401
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Yang R, Cheng S, Luo N, Gao R, Yu K, Kang B, Wang L, Zhang Q, Fang Q, Zhang L, Li C, He A, Hu X, Peng J, Ren X, Zhang Z. Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biol 2019; 21:2. [PMID: 31892342 PMCID: PMC6937914 DOI: 10.1186/s13059-019-1921-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tumor-reactive CD8+ tumor-infiltrating lymphocytes (TILs) represent a subtype of T cells that can recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. RESULTS In this study, we segregate tumor-reactive and bystander CD8+ TILs, as well as naïve and effector memory CD8+ T cell subtypes as controls from colorectal cancer patients, to compare their transcriptome and methylome characteristics. Transcriptome profiling confirms previous conclusions that tumor-reactive TILs have an exhausted tissue-resident memory signature. Whole-genome methylation profiling identifies a distinct methylome pattern of tumor-reactive CD8+ T cells, with tumor-reactive markers CD39 and CD103 being specifically demethylated. In addition, dynamic changes are observed during the transition of naïve T cells into tumor-reactive CD8+ T cells. Transcription factor binding motif enrichment analysis identifies several immune-related transcription factors, including three exhaustion-related genes (NR4A1, BATF, and EGR2) and VDR, which potentially play an important regulatory role in tumor-reactive CD8+ T cells. CONCLUSION Our study supports the involvement of DNA methylation in shaping tumor-reactive and bystander CD8+ TILs, and provides a valuable resource for the development of novel DNA methylation markers and future therapeutics.
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Affiliation(s)
- Rui Yang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Sijin Cheng
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Nan Luo
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Surgery, Peking University Ninth School of Clinical Medicine, Beijing, China
| | - Ranran Gao
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Kezhuo Yu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Boxi Kang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Li Wang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Qiming Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Qiao Fang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Lei Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Li
- Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
| | - Aibin He
- Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
| | - Xueda Hu
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China
| | - Jirun Peng
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China.
- Department of Surgery, Peking University Ninth School of Clinical Medicine, Beijing, China.
| | - Xianwen Ren
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China.
| | - Zemin Zhang
- BIOPIC, Beijing Advanced Innovation Center for Genomics, and School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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402
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The alternative cap-binding complex is required for antiviral defense in vivo. PLoS Pathog 2019; 15:e1008155. [PMID: 31856218 PMCID: PMC6946169 DOI: 10.1371/journal.ppat.1008155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/07/2020] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Cellular response to environmental challenges requires immediate and precise regulation of transcriptional programs. During viral infections, this includes the expression of antiviral genes that are essential to combat the pathogen. Transcribed mRNAs are bound and escorted to the cytoplasm by the cap-binding complex (CBC). We recently identified a protein complex consisting of NCBP1 and NCBP3 that, under physiological conditions, has redundant function to the canonical CBC, consisting of NCBP1 and NCBP2. Here, we provide evidence that NCBP3 is essential to mount a precise and appropriate antiviral response. Ncbp3-deficient cells allow higher virus growth and elicit a reduced antiviral response, a defect happening on post-transcriptional level. Ncbp3-deficient mice suffered from severe lung pathology and increased morbidity after influenza A virus challenge. While NCBP3 appeared to be particularly important during viral infections, it may be more broadly involved to ensure proper protein expression.
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403
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Aiello A, Giannessi F, Percario ZA, Affabris E. An emerging interplay between extracellular vesicles and cytokines. Cytokine Growth Factor Rev 2019; 51:49-60. [PMID: 31874738 DOI: 10.1016/j.cytogfr.2019.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Extracellular vesicles (EVs) are small membrane-bound particles that are naturally released from cells. They are recognized as potent vehicles of intercellular communication both in prokaryotes and eukaryotes. Because of their capacity to carry biological macromolecules such as proteins, lipids and nucleic acids, EVs influence different physiological and pathological functions of both parental and recipient cells. Although multiple pathways have been proposed for cytokine secretion beyond the classical ER/Golgi route, EVs have recently recognized as an alternative secretory mechanism. Interestingly, cytokines/chemokines exploit these vesicles to be released into the extracellular milieu, and also appear to modulate their release, trafficking and/or content. In this review, we provide an overview of the cytokines/chemokines that are known to be associated with EVs or their regulation with a focus on TNFα, IL-1β and IFNs.
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404
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Zhang Y, Thery F, Wu NC, Luhmann EK, Dussurget O, Foecke M, Bredow C, Jiménez-Fernández D, Leandro K, Beling A, Knobeloch KP, Impens F, Cossart P, Radoshevich L. The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection. Nat Commun 2019; 10:5383. [PMID: 31772204 PMCID: PMC6879477 DOI: 10.1038/s41467-019-13393-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/07/2019] [Indexed: 12/28/2022] Open
Abstract
ISG15 is an interferon-stimulated, ubiquitin-like protein, with anti-viral and anti-bacterial activity. Here, we map the endogenous in vivo ISGylome in the liver following Listeria monocytogenes infection by combining murine models of reduced or enhanced ISGylation with quantitative proteomics. Our method identifies 930 ISG15 sites in 434 proteins and also detects changes in the host ubiquitylome. The ISGylated targets are enriched in proteins which alter cellular metabolic processes, including upstream modulators of the catabolic and antibacterial pathway of autophagy. Computational analysis of substrate structures reveals that a number of ISG15 modifications occur at catalytic sites or dimerization interfaces of enzymes. Finally, we demonstrate that animals and cells with enhanced ISGylation have increased basal and infection-induced autophagy through the modification of mTOR, WIPI2, AMBRA1, and RAB7. Taken together, these findings ascribe a role of ISGylation to temporally reprogram organismal metabolism following infection through direct modification of a subset of enzymes in the liver.
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Affiliation(s)
- Yifeng Zhang
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Fabien Thery
- Center for Medical Biotechnology, VIB, 9000, Gent, Belgium
- Department for Biomolecular Medicine, Gent University, 9000, Gent, Belgium
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Emma K Luhmann
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Olivier Dussurget
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, 75015, Paris, France
- Inserm, U604, 75015, Paris, France
- National Institute for Agronomic Research (INRA), Unité sous-contrat 2020, 75015, Paris, France
| | - Mariko Foecke
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, 75015, Paris, France
- Inserm, U604, 75015, Paris, France
- National Institute for Agronomic Research (INRA), Unité sous-contrat 2020, 75015, Paris, France
| | - Clara Bredow
- Charité-Universitäts medizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Biochemistry, Berlin, Germany
| | | | - Kevin Leandro
- Center for Medical Biotechnology, VIB, 9000, Gent, Belgium
- Department for Biomolecular Medicine, Gent University, 9000, Gent, Belgium
| | - Antje Beling
- Charité-Universitäts medizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Biochemistry, Berlin, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), Partner Site Berlin, Berlin, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Francis Impens
- Center for Medical Biotechnology, VIB, 9000, Gent, Belgium.
- Department for Biomolecular Medicine, Gent University, 9000, Gent, Belgium.
- VIB Proteomics Core, VIB, 9000, Gent, Belgium.
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, 75015, Paris, France.
- Inserm, U604, 75015, Paris, France.
- National Institute for Agronomic Research (INRA), Unité sous-contrat 2020, 75015, Paris, France.
| | - Lilliana Radoshevich
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
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405
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Kim MS, Kim KH. Effect of CRISPR/Cas9-mediated knockout of either Mx1 or ISG15 gene in EPC cells on resistance against VHSV infection. FISH & SHELLFISH IMMUNOLOGY 2019; 93:1041-1046. [PMID: 31465870 DOI: 10.1016/j.fsi.2019.08.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 06/10/2023]
Abstract
Although the type I interferon-mediated increase of Mx1 and ISG15 gene expression in Epithelioma papulosum cyprini (EPC) cells has been reported, the antiviral role of Mx1 and ISG15 in EPC cells has not been investigated. In this study, to know the anti-viral hemorrhagic septicemia virus (VHSV) role of Mx1 and ISG15 of EPC cells, either Mx1 or ISG15 gene was knocked-out using a CRISPR/Cas9 system, and the progression of cytopathic effects (CPE) and viral growth were analyzed. Mx1 gene and ISG15 gene knockout EPC cells were successfully produced via CRISPR/Cas9 coupled with a single-cell cloning. Through the sequence analysis, one clone showing two heterozygous indel patterns in Mx1 gene and a clone showing three heterozygous indel patterns in ISG15 gene were selected for further analyses. Mx1 knockout EPC cells did not show any differences in VHSV-mediated CPE progression, even when pre-treated with polyinosinic:polycytidylic acid (poly I:C), compared to control EPC cells. These results suggest that Mx1 in EPC cells may be unfunctional to cytoplasmic RNA viruses. In contrast to Mx1, ISG15 knockout cells showed clearly hampered anti-VHSV activity even when pre-treated with poly I:C, indicating that ISG15 plays an important role in type I interferon-mediated anti-viral activity in EPC cells, which allowed VHSV to replicate more efficiently in ISG15 knockout cells than Mx1 knockout and control cells.
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Affiliation(s)
- Min Sun Kim
- Department of Integrative Bio-industrial Engineering, Sejong University, Seoul, 05006, South Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 48513, South Korea.
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406
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Liu C, Oveissi S, Downs R, Kirby J, Nedeva C, Puthalakath H, Faou P, Duan M, Chen W. Semiquantitative Proteomics Enables Mapping of Murine Neutrophil Dynamics following Lethal Influenza Virus Infection. THE JOURNAL OF IMMUNOLOGY 2019; 203:1064-1075. [PMID: 31308090 DOI: 10.4049/jimmunol.1900337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 12/31/2022]
Abstract
Neutrophils are rapidly deployed innate immune cells, and excessive recruitment is causally associated with influenza-induced pathologic conditions. Despite this, the complete set of influenza lethality-associated neutrophil effector proteins is currently unknown. Whether the expression of these proteins is predetermined during bone marrow (BM) neutrophil maturation or further modulated by tissue compartment transitions has also not been comprehensively characterized at a proteome-wide scale. In this study, we used high-resolution mass spectrometry to map how the proteomes of murine neutrophils change comparatively across BM, blood, and the alveolar airspaces to deploy an influenza lethality-associated response. Following lethal influenza infection, mature neutrophils undergo two infection-dependent and one context-independent compartmental transitions. Translation of type I IFN-stimulated genes is first elevated in the BM, preceding the context-independent downregulation of ribosomal proteins observed in blood neutrophils. Following alveolar airspace infiltration, the bronchoalveolar lavage (BAL) neutrophil proteome is further characterized by a limited increase in type I IFN-stimulated and metal-sequestering proteins as well as a decrease in degranulation-associated proteins. An influenza-selective and dose-dependent increase in antiviral and lipid metabolism-associated proteins was also observed in BAL neutrophils, indicative of a modest capacity for pathogen response tuning. Altogether, our study provides new and comprehensive evidence that the BAL neutrophil proteome is shaped by BM neutrophil maturation as well as subsequent compartmental transitions following lethal influenza infection.
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Affiliation(s)
- Chuanxin Liu
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Sara Oveissi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Rachael Downs
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Jason Kirby
- Land and Water, Commonwealth Scientific and Industrial Research Organisation, Urrbrae, South Australia 5064, Australia
| | - Christina Nedeva
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Hamsa Puthalakath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Pierre Faou
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia; and
| | - Mubing Duan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia;
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407
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Chandler LC, Barnard AR, Caddy SL, Patrício MI, McClements ME, Fu H, Rada C, MacLaren RE, Xue K. Enhancement of Adeno-Associated Virus-Mediated Gene Therapy Using Hydroxychloroquine in Murine and Human Tissues. Mol Ther Methods Clin Dev 2019; 14:77-89. [PMID: 31309129 PMCID: PMC6606965 DOI: 10.1016/j.omtm.2019.05.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/20/2019] [Indexed: 12/20/2022]
Abstract
The therapeutic effects of gene therapy using adeno-associated virus (AAV) vectors are dependent on the efficacy of viral transduction. Currently, we have reached the safe limits of AAV vector dose, beyond which damaging inflammatory responses are seen. To improve the efficacy of AAV transduction, we treated mouse embryonic fibroblasts, primate retinal pigment epithelial cells, and human retinal explants with hydroxychloroquine (HCQ) 1 h prior to transduction with an AAV2 vector encoding GFP driven by a ubiquitous CAG promoter. This led to a consistent increase in GFP expression, up to 3-fold, compared with vector alone. Comparing subretinal injections of AAV2.CAG.GFP vector alone versus co-injection with 18.75 μM HCQ in paired eyes in mice, mean GFP expression was 4.6-fold higher in retinae co-treated with HCQ without retinal toxicity. A comparative 5.9-fold effect was seen with an AAV8(Y733F).GRK1.GFP vector containing the photoreceptor-specific rhodopsin kinase promoter. While the mechanism of action remains to be fully elucidated, our data suggest that a single pulse of adjunctive HCQ could safely improve AAV transduction in vivo, thus providing a novel strategy for enhancing the clinical effects of gene therapy.
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Affiliation(s)
- Laurel C. Chandler
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Sarah L. Caddy
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Maria I. Patrício
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Howell Fu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Cristina Rada
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford OX3 9DU, UK
| | - Kanmin Xue
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, NIHR Biomedical Research Centre, Oxford OX3 9DU, UK
- Corresponding author: Kanmin Xue, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Level 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK.
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408
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Involvement of Interferon Regulatory Factor 7 in Nicotine's Suppression of Antiviral Immune Responses. J Neuroimmune Pharmacol 2019; 14:551-564. [PMID: 31154625 DOI: 10.1007/s11481-019-09845-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 03/05/2019] [Indexed: 01/16/2023]
Abstract
Nicotine, the active ingredient in tobacco smoke, suppresses antiviral responses. Interferon regulatory factors (IRFs) regulate transcription of type I interferons (IFNs) and IFN-stimulated genes (ISGs) in this response. IRF7 is a key member of the IRF family. Expression of Irf7 is elevated in the brains of virus-infected animals, including human immunodeficiency virus-1 transgenic (HIV-1Tg) rats. We hypothesized that IRF7 affects nicotine's modulation of antiviral responses. Using CRISPR/Cas9 system, IRF7-mutant cell lines were created from human embryonic kidney 293FT cells in which 16 nicotinic acetylcholine receptors (nAChRs) were detected. Decreased expression of IRF7 was confirmed at both the mRNA and protein levels, as was IRF7-regulated cell growth in two IRF7-mutant cell lines, designated IRF7-Δ7 and IRF7-Δ11. In IRF7-Δ7 cells, expression of two nAChR genes, CHRNA3 and CHRNA9, changed modestly. After stimulation with polyinosinic-polycytidylic acid (poly I:C) (0.25 μg/ml) for 4 h to mimic viral infection, 293FT wild-type (WT) and IRF7-Δ7 cells were treated with 0, 1, or 100 μM nicotine for 24 h, which increased IFN-β expression in both types of cells but elevation was higher in WT cells (p < 0.001). Expression was significantly suppressed in WT cells (p < 0.001) but not in IRF7-Δ7 cells by 24-h nicotine exposure. Poly I:C stimulation increased mRNA expression of retinoic-acid-inducible protein I (RIG-I), melanoma-differentiation-associated gene 5 (MDA5), IFN-stimulated gene factor 3 (ISG3) complex, and IFN-stimulated genes (IRF7, ISG15, IFIT1, OAS1); nicotine attenuated mRNA expression only in WT cells. Overall, IRF7 is critical to nicotine's effect on the antiviral immune response. Graphical Abstract Involvement of IRF7 in nicotine's suppression of poly I:C-induced antiviral immune responses. PAMPs, such as a synthetic viral analogue of dsRNA poly I:C attack cells, will be recognized by PRRs, and the host innate immunity against viral infection will be activated. PRRs signaling trigger phosphorylation of IRF7 and IRF3 to induce their translocation to the nucleus and result in the production of type I IFNs. Then IFNs bind to IFNAR to activate the transcription factor ISGF3, a complex consisting of STAT1, STAT2, and IRF9. Further, it induces the expression of ISGs, including IFIT1, OAS1, IRF7, ISG15, etc. Nicotine suppresses the immune responses stimulated by poly I:C. In the IRF7-mutant cells, nicotine's suppressive effects on poly I:C-stimulated immune responses were restrained.
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409
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Galinato M, Shimoda K, Aguiar A, Hennig F, Boffelli D, McVoy MA, Hertel L. Single-Cell Transcriptome Analysis of CD34 + Stem Cell-Derived Myeloid Cells Infected With Human Cytomegalovirus. Front Microbiol 2019; 10:577. [PMID: 30949159 PMCID: PMC6437045 DOI: 10.3389/fmicb.2019.00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Myeloid cells are important sites of lytic and latent infection by human cytomegalovirus (CMV). We previously showed that only a small subset of myeloid cells differentiated from CD34+ hematopoietic stem cells is permissive to CMV replication, underscoring the heterogeneous nature of these populations. The exact identity of resistant and permissive cell types, and the cellular features characterizing the latter, however, could not be dissected using averaging transcriptional analysis tools such as microarrays and, hence, remained enigmatic. Here, we profile the transcriptomes of ∼7000 individual cells at day 1 post-infection using the 10× genomics platform. We show that viral transcripts are detectable in the majority of the cells, suggesting that virion entry is unlikely to be the main target of cellular restriction mechanisms. We further show that viral replication occurs in a small but specific sub-group of cells transcriptionally related to, and likely derived from, a cluster of cells expressing markers of Colony Forming Unit – Granulocyte, Erythrocyte, Monocyte, Megakaryocyte (CFU-GEMM) oligopotent progenitors. Compared to the remainder of the population, CFU-GEMM cells are enriched in transcripts with functions in mitochondrial energy production, cell proliferation, RNA processing and protein synthesis, and express similar or higher levels of interferon-related genes. While expression levels of the former are maintained in infected cells, the latter are strongly down-regulated. We thus propose that the preferential infection of CFU-GEMM cells may be due to the presence of a pre-established pro-viral environment, requiring minimal optimization efforts from viral effectors, rather than to the absence of specific restriction factors. Together, these findings identify a potentially new population of myeloid cells permissive to CMV replication, and provide a possible rationale for their preferential infection.
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Affiliation(s)
- Melissa Galinato
- Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, CA, United States
| | - Kristen Shimoda
- Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, CA, United States
| | - Alexis Aguiar
- Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, CA, United States
| | - Fiona Hennig
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, United States
| | - Dario Boffelli
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, United States
| | - Michael A McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, United States
| | - Laura Hertel
- Center for Immunobiology and Vaccine Development, Children's Hospital Oakland Research Institute, Oakland, CA, United States
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410
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Shen B, Wei K, Guo S, Liu C, Zhang J. Molecular characterization and expression analyses of two homologues of interferon-stimulated gene ISG15 in Larimichthys crocea (Family: Sciaenidae). FISH & SHELLFISH IMMUNOLOGY 2019; 86:846-857. [PMID: 30576775 DOI: 10.1016/j.fsi.2018.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 12/10/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
In this study, we sequenced and characterized two homologues of interferon-stimulated gene ISG15, termed as LcISG15-1 and LcISG15-2, from the large yellow croaker (Larimichthys crocea). The LcISG15-1 encodes 159 amino acids and the LcISG15-2 encodes 155 amino acids, both of which contain two tandem ubiquitin-like domains and the conserved C-terminal LRGG conjugation motif. The sequence analyses showed that both the LcISG15-1 and LcISG15-2 exhibit high similarity with ISG15 from other fishes. A putative IFN-stimulatory response element (ISRE) was detected in promoter regions of both the LcISG15-1 and LcISG15-2. Phylogenetic analyses revealed a close evolutionary relationship of both the LcISG15-1 and LcISG15-2 with other teleostean ISG15. Molecular evolutionary analyses suggested a gene duplication event of ISG15 in the ancestor of the Sciaenidae, with a signature of positive selection was found in the ISG15-2 gene copy of sciaenid fishes. The Real-time PCR analyses showed that the LcISG15-1 and LcISG15-2 were both found to be ubiquitously expressed in ten examined organs in large yellow croaker, with predominant expressions both in peripheral blood. Expression analyses showed that both the LcISG15-1 and LcISG15-2 were rapidly and significantly upregulated in vivo after poly (I:C) challenge in liver and spleen organs. However, the LcISG15-1 and LcISG15-2 were both significantly induced after pathogen Vibrio parahemolyticus infection only in the liver but not in the spleen. These results indicated that there are two ISG15 homologues in the large yellow croaker, both of which are likely to be involved in host immune defense against viral and bacterial infection.
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Affiliation(s)
- Bin Shen
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316004, China.
| | - Ke Wei
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Shaoyu Guo
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Cheng Liu
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316004, China
| | - Jianshe Zhang
- National Engineering Research Center of Marine Facilities Aquaculture, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316004, China.
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411
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The Abundant Tegument Protein pUL25 of Human Cytomegalovirus Prevents Proteasomal Degradation of pUL26 and Supports Its Suppression of ISGylation. J Virol 2018; 92:JVI.01180-18. [PMID: 30282718 DOI: 10.1128/jvi.01180-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022] Open
Abstract
The tegument of human cytomegalovirus (HCMV) virions contains proteins that interfere with both the intrinsic and the innate immunity. One protein with a thus far unknown function is pUL25. The deletion of pUL25 in a viral mutant (Towne-ΔUL25) had no impact on the release of virions and subviral dense bodies or on virion morphogenesis. Proteomic analyses showed few alterations in the overall protein composition of extracellular particles. A surprising result, however, was the almost complete absence of pUL26 in virions and dense bodies of Towne-ΔUL25 and a reduction of the large isoform pUL26-p27 in mutant virus-infected cells. pUL26 had been shown to inhibit protein conjugation with the interferon-stimulated gene 15 protein (ISG15), thereby supporting HCMV replication. To test for a functional relationship between pUL25 and pUL26, we addressed the steady-state levels of pUL26 and found them to be reduced in Towne-ΔUL25-infected cells. Coimmunoprecipitation experiments proved an interaction between pUL25 and pUL26. Surprisingly, the overall protein ISGylation was enhanced in Towne-ΔUL25-infected cells, thus mimicking the phenotype of a pUL26-deleted HCMV mutant. The functional relevance of this was confirmed by showing that the replication of Towne-ΔUL25 was more sensitive to beta interferon. The increase of protein ISGylation was also seen in cells infected with a mutant lacking the tegument protein pp65. Upon retesting, we found that pUL26 degradation was also increased when pp65 was unavailable. Our experiments show that both pUL25 and pp65 regulate pUL26 degradation and the pUL26-dependent reduction of ISGylation and add pUL25 as another HCMV tegument protein that interferes with the intrinsic immunity of the host cell.IMPORTANCE Human cytomegalovirus (HCMV) expresses a number of tegument proteins that interfere with the intrinsic and the innate defense mechanisms of the cell. Initial induction of the interferon-stimulated gene 15 protein (ISG15) and conjugation of proteins with ISG15 (ISGylation) by HCMV infection are subsequently attenuated by the expression of the viral IE1, pUL50, and pUL26 proteins. This study adds pUL25 as another factor that contributes to suppression of ISGylation. The tegument protein interacts with pUL26 and prevents its degradation by the proteasome. By doing this, it supports its restrictive influence on ISGylation. In addition, a lack of pUL25 enhances the levels of free ISG15, indicating that the tegument protein may interfere with the interferon response on levels other than interacting with pUL26. Knowledge obtained in this study widens our understanding of HCMV immune evasion and may also provide a new avenue for the use of pUL25-negative strains for vaccine production.
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412
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Lata S, Mishra R, Banerjea AC. Proteasomal Degradation Machinery: Favorite Target of HIV-1 Proteins. Front Microbiol 2018; 9:2738. [PMID: 30524389 PMCID: PMC6262318 DOI: 10.3389/fmicb.2018.02738] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022] Open
Abstract
Proteasomal degradation pathways play a central role in regulating a variety of protein functions by controlling not only their turnover but also the physiological behavior of the cell. This makes it an attractive target for the pathogens, especially viruses which rely on the host cellular machinery for their propagation and pathogenesis. Viruses have evolutionarily developed various strategies to manipulate the host proteasomal machinery thereby creating a cellular environment favorable for their own survival and replication. Human immunodeficiency virus-1 (HIV-1) is one of the most dreadful viruses which has rapidly spread throughout the world and caused high mortality due to its high evolution rate. Here, we review the various mechanisms adopted by HIV-1 to exploit the cellular proteasomal machinery in order to escape the host restriction factors and components of host immune system for supporting its own multiplication, and successfully created an infection.
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Affiliation(s)
- Sneh Lata
- Virology Lab II, National Institute of Immunology, New Delhi, India
| | - Ritu Mishra
- Virology Lab II, National Institute of Immunology, New Delhi, India
| | - Akhil C Banerjea
- Virology Lab II, National Institute of Immunology, New Delhi, India
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413
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Albert M, Bécares M, Falqui M, Fernández-Lozano C, Guerra S. ISG15, a Small Molecule with Huge Implications: Regulation of Mitochondrial Homeostasis. Viruses 2018; 10:v10110629. [PMID: 30428561 PMCID: PMC6265978 DOI: 10.3390/v10110629] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 12/12/2022] Open
Abstract
Viruses are responsible for the majority of infectious diseases, from the common cold to HIV/AIDS or hemorrhagic fevers, the latter with devastating effects on the human population. Accordingly, the development of efficient antiviral therapies is a major goal and a challenge for the scientific community, as we are still far from understanding the molecular mechanisms that operate after virus infection. Interferon-stimulated gene 15 (ISG15) plays an important antiviral role during viral infection. ISG15 catalyzes a ubiquitin-like post-translational modification termed ISGylation, involving the conjugation of ISG15 molecules to de novo synthesized viral or cellular proteins, which regulates their stability and function. Numerous biomedically relevant viruses are targets of ISG15, as well as proteins involved in antiviral immunity. Beyond their role as cellular powerhouses, mitochondria are multifunctional organelles that act as signaling hubs in antiviral responses. In this review, we give an overview of the biological consequences of ISGylation for virus infection and host defense. We also compare several published proteomic studies to identify and classify potential mitochondrial ISGylation targets. Finally, based on our recent observations, we discuss the essential functions of mitochondria in the antiviral response and examine the role of ISG15 in the regulation of mitochondrial processes, specifically OXPHOS and mitophagy.
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Affiliation(s)
- Manuel Albert
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
| | - Martina Bécares
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
| | - Michela Falqui
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
| | - Carlos Fernández-Lozano
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
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414
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Transcriptomics Reveal Antiviral Gene Induction in the Egyptian Rousette Bat Is Antagonized In Vitro by Marburg Virus Infection. Viruses 2018; 10:v10110607. [PMID: 30400182 PMCID: PMC6266330 DOI: 10.3390/v10110607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/27/2022] Open
Abstract
The Egyptian rousette bat (ERB) is the only known Marburg virus (MARV) reservoir host. ERBs develop a productive MARV infection with low viremia and shedding but no overt disease, suggesting this virus is efficiently controlled by ERB antiviral responses. This dynamic would contrast with humans, where MARV-mediated interferon (IFN) antagonism early in infection is thought to contribute to the severe, often fatal disease. The newly-annotated ERB genome and transcriptome have now enabled us to use a custom-designed NanoString nCounter ERB CodeSet in conjunction with RNA-seq to investigate responses in a MARV-infected ERB cell line. Both transcriptomic platforms correlated well and showed that MARV inhibited the antiviral program in ERB cells, while an IFN antagonism-impaired MARV was less efficient at suppressing the response gene induction, phenotypes previously reported for primate cells. Interestingly, and despite the expansion of IFN loci in the ERB genome, neither MARV showed specific induction of almost any IFN gene. However, we detected an upregulation of putative, unannotated ERB antiviral paralogs, as well as an elevated basal expression in uninfected ERB cells of key antiviral genes.
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415
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Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a widely distributed hemorrhagic fever virus and the cause of hemorrhagic disease in Africa, Southern and Eastern Europe, the Middle East, India and Asia. Recent emergence of CCHFV into Spain indicates that the geographic range of this virus is expanding and the presence of its tick vector in several countries without reported disease suggest that CCHFV will continue to spread. Research into CCHFV was historically limited by a lack of suitable animal models and tools to study viral pathogenesis. However, in the past few years the toolset for studying CCHFV has expanded with small animal and non-human primate models for CCHFV being developed along with a reverse genetics system that allows for investigation of viral determinants of disease. These tools have been utilized to understand how CCHFV antagonizes host restriction factors and to develop novel vaccine candidates that may help limit the substantial morbidity and mortality in humans caused by CCHFV.
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Affiliation(s)
- David W Hawman
- Laboratory of Virology, Division of Intramural Research, NIAID/NIH, Hamilton, Montana, 59840, USA
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, NIAID/NIH, Hamilton, Montana, 59840, USA
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416
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Who's Driving? Human Cytomegalovirus, Interferon, and NFκB Signaling. Viruses 2018; 10:v10090447. [PMID: 30134546 PMCID: PMC6163874 DOI: 10.3390/v10090447] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/17/2018] [Accepted: 08/18/2018] [Indexed: 12/16/2022] Open
Abstract
As essential components of the host's innate immune response, NFκB and interferon signaling are critical determinants of the outcome of infection. Over the past 25 years, numerous Human Cytomegalovirus (HCMV) genes have been identified that antagonize or modulate the signaling of these pathways. Here we review the biology of the HCMV factors that alter NFκB and interferon signaling, including what is currently known about how these viral genes contribute to infection and persistence, as well as the major outstanding questions that remain.
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