Greenhalgh DG, Cho K. ERE database: a database of genomic maps and biological properties of endogenous retroviral elements in the C57BL/6J mouse genome. Genomics 2012; 100:157-61. [PMID: 22691267 DOI: 10.1016/j.ygeno.2012.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/31/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022]
Abstract
Endogenous retroviral elements (EREs), a family of transposable elements, constitute a substantial fraction of mammalian genomes. It is expected that profiles of the ERE sequences and their genomic locations are unique for each individual. Comprehensive characterization of the EREs' genomic locations and their biological properties is essential for understanding their roles in the pathophysiology of the host. In this study, we identified and mapped putative EREs (a total of 111 endogenous retroviruses [ERVs] and 488 solo long terminal repeats [sLTRs]) within the C57BL/6J mouse genome. The biological properties of individual ERE isolates (both ERVs and sLTRs) were then characterized in the following aspects: transcription potential, tropism trait, coding potential, recombination event, integration age, and primer binding site for replication. In addition, a suite of database management system programs was developed to organize and update the data acquired from current and future studies and to make the data accessible via internet.
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Affiliation(s)
- Damian Kao
- Burn Research, Shriners Hospitals for Children Northern California, Sacramento, CA 95817, USA
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Lai OY, Chen H, Michaud HA, Hayashi G, Kuebler PJ, Hultman GK, Ariza ME, Williams MV, Batista MD, Nixon DF, Foerster J, Bowcock AM, Liao W. Protective effect of human endogenous retrovirus K dUTPase variants on psoriasis susceptibility. J Invest Dermatol 2012; 132:1833-40. [PMID: 22437317 PMCID: PMC3375357 DOI: 10.1038/jid.2012.69] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Previous genetic and functional studies have implicated the human endogenous retrovirus K (HERV-K) dUTPase located within the PSORS1 locus in the major histocompatibility complex region as a candidate psoriasis gene. Here, we describe a variant discovery and case-control association study of HERV-K dUTPase variants in 708 psoriasis cases and 349 healthy controls. Five common HERV-K dUTPase variants were found to be highly associated with psoriasis, with the strongest association occurring at the missense single-nucleotide polymorphism (SNP) rs3134774 (K158R, P=3.28 × 10(-15), odds ratio =2.36 (95% confidence interval: 1.91-2.92)). After adjusting the association of the HERV-K dUTPase variants for the potential confounding effects of HLA alleles associated with psoriasis, the HERV-K SNPs rs9264082 and rs3134774 remained significantly associated. Haplotype analysis revealed that HERV-K haplotypes containing the non-risk alleles for rs3134774 and rs9264082 significantly reduced the risk of psoriasis. Functional testing showed higher antibody responses against recombinant HERV-K dUTPase in psoriasis patients compared with controls (P<0.05), as well as higher T-cell responses against a single HERV-K dUTPase peptide (P<0.05). Our data support an independent role for the HERV-K dUTPase on psoriasis susceptibility, and suggest the need for additional studies to clarify the role of this dUTPase in the pathogenesis of psoriasis.
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Affiliation(s)
- Olivia Y Lai
- Department of Dermatology, University of California, San Francisco, San Francisco, California, USA
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The biological significance of evolution in autoimmune phenomena. Autoimmune Dis 2012; 2012:784315. [PMID: 22482039 PMCID: PMC3312230 DOI: 10.1155/2012/784315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/28/2011] [Indexed: 01/16/2023] Open
Abstract
It is an inherent part of living to be in constant modification, which are due to answers resulting from environmental changes. The different systems make adaptations based on natural selection. With respect to the immune system of mammals, these changes have a lot to do with the interactions that occur continuously with other living species, especially microorganisms. The immune system is primarily designed to defend from germs and this response triggers inflammatory reactions which must be regulated in order not to generate damage to healthy tissue. The regulatory processes were added over time to prevent such damage. Through evolution the species have stored “an immunological experience,” which provides information that is important for developing effective responses in the future. The human species, which is at a high level of evolutionary immunological accumulation, have multiple immune defense strategies which, in turn, are highly regulated. Imbalances in these can result in autoimmunity. “There is nothing permanent except change.” (Heraclitus)
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Paul S, Planque SA, Nishiyama Y, Hanson CV, Massey RJ. Nature and nurture of catalytic antibodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 750:56-75. [PMID: 22903666 DOI: 10.1007/978-1-4614-3461-0_5] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Immunoglobulins (antibodies) frequently express constitutive functions. Two such functions are nucleophilic catalysis and the reversible binding to B-cell superantigens. Constitutive or "naturally-occurring" antibodies are produced spontaneously from germline genetic information. The antibody structural elements mediating the constitutive functions have originated over millions of years of phylogenic evolution, contrasting with antigen-driven, somatic sequence diversification of the complementarity determining regions (CDR) that underlies the better-known high affinity antigen binding function of antibodies. Often, the framework regions (FRs) play a dominant role in antibody constitutive functions. Catalytic antibody subsets with promiscuous, autoantigen-directed and microbe-directed specificities have been identified. Mucosal antibodies may be specialized to express high-level catalytic activity against microbes transmitted by the mucosal route, exemplified by constitutive production of IgA class antibodies in mucosal secretions that catalyze the cleavage of HIV gp120. Catalytic specificity can be gained by constitutive noncovalent superantigen binding at the FRs and by adaptive development of noncovalent classical antigen or superantigen binding, respectively, at the CDRs and FRs. Growing evidence suggests important functional roles for catalytic antibodies in homeostasis, autoimmune disease and protection against infection. Adaptive antibody responses to microbial superantigens are proscribed underphysiological circumstances. Covalent electrophilic immunogen binding to constitutively expressed nucleophilic sites in B-cell receptors bypasses the restriction on adaptive antibody production, and simultaneous occupancy of the CDR binding site by a stimulatory antigenic epitope can also overcome the downregulatory effect of superantigen binding at the FRs. These concepts may be useful for developing novel vaccines that capitalize and improve on constitutive antibody functions for protection against microbes.
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Affiliation(s)
- Sudhir Paul
- Chemical Immunology Research Center, Department of Pathology, University of Texas-Houston Medical School, Texas, USA.
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George M, Schwecke T, Beimforde N, Hohn O, Chudak C, Zimmermann A, Kurth R, Naumann D, Bannert N. Identification of the protease cleavage sites in a reconstituted Gag polyprotein of an HERV-K(HML-2) element. Retrovirology 2011; 8:30. [PMID: 21554716 PMCID: PMC3114732 DOI: 10.1186/1742-4690-8-30] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 05/09/2011] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The human genome harbors several largely preserved HERV-K(HML-2) elements. Although this retroviral family comes closest of all known HERVs to producing replication competent virions, mutations acquired during their chromosomal residence have rendered them incapable of expressing infectious particles. This also holds true for the HERV-K113 element that has conserved open reading frames (ORFs) for all its proteins in addition to a functional LTR promoter. Uncertainty concerning the localization and impact of post-insertional mutations has greatly hampered the functional characterization of these ancient retroviruses and their proteins. However, analogous to other betaretroviruses, it is known that HERV-K(HML-2) virions undergo a maturation process during or shortly after release from the host cell. During this process, the subdomains of the Gag polyproteins are released by proteolytic cleavage, although the nature of the mature HERV-K(HML-2) Gag proteins and the exact position of the cleavage sites have until now remained unknown. RESULTS By aligning the amino acid sequences encoded by the gag-pro-pol ORFs of HERV-K113 with the corresponding segments from 10 other well-preserved human specific elements we identified non-synonymous post-insertional mutations that have occurred in this region of the provirus. Reversion of these mutations and a partial codon optimization facilitated the large-scale production of maturation-competent HERV-K113 virus-like particles (VLPs). The Gag subdomains of purified mature VLPs were separated by reversed-phase high-pressure liquid chromatography and initially characterized using specific antibodies. Cleavage sites were identified by mass spectrometry and N-terminal sequencing and confirmed by mutagenesis. Our results indicate that the gag gene product Pr74Gag of HERV-K(HML-2) is processed to yield p15-MA (matrix), SP1 (spacer peptide of 14 amino acids), p15, p27-CA (capsid), p10-NC (nucleocapsid) and two C-terminally encoded glutamine- and proline-rich peptides, QP1 and QP2, spanning 23 and 19 amino acids, respectively. CONCLUSIONS Expression of reconstituted sequences of original HERV elements is an important tool for studying fundamental aspects of the biology of these ancient viruses. The analysis of HERV-K(HML-2) Gag processing and the nature of the mature Gag proteins presented here will facilitate further studies of the discrete functions of these proteins and of their potential impact on the human host.
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Affiliation(s)
- Maja George
- Center for HIV and Retrovirology, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Different transcription activity of HERV-K LTR-containing and LTR-lacking genes of the KIAA1245/NBPF gene subfamily. Genetica 2011; 139:733-41. [PMID: 21544646 DOI: 10.1007/s10709-011-9577-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 04/15/2011] [Indexed: 10/18/2022]
Abstract
Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) located near or within genes might affect their expression. We used the KIAA1245/NBPF human gene subfamily in an attempt to assess the regulatory potential of HERV LTRs. The subfamily includes five closely related paralogous genes: three of them contain an LTR in the second intron, and two genes lack it. Earlier we reported that the second and third exons of only LTR-containing genes of this subfamily could be detected in mature mRNAs of various cell lines and human tissues. The corresponding parts of mRNA of LTR-lacking genes analyzed in our study were absent from EST libraries, but other fragments of their mRNAs were available in EST databases. For a more unbiased view on the correlation between gene transcription and the intronic LTRs, in the present work we analyzed non-spliced pre-mRNA thus avoiding splicing effects. Based on RT-PCR analysis, we demonstrated that the KIAA1245/NBPF LTR-lacking gene AL592309/NBPF3 was transcriptionally active, but the LTR-containing genes showed significantly higher transcription levels. The data are in agreement with the suggestion that HERV-K LTRs within the second intron of the KIAA1245/NBPF subfamily genes might affect their transcriptional activity. However, it still remains to be investigated whether the revealed effect is due just to the LTR insertion or other factors are responsible for the difference.
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Abstract
Lentiviral vectors are now in clinical trials for a variety of inherited and acquired disorders. A challenge for moving any viral vector into the clinic is the ability to screen the vector product for the presence of replication-competent virus. Assay development for replication-competent lentivirus (RCL) is particularly challenging because recombination of vector packaging plasmids and cellular DNA leading to RCL has not been reported with the current viral vector systems. Therefore, the genomic structure of a RCL remains theoretical. In this report, we describe a highly sensitive RCL assay suitable for screening vector product and have screened large-scale vector supernatant, cells used in vector production, and cells transduced with clinical grade vector. We discuss the limitations and challenges of the current assay, and suggest modifications that may improve the suitability of this assay for screening US Food and Drug Administration (US FDA)-licensed products.
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Paul S, Planque S, Nishiyama Y, Escobar M, Hanson C. Back to the future: covalent epitope-based HIV vaccine development. Expert Rev Vaccines 2010; 9:1027-43. [PMID: 20822346 DOI: 10.1586/erv.10.77] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Traditional HIV vaccine approaches have proved ineffective because the immunodominant viral epitopes are mutable and the conserved epitopes necessary for infection are not sufficiently immunogenic. The CD4 binding site expressed by the HIV envelope protein of glycoprotein 120 is essential for viral entry into host cells. In this article, we review the B-cell superantigenic character of the CD4 binding site as the cause of its poor immunogenicity. We summarize evidence supporting development of covalent immunization as the first vaccine strategy with the potential to induce an antibody response to a conserved HIV epitope that neutralizes genetically divergent HIV strains.
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Affiliation(s)
- Sudhir Paul
- Department of Pathology and Laboratory Medicine, Chemical Immunology Research Center, University of Texas-Houston Medical School, 6431 Fannin, MSB 2.230A, Houston, TX 77030, USA.
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Antony JM, Deslauriers AM, Bhat RK, Ellestad KK, Power C. Human endogenous retroviruses and multiple sclerosis: innocent bystanders or disease determinants? Biochim Biophys Acta Mol Basis Dis 2010; 1812:162-76. [PMID: 20696240 PMCID: PMC7172332 DOI: 10.1016/j.bbadis.2010.07.016] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 07/14/2010] [Accepted: 07/26/2010] [Indexed: 12/21/2022]
Abstract
Human endogenous retroviruses (HERVs) constitute 5–8% of human genomic DNA and are replication incompetent despite expression of individual HERV genes from different chromosomal loci depending on the specific tissue. Several HERV genes have been detected as transcripts and proteins in the central nervous system, frequently in the context of neuroinflammation. The HERV-W family has received substantial attention in large part because of associations with diverse syndromes including multiple sclerosis (MS) and several psychiatric disorders. A HERV-W-related retroelement, multiple sclerosis retrovirus (MSRV), has been reported in MS patients to be both a biomarker as well as an effector of aberrant immune responses. HERV-H and HERV-K have also been implicated in MS and other neurological diseases but await delineation of their contributions to disease. The HERV-W envelope-encoded glycosylated protein, syncytin-1, is encoded by chromosome 7q21 and exhibits increased glial expression within MS lesions. Overexpression of syncytin-1 in glia induces endoplasmic reticulum stress leading to neuroinflammation and the induction of free radicals, which damage proximate cells. Syncytin-1's receptor, ASCT1 is a neutral amino acid transporter expressed on glia and is suppressed in white matter of MS patients. Of interest, antioxidants ameliorate syncytin-1's neuropathogenic effects raising the possibility of using these agents as therapeutics for neuroinflammatory diseases. Given the multiple insertion sites of HERV genes as complete and incomplete open reading frames, together with their differing capacity to be expressed and the complexities of individual HERVs as both disease markers and bioactive effectors, HERV biology is a compelling area for understanding neuropathogenic mechanisms and developing new therapeutic strategies.
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Ashlock W, Datta S. Using Fourier phase analysis on genomic sequences to identify retroviruses. PROCEEDINGS OF THE FIRST ACM INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2010. [DOI: 10.1145/1854776.1854841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Crowhurst G. XMRV: does this virus hold the key to myalgic encephalomyelitis/CFS? ACTA ACUST UNITED AC 2010; 19:919-22. [DOI: 10.12968/bjon.2010.19.14.49051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Ashlock W, Datta S. Detecting retroviruses using reading frame information and side effect machines. 2010 IEEE SYMPOSIUM ON COMPUTATIONAL INTELLIGENCE IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2010. [DOI: 10.1109/cibcb.2010.5510699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Beck J, Urnovitz HB, Mitchell WM, Schütz E. Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls. Mol Cancer Res 2010; 8:335-42. [PMID: 20215424 DOI: 10.1158/1541-7786.mcr-09-0314] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Circulating nucleic acids (CNA) isolated from serum or plasma are increasingly recognized as biomarkers for cancers. Recently developed next generation sequencing provides high numbers of DNA sequences to detect the trace amounts of unique serum biomarkers associated with breast carcinoma. Serum CNA of 38 women with ductal carcinoma was extracted and sequenced on a 454/Roche high-throughput GS-FLX platform and compared with healthy controls and patients with other medical conditions. Repetitive elements present in CNA were detected and classified, and each repetitive element was normalized based on total sequence count or repeat count. Multivariate regression models were calculated using an information-theoretical approach and multimodel inference. A total of 423,150 and 953,545 sequences for the cancer patients and controls, respectively, were obtained. Data from 26 patients with stages II to IV tumors and from 67 apparently healthy female controls were used as the training data set. Using a bootstrap method to avoid sampling bias, a five-parameter model was developed. When this model was applied to a validation data set consisting of patients with tumor stage I (n = 10) compared with healthy and nonmalignant disease controls (n = 87; 1,261,561 sequences) a sensitivity of 70% at a specificity of 100% was obtained. At a diagnostic specificity level of 95%, a sensitivity of 90% was calculated. Identification of specific breast cancer-related CNA sequences provides the basis for the development of a serum-based routine laboratory test for breast cancer screening and monitoring.
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Affiliation(s)
- Julia Beck
- Chronix Biomedical GmbH, Goettingen, Germany
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42
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Boucher CA. Retroviruses and retroviral infections. Infect Dis (Lond) 2010. [DOI: 10.1016/b978-0-323-04579-7.00163-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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CLONING AND CHARACTERIZATION OF ENDOGENOUS RETROVIRUSES ASSOCIATED WITH POSTINJURY STRESS SIGNALS IN LYMPHOID TISSUES. Shock 2009; 32:80-8. [DOI: 10.1097/shk.0b013e31818bc193] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Retroviral vectors based on murine leukemia viruses (MuLV) have been used in clinical investigations for over a decade. Alternative retroviruses, most notably vectors based on HIV-1 and other lentiviruses, are now entering into clinical trials. Although vectors are designed to be replication defective, recombination events during vector production could lead to the generation of replication competent retroviruses (RCR) or replication competent lentiviruses (RCL). Careful screening of vector prior to human use must insure that patients are not inadvertently exposed to RCR or RCL. We describe methods capable of detecting low levels of virus contamination and discuss the current regulatory guidelines for screening gene therapy products intended for human use.
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Affiliation(s)
- Lakshmi Sastry
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
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Gordon PMK, Schütz E, Beck J, Urnovitz HB, Graham C, Clark R, Dudas S, Czub S, Sensen M, Brenig B, Groschup MH, Church RB, Sensen CW. Disease-specific motifs can be identified in circulating nucleic acids from live elk and cattle infected with transmissible spongiform encephalopathies. Nucleic Acids Res 2008; 37:550-6. [PMID: 19059996 PMCID: PMC2632913 DOI: 10.1093/nar/gkn963] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To gain insight into the disease progression of transmissible spongiform encephalopathies (TSE), we searched for disease-specific patterns in circulating nucleic acids (CNA) in elk and cattle. In a 25-month time-course experiment, CNAs were isolated from blood samples of 24 elk (Cervus elaphus) orally challenged with chronic wasting disease (CWD) infectious material. In a separate experiment, blood-sample CNAs from 29 experimental cattle (Bos taurus) 40 months post-inoculation with clinical bovine spongiform encephalopathy (BSE) were analyzed according to the same protocol. Next-generation sequencing provided broad elucidation of sample CNAs: we detected infection-specific sequences as early as 11 months in elk (i.e. at least 3 months before the appearance of the first clinical signs) and we established CNA patterns related to BSE in cattle at least 4 months prior to clinical signs. In elk, a progression of CNA sequence patterns was found to precede and correlate with macro-observable disease progression, including delayed CWD progression in elk with PrP genotype LM. Some of the patterns identified contain transcription-factor-binding sites linked to endogenous retroviral integration. These patterns suggest that retroviruses may be connected to the manifestation of TSEs. Our results may become useful for the early diagnosis of TSE in live elk and cattle.
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Affiliation(s)
- Paul M K Gordon
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Sun Center of Excellence for Visual Genomics, University of Calgary, Calgary, AB, Canada T2N 4N1
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Abstract
Infection of germline cells with retroviruses initiates permanent proviral colonization of the germline genome. The germline-integrated proviruses, called endogenous retroviruses (ERVs), are inherited to offspring in a Mendelian order and belong to the transposable element family. Endogenous retroviruses and other long terminal repeat retroelements constitute ~8% and ~10% of the human and mouse genomes, respectively. It is likely that each individual has a distinct genomic ERV profile. Recent studies have revealed that a substantial fraction of ERVs retains the coding potentials necessary for virion assembly and replication. There are several layers of potential mechanisms controlling ERV expression: intracellular transcription environment (e.g., transcription factor pool, splicing machinery, hormones), epigenetic status of the genome (e.g., proviral methylation, histone acetylation), profile of transcription regulatory elements on each ERV's promoter, and a range of stress signals (e.g., injury, infection, environment). Endogenous retroviruses may exert pathophysiologic effects by infection followed by random reintegration into the genome, by their gene products (e.g., envelope, superantigen), and by altering the expression of neighboring genes. Several studies have provided evidence that ERVs are associated with a range of pathogenic processes involving multiple sclerosis, systemic lupus erythematosus, breast cancer, and the response to burn injury. For instance, the proinflammatory properties of the human ERV-W envelope protein play a central role in demyelination of oligodendrocytes. As reviewed in this article, recent advances in ERV biology and mammalian genomics suggest that ERVs may have a profound influence on various pathogenic processes including the response to injury and infection. Understanding the roles of ERVs in the pathogenesis of injury and infection will broaden insights into the underlying mechanisms of systemic immune disorder and organ failure in these patients.
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Transcriptional regulation of GSDML gene by antisense-oriented HERV-H LTR element. Arch Virol 2008; 153:1201-5. [DOI: 10.1007/s00705-008-0105-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2006] [Accepted: 04/02/2008] [Indexed: 11/25/2022]
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Abstract
Immunoglobulins (Igs) in uninfected humans recognize residues 421-433 located in the B cell superantigenic site (SAg) of the HIV envelope protein gp120 and catalyze its hydrolysis by a serine protease-like mechanism. The catalytic activity is encoded by germline Ig variable (V) region genes, and is expressed at robust levels by IgMs and IgAs but poorly by IgGs. Mucosal IgAs are highly catalytic and neutralize HIV, suggesting that they constitute a first line of defense against HIV. Lupus patients produce the Igs at enhanced levels. Homology of the 421-433 region with an endogenous retroviral sequence and a bacterial protein may provide clues about the antigen driving anti-SAg synthesis in lupus patients and uninfected subjects. The potency and breadth of HIV neutralization revives hopes of clinical application of catalytic anti-421-433 Igs as immunotherapeutic and topical microbicide reagents. Adaptive improvement of anti-SAg catalytic Igs in HIV infected subjects is not customary. Further study of the properties of the naturally occurring anti-SAg catalytic Igs should provide valuable guidance in designing a prophylactic vaccine that amplifies protective catalytic immunity to HIV.
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Abstract
The capacity to integrate into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be vertically transmitted from generation to generation and eventually become fixed in the genomes of the entire population. This has been independently accomplished by several ancient retroviruses that invaded the genomes of our early and more recent primate and hominoid ancestors. Some of the inherited elements then proliferated in the genome, resulting in a number of lineages with complex phylogenetic patterns. Although the vast majority of chromosomally integrated retroelements have suffered inactivating mutations and deletions, a significant impact on various aspects of human biology has been recently revealed and evidence for the present activity of at least one human endogenous retrovirus family continues to accumulate.
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Pessina A, Bonomi A, Baglio C, Cavicchini L, Sisto F, Neri MG, Gribaldo L. Microbiological risk assessment in stem cell manipulation. Crit Rev Microbiol 2008; 34:1-12. [PMID: 18259977 DOI: 10.1080/10408410701683599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cell therapy based on the use of human stem cells is more complicated than transfusion or organ transplantation because cells may undergo many additional manipulations due to different treatments for isolation, expansion, differentiation, and other types of biological changes. These manipulations require the approval of regulatory agencies (other than ethical) and the processes must be monitored with more tests than the ones applied for minimally manipulated cells. The clinical safety and efficacy of transplanted cells depend on several factors such as homologous or non-homologous sources, extent of manipulation, and culture conditions. Moreover, the kind of information needed to address these issues may differ depending on whether the cells are to be used for tissue reconstruction or repair, or to recover metabolic functions. Also anatomical site, functional integration as well as duration of therapy, are crucial points that indirectly can influence safety. Many important assays have been suggested for environmental monitoring as well as to standardize microbiological controls in stem cell banks to prevent contamination. In order to guarantee safety two main aspects must be considered: one is related to the source of cells (the donor) and the other is depending on cell collection and processing. In this review we critically analyze the steps of the processes (from collection to banking) and consider the main factors involved in the clinical research (continuously in evolution) by suggesting a standardized facsimile form to use in the laboratory for the assessment of the microbiological risk related to the cell manipulations.
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Affiliation(s)
- Augusto Pessina
- Department of Public Health-Microbiology-Virology, University of Milan, Italy.
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