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Pratt HE, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal MJ, Geschwind DH, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. SCIENCE ADVANCES 2024; 10:eadj4452. [PMID: 38781344 PMCID: PMC11114231 DOI: 10.1126/sciadv.adj4452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Most genetic variants associated with psychiatric disorders are located in noncoding regions of the genome. To investigate their functional implications, we integrate epigenetic data from the PsychENCODE Consortium and other published sources to construct a comprehensive atlas of candidate brain cis-regulatory elements. Using deep learning, we model these elements' sequence syntax and predict how binding sites for lineage-specific transcription factors contribute to cell type-specific gene regulation in various types of glia and neurons. The elements' evolutionary history suggests that new regulatory information in the brain emerges primarily via smaller sequence mutations within conserved mammalian elements rather than entirely new human- or primate-specific sequences. However, primate-specific candidate elements, particularly those active during fetal brain development and in excitatory neurons and astrocytes, are implicated in the heritability of brain-related human traits. Additionally, we introduce PsychSCREEN, a web-based platform offering interactive visualization of PsychENCODE-generated genetic and epigenetic data from diverse brain cell types in individuals with psychiatric disorders and healthy controls.
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Affiliation(s)
- Henry E. Pratt
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gregory Andrews
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicole Shedd
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nishigandha Phalke
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Tongxin Li
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Khoury College of Computer Science, Northeastern University, Boston, MA 02115, USA
| | - Anusri Pampari
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Jensen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Michael J. Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute of Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Jill Moore
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Andrés Colubri
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Department of Genomics and Computational Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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O’Connor KW, Liu T, Kim S, Briseño CG, Georgopoulos K, Murphy TL, Murphy KM. Bcl6, Irf2, and Notch2 promote nonclassical monocyte development. Proc Natl Acad Sci U S A 2023; 120:e2220853120. [PMID: 37607223 PMCID: PMC10469339 DOI: 10.1073/pnas.2220853120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
Ly6Clo monocytes are a myeloid subset that specializes in the surveillance of vascular endothelium. Ly6Clo monocytes have been shown to derive from Ly6Chi monocytes. NOTCH2 signaling has been implicated as a trigger for Ly6Clo monocyte development, but the basis for this effect is unclear. Here, we examined the impact of NOTCH2 signaling of myeloid progenitors on the development of Ly6Clo monocytes in vitro. NOTCH2 signaling induced by delta-like ligand 1 (DLL1) efficiently induced the transition of Ly6Chi TREML4- monocytes into Ly6Clo TREML4+ monocytes. We further identified two additional transcriptional requirements for development of Ly6Clo monocytes. Deletion of BCL6 from myeloid progenitors abrogated development of Ly6Clo monocytes. IRF2 was also required for Ly6Clo monocyte development in a cell-intrinsic manner. DLL1-induced in vitro transition into Ly6Clo TREML4+ monocytes required IRF2 but unexpectedly could occur in the absence of NUR77 or BCL6. These results imply a transcriptional hierarchy for these factors in controlling Ly6Clo monocyte development.
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Affiliation(s)
- Kevin W. O’Connor
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
| | - Tiantian Liu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
| | - Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
| | - Carlos G. Briseño
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
| | - Katia Georgopoulos
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA02114
| | - Theresa L. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
| | - Kenneth M. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO63110
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Sadhu S, Dalal R, Dandotiya J, Binayke A, Singh V, Tripathy MR, Das V, Goswami S, Kumar S, Rizvi ZA, Awasthi A. IL-9 aggravates SARS-CoV-2 infection and exacerbates associated airway inflammation. Nat Commun 2023; 14:4060. [PMID: 37429848 DOI: 10.1038/s41467-023-39815-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 06/30/2023] [Indexed: 07/12/2023] Open
Abstract
SARS-CoV-2 infection is known for causing broncho-alveolar inflammation. Interleukin 9 (IL-9) induces airway inflammation and bronchial hyper responsiveness in respiratory viral illnesses and allergic inflammation, however, IL-9 has not been assigned a pathologic role in COVID-19. Here we show, in a K18-hACE2 transgenic (ACE2.Tg) mouse model, that IL-9 contributes to and exacerbates viral spread and airway inflammation caused by SARS-CoV-2 infection. ACE2.Tg mice with CD4+ T cell-specific deficiency of the transcription factor Forkhead Box Protein O1 (Foxo1) produce significantly less IL-9 upon SARS-CoV-2 infection than the wild type controls and they are resistant to the severe inflammatory disease that characterises the control mice. Exogenous IL-9 increases airway inflammation in Foxo1-deficient mice, while IL-9 blockade reduces and suppresses airway inflammation in SARS-CoV-2 infection, providing further evidence for a Foxo1-Il-9 mediated Th cell-specific pathway playing a role in COVID-19. Collectively, our study provides mechanistic insight into an important inflammatory pathway in SARS-CoV-2 infection, and thus represents proof of principle for the development of host-directed therapeutics to mitigate disease severity.
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Affiliation(s)
- Srikanth Sadhu
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
- Immunology-Core Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Rajdeep Dalal
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Jyotsna Dandotiya
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Akshay Binayke
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Virendra Singh
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Manas Ranjan Tripathy
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
- Immunology-Core Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Vinayaka Das
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Sandeep Goswami
- Immunology-Core Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Shakti Kumar
- Centre for Human Microbiome and Anti-Microbial Resistance, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Zaigham Abbas Rizvi
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
- Immunology-Core Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India
| | - Amit Awasthi
- Centre for Immunobiology and Immunotherapy, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India.
- Immunology-Core Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad, 121 001, Haryana, India.
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Qiu H, Yang B, Chen Y, Zhu Q, Wen F, Peng M, Wang G, Guo G, Chen B, Maarouf M, Fang M, Chen JL. Influenza A Virus-Induced circRNA circMerTK Negatively Regulates Innate Antiviral Responses. Microbiol Spectr 2023; 11:e0363722. [PMID: 36847523 PMCID: PMC10100971 DOI: 10.1128/spectrum.03637-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023] Open
Abstract
Circular RNAs (circRNAs) are an important subclass of noncoding RNAs implicated in the regulation of multiple biological processes. However, the functional involvement of circRNAs in the pathogenesis of influenza A viruses (IAVs) remains largely unknown. Here, we employed RNA sequencing (RNA-Seq) to examine the differentially expressed circRNAs in mouse lung tissues challenged or not challenged with IAV to evaluate the impact of viral infection on circRNAs in vivo. We observed that 413 circRNAs exhibited significantly altered levels following IAV infection. Among these, circMerTK, the derivative of myeloid-epithelial-reproductive tyrosine kinase (MerTK) pre-mRNA, was highly induced by IAV. Interestingly, circMerTK expression was also increased upon infection with multiple DNA and RNA viruses in human and animal cell lines, and thus it was selected for further studies. Poly(I:C) and interferon β (IFN-β) stimulated circMerTK expression, while RIG-I knockout and IFNAR1 knockout cell lines failed to elevate circMerTK levels after IAV infection, demonstrating that circMerTK is regulated by IFN signaling. Furthermore, circMerTK overexpression or silencing accelerated or impeded IAV and Sendai virus replication, respectively. Silencing circMerTK enhanced the production of type I IFNs and interferon-stimulating genes (ISGs), whereas circMerTK overexpression suppressed their expression at both the mRNA and protein levels. Notably, altering circMerTK expression had no effect on the MerTK mRNA level in cells infected or not infected with IAV, and vice versa. In addition, human circMerTK and mouse homologs functioned similarly in antiviral responses. Together, these results identify circMerTK as an enhancer of IAV replication through suppression of antiviral immunity. IMPORTANCE CircRNAs are an important class of noncoding RNAs characterized by a covalently closed circular structure. CircRNAs have been proven to impact numerous cellular processes, where they conduct specialized biological activities. In addition, circRNAs are believed to play a crucial role in regulating immune responses. Nevertheless, the functions of circRNAs in the innate immunity against IAV infection remain obscure. In this study, we employed transcriptomic analysis to investigate the alterations in circRNAs expression following IAV infection in vivo. It was found that expression of 413 circRNAs was significantly altered, of which 171 were upregulated, and 242 were downregulated following the IAV infection. Interestingly, circMerTK was identified as a positive regulator of IAV replication in both human and mouse hosts. CircMerTK was shown to influence IFN-β production and its downstream signaling, enhancing IAV replication. This finding provides new insights into the critical roles of circRNAs in regulating antiviral immunity.
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Affiliation(s)
- Haori Qiu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bincai Yang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhai Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qianwen Zhu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Faxin Wen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Min Peng
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guoqing Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guijie Guo
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Mohamed Maarouf
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Egypt
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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5
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Persyn E, Wahlen S, Kiekens L, Van Loocke W, Siwe H, Van Ammel E, De Vos Z, Van Nieuwerburgh F, Matthys P, Taghon T, Vandekerckhove B, Van Vlierberghe P, Leclercq G. IRF2 is required for development and functional maturation of human NK cells. Front Immunol 2022; 13:1038821. [PMID: 36544762 PMCID: PMC9762550 DOI: 10.3389/fimmu.2022.1038821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Natural killer (NK) cells are cytotoxic and cytokine-producing lymphocytes that play an important role in the first line of defense against malignant or virus-infected cells. A better understanding of the transcriptional regulation of human NK cell differentiation is crucial to improve the efficacy of NK cell-mediated immunotherapy for cancer treatment. Here, we studied the role of the transcription factor interferon regulatory factor (IRF) 2 in human NK cell differentiation by stable knockdown or overexpression in cord blood hematopoietic stem cells and investigated its effect on development and function of the NK cell progeny. IRF2 overexpression had limited effects in these processes, indicating that endogenous IRF2 expression levels are sufficient. However, IRF2 knockdown greatly reduced the cell numbers of all early differentiation stages, resulting in decimated NK cell numbers. This was not caused by increased apoptosis, but by decreased proliferation. Expression of IRF2 is also required for functional maturation of NK cells, as the remaining NK cells after silencing of IRF2 had a less mature phenotype and showed decreased cytotoxic potential, as well as a greatly reduced cytokine secretion. Thus, IRF2 plays an important role during development and functional maturation of human NK cells.
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Affiliation(s)
- Eva Persyn
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sigrid Wahlen
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Laura Kiekens
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Hannah Siwe
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Els Van Ammel
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Zenzi De Vos
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Patrick Matthys
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, K.U. Leuven, Leuven, Belgium
| | - Tom Taghon
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bart Vandekerckhove
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Georges Leclercq
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium,Cancer Research Institute Ghent (CRIG), Ghent, Belgium,*Correspondence: Georges Leclercq,
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6
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IRF2 Cooperates with Phosphoprotein of Spring Viremia of Carp Virus to Suppress Antiviral Response in Zebrafish. J Virol 2022; 96:e0131422. [PMID: 36314827 PMCID: PMC9683000 DOI: 10.1128/jvi.01314-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
IFN regulatory factor (IRF) 2 belongs to the IRF1 subfamily, and its functions are not yet fully understood. In this study, we showed that IRF2a was a negative regulator of the interferon (IFN) response induced by spring viremia of carp virus (SVCV). Irf2a-/- knockout zebrafish were less susceptible to SVCV than wild-type fish. Transcriptomic analysis reveals that differentially expressed genes (DEGs) in the irf2a-/- and irf2a+/+ cells derived caudal fins were mainly involved in cytokine-cytokine receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, and transforming growth factor-beta (TGF-beta) signaling pathway. Interestingly, the basal expression levels of interferon stimulating genes (ISGs), including pkz, mx, apol, and stat1 were higher in the irf2a-/- cells than irf2a+/+ cells, suggesting that they may contribute to the increased viral resistance of the irf2a-/- cells. Overexpression of IRF2a inhibited the activation of ifnφ1 and ifnφ3 induced by SVCV and poly(I:C) in the epithelioma papulosum cyprini (EPC) cells. Further, it was found that SVCV phosphoprotein (SVCV-P) could interact with IRF2a to promote IRF2a nuclear translocation and protein stability via suppressing K48-linked ubiquitination of IRF2a. Both IRF2a and SVCV-P not only destabilized STAT1a but reduced its translocation into the nucleus. Our work demonstrates that IRF2a cooperates with SVCV-P to suppress host antiviral response against viral infection in zebrafish. IMPORTANCE Interferon regulatory factors (IRFs) are central in the regulation of interferon-mediated antiviral immunity. Here, we reported that IRF2a suppressed interferon response and promoted virus replication in zebrafish. The suppressive effects were enhanced by the phosphoprotein of the spring viremia of carp virus (SVCV) via inhibition of K48-linked ubiquitination of IRF2a. IRF2a and SVCV phosphoprotein cooperated to degrade STAT1 and block its nuclear translocation. Our work demonstrated that IRFs and STATs were targeted by the virus through posttranslational modifications to repress interferon-mediated antiviral response in lower vertebrates.
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7
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Cardani‐Boulton A, Boylan BT, Stetsenko V, Bergmann CC. B cells going viral in the CNS: Dynamics, complexities, and functions of B cells responding to viral encephalitis. Immunol Rev 2022; 311:75-89. [PMID: 35984298 PMCID: PMC9804320 DOI: 10.1111/imr.13124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A diverse number of DNA and RNA viruses have the potential to invade the central nervous system (CNS), causing inflammation and injury to cells that have a limited capacity for repair and regeneration. While rare, viral encephalitis in humans is often fatal and survivors commonly suffer from permanent neurological sequelae including seizures. Established treatment options are extremely limited, predominantly relying on vaccines, antivirals, or supportive care. Many viral CNS infections are characterized by the presence of antiviral antibodies in the cerebral spinal fluid (CSF), indicating local maintenance of protective antibody secreting cells. However, the mechanisms maintaining these humoral responses are poorly characterized. Furthermore, while both viral and autoimmune encephalitis are associated with the recruitment of diverse B cell subsets to the CNS, their protective and pathogenic roles aside from antibody production are just beginning to be understood. This review will focus on the relevance of B cell responses to viral CNS infections, with an emphasis on the importance of intrathecal immunity and the potential contribution to autoimmunity. Specifically, it will summarize the newest data characterizing B cell activation, differentiation, migration, and localization in clinical samples as well as experimental models of acute and persistent viral encephalitis.
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Affiliation(s)
| | - Brendan T. Boylan
- Cleveland Clinic Lerner Research Institute, NeuroscienceClevelandOhioUSA,Case Western Reserve University School of Medicine, PathologyClevelandOhioUSA
| | - Volodymyr Stetsenko
- Cleveland Clinic Lerner Research Institute, NeuroscienceClevelandOhioUSA,Kent State University, School of Biomedical SciencesKentOhioUSA
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8
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Kafai NM, Diamond MS, Fox JM. Distinct Cellular Tropism and Immune Responses to Alphavirus Infection. Annu Rev Immunol 2022; 40:615-649. [PMID: 35134315 DOI: 10.1146/annurev-immunol-101220-014952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alphaviruses are emerging and reemerging viruses that cause disease syndromes ranging from incapacitating arthritis to potentially fatal encephalitis. While infection by arthritogenic and encephalitic alphaviruses results in distinct clinical manifestations, both virus groups induce robust innate and adaptive immune responses. However, differences in cellular tropism, type I interferon induction, immune cell recruitment, and B and T cell responses result in differential disease progression and outcome. In this review, we discuss aspects of immune responses that contribute to protective or pathogenic outcomes after alphavirus infection. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Natasha M Kafai
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; , .,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael S Diamond
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA; , .,Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA.,Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Julie M Fox
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA;
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9
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Okubo Y, Tokumaru S, Yamamoto Y, Miyagawa SI, Sanjo H, Taki S. Generation of a common innate lymphoid cell progenitor requires interferon regulatory factor 2. Int Immunol 2019; 31:489-498. [DOI: 10.1093/intimm/dxz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
Innate lymphoid cells (ILCs), composed of heterogeneous populations of lymphoid cells, contribute critically to immune surveillance at mucosal surfaces. ILC subsets develop from common lymphoid progenitors through stepwise lineage specification. However, the composition and temporal regulation of the transcription factor network governing such a process remain incompletely understood. Here, we report that deletion of the transcription factor interferon regulatory factor 2 (IRF-2), known also for its importance in the maturation of conventional NK cells, resulted in an impaired generation of ILC1, ILC2 and ILC3 subsets with lymphoid tissue inducer (LTi)-like cells hardly affected. In IRF-2-deficient mice, PD-1hi ILC precursors (ILCPs) that generate these three ILCs but not LTi-like cells were present at normal frequency, while their sub-population expressing high amounts of PLZF, another marker for ILCPs, was severely reduced. Notably, these IRF-2-deficient ILCPs contained normal quantities of PLZF-encoding Zbtb16 messages, and PLZF expression in developing invariant NKT cells within the thymus was unaffected in these mutant mice. These results point to a unique, cell-type selective role for IRF-2 in ILC development, acting at a discrete step critical for the generation of functionally competent ILCPs.
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Affiliation(s)
- Yohei Okubo
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
- Department of Surgery, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Shigeo Tokumaru
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
- Department of Surgery, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Yuta Yamamoto
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
- Department of Surgery, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Shin-ichi Miyagawa
- Department of Surgery, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Hideki Sanjo
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
| | - Shinsuke Taki
- Department of Molecular and Cellular Immunology, Shinshu University School of Medicine, Asahi, Matsumoto, Japan
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Cellular microRNA bta-miR-222 suppresses caprine parainfluenza virus type 3 replication via downregulation of interferon regulatory factor 2. Vet Microbiol 2018; 224:58-65. [DOI: 10.1016/j.vetmic.2018.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 12/23/2022]
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11
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Abstract
Alphaviruses, members of the positive-sense, single-stranded RNA virus family Togaviridae, represent a re-emerging public health concern worldwide as mosquito vectors expand into new geographic ranges. Members of the alphavirus genus tend to induce clinical disease characterized by rash, arthralgia, and arthritis (chikungunya virus, Ross River virus, and Semliki Forest virus) or encephalomyelitis (eastern equine encephalitis virus, western equine encephalitis virus, and Venezuelan equine encephalitis virus), though some patients who recover from the initial acute illness may develop long-term sequelae, regardless of the specific infecting virus. Studies examining the natural disease course in humans and experimental infection in cell culture and animal models reveal that host genetics play a major role in influencing susceptibility to infection and severity of clinical disease. Genome-wide genetic screens, including loss of function screens, microarrays, RNA-sequencing, and candidate gene studies, have further elucidated the role host genetics play in the response to virus infection, with the immune response being found in particular to majorly influence the outcome. This review describes the current knowledge of the mechanisms by which host genetic factors influence alphavirus pathogenesis and discusses emerging technologies that are poised to increase our understanding of the complex interplay between viral and host genetics on disease susceptibility and clinical outcome.
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12
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Deletion of interferon-regulatory factor-1 results in cognitive impairment. Hypertens Res 2018; 41:809-816. [PMID: 30082820 DOI: 10.1038/s41440-018-0080-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/19/2018] [Accepted: 03/25/2018] [Indexed: 11/09/2022]
Abstract
Interferon-regulatory factor (IRF)-1-dependent genes in neurons play a role in ischemic neuronal death; however, the roles of IRF-1 in dementia are not well investigated. Therefore, we assessed the effect of IRF-1 on cognitive function using a vascular cognitive impairment mouse model created by chronic cerebral hypoperfusion. Male 10-week-old C57BL/6 (wild-type; WT) and IRF-1-knockout (IRF-1KO) mice were used in this study. A chronic cerebral hypoperfusion mouse model was generated by bilateral common carotid artery stenosis (BCAS) treatment. After 6 weeks of BCAS, the mice were subjected to the Morris water maze test five times a day for 5 days. In the Morris water maze task, escape latency was significantly prolonged in sham-operated IRF-1KO mice compared with sham-operated WT mice. However, BCAS treatment cancelled such difference in spatial learning between WT and IRF-1KO mice. BCAS treatment decreased CBF, but no significant difference was observed between the two strains after BCAS. Sham-operated IRF-1KO mice showed a decrease in mRNA expression of caspase-1 and an increase in IRF-2 expression in the hippocampus. Expression of angiotensin II type 2 (AT2) receptor, which induces better cognitive function, is regulated by IRF-1; however, no obvious difference in AT2 receptor expression was observed between the two strains even after BCAS. These results suggest that IRF-1 has a protective effect on cognitive decline in a normal condition; however, there was no obvious effect on cognition after chronic cerebral hypoperfusion treatment.
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