51
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Ohsugi T, Yamaguchi K, Zhu C, Ikenoue T, Takane K, Shinozaki M, Tsurita G, Yano H, Furukawa Y. Anti-apoptotic effect by the suppression of IRF1 as a downstream of Wnt/β-catenin signaling in colorectal cancer cells. Oncogene 2019; 38:6051-6064. [PMID: 31292489 DOI: 10.1038/s41388-019-0856-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 02/27/2019] [Accepted: 04/16/2019] [Indexed: 12/29/2022]
Abstract
Impaired Wnt signaling pathway plays a crucial role in the development of colorectal cancer through activation of the β-catenin/TCF7L2 complex. Although genes upregulated by Wnt/β-catenin signaling have been intensively studied, the roles of downregulated genes are poorly understood. Previously, we reported that interferon-induced proteins with tetratricopeptide repeats 2 (IFIT2) was downregulated by the Wnt/β-catenin signaling, and that the suppressed expression of IFIT2 conferred antiapoptotic property to colorectal cancer (CRC) cells. However, the mechanisms underlying how Wnt/β-catenin signaling regulates IFIT2 remain to be elucidated. In this study, we have uncovered that the expression of IFIT2 is induced by IRF1, which is negatively regulated by the Wnt/β-catenin signaling. In addition, we found that downregulation of IRF1 is mediated by its degradation through the ubiquitination-proteasome pathway, and that decreased activity of a deubiquitinase complex containing USP1 and UAF1 is involved in the degradation of IRF1 by Wnt/β-catenin signaling. These data should provide better understanding of the Wnt signaling pathway and human carcinogenesis.
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Affiliation(s)
- Tomoyuki Ohsugi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Chi Zhu
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Tsuneo Ikenoue
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Kiyoko Takane
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Masaru Shinozaki
- Department of Surgery, IMSUT Hospital, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Giichiro Tsurita
- Department of Surgery, IMSUT Hospital, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan
| | - Hideaki Yano
- Department of Surgery, Center Hospital of the National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, Institute of Medical Science, the University of Tokyo, Tokyo, 108-8639, Japan.
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Kayagaki N, Lee BL, Stowe IB, Kornfeld OS, O'Rourke K, Mirrashidi KM, Haley B, Watanabe C, Roose-Girma M, Modrusan Z, Kummerfeld S, Reja R, Zhang Y, Cho V, Andrews TD, Morris LX, Goodnow CC, Bertram EM, Dixit VM. IRF2 transcriptionally induces GSDMD expression for pyroptosis. Sci Signal 2019; 12:12/582/eaax4917. [DOI: 10.1126/scisignal.aax4917] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gasdermin-D (GSDMD) is cleaved by caspase-1, caspase-4, and caspase-11 in response to canonical and noncanonical inflammasome activation. Upon cleavage, GSDMD oligomerizes and forms plasma membrane pores, resulting in interleukin-1β (IL-1β) secretion, pyroptotic cell death, and inflammatory pathologies, including periodic fever syndromes and septic shock—a plague on modern medicine. Here, we showed that IRF2, a member of the interferon regulatory factor (IRF) family of transcription factors, was essential for the transcriptional activation of GSDMD. A forward genetic screen with N-ethyl-N-nitrosourea (ENU)–mutagenized mice linked IRF2 to inflammasome signaling. GSDMD expression was substantially attenuated in IRF2-deficient macrophages, endothelial cells, and multiple tissues, which corresponded with reduced IL-1β secretion and inhibited pyroptosis. Mechanistically, IRF2 bound to a previously uncharacterized but unique site within the GSDMD promoter to directly drive GSDMD transcription for the execution of pyroptosis. Disruption of this single IRF2-binding site abolished signaling by both the canonical and noncanonical inflammasomes. Together, our data illuminate a key transcriptional mechanism for expression of the gene encoding GSDMD, a critical mediator of inflammatory pathologies.
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Abstract
The Interferon regulatory factors (IRFs) are a family of transcription factors that play pivotal roles in many aspects of the immune response, including immune cell development and differentiation and regulating responses to pathogens. Three family members, IRF3, IRF5, and IRF7, are critical to production of type I interferons downstream of pathogen recognition receptors that detect viral RNA and DNA. A fourth family member, IRF9, regulates interferon-driven gene expression. In addition, IRF4, IRF8, and IRF5 regulate myeloid cell development and phenotype, thus playing important roles in regulating inflammatory responses. Thus, understanding how their levels and activity is regulated is of critical importance given that perturbations in either can result in dysregulated immune responses and potential autoimmune disease. This review will focus the role of IRF family members in regulating type I IFN production and responses and myeloid cell development or differentiation, with particular emphasis on how regulation of their levels and activity by ubiquitination and microRNAs may impact autoimmune disease.
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Affiliation(s)
- Caroline A Jefferies
- Department of Medicine, Division of Rheumatology and Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, United States
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54
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Krishnakumar V, Durairajan SSK, Alagarasu K, Li M, Dash AP. Recent Updates on Mouse Models for Human Immunodeficiency, Influenza, and Dengue Viral Infections. Viruses 2019; 11:E252. [PMID: 30871179 PMCID: PMC6466164 DOI: 10.3390/v11030252] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/09/2019] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Well-developed mouse models are important for understanding the pathogenesis and progression of immunological response to viral infections in humans. Moreover, to test vaccines, anti-viral drugs and therapeutic agents, mouse models are fundamental for preclinical investigations. Human viruses, however, seldom infect mice due to differences in the cellular receptors used by the viruses for entry, as well as in the innate immune responses in mice and humans. In other words, a species barrier exists when using mouse models for investigating human viral infections. Developing transgenic (Tg) mice models expressing the human genes coding for viral entry receptors and knock-out (KO) mice models devoid of components involved in the innate immune response have, to some extent, overcome this barrier. Humanized mouse models are a third approach, developed by engrafting functional human cells and tissues into immunodeficient mice. They are becoming indispensable for analyzing human viral diseases since they nearly recapitulate the human disease. These mouse models also serve to test the efficacy of vaccines and antiviral agents. This review provides an update on the Tg, KO, and humanized mouse models that are used in studies investigating the pathogenesis of three important human-specific viruses, namely human immunodeficiency (HIV) virus 1, influenza, and dengue.
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Affiliation(s)
- Vinodhini Krishnakumar
- Department of Microbiology, School of Life Sciences, Central University of Tamilnadu, Tiruvarur 610 005, India.
| | | | - Kalichamy Alagarasu
- Dengue/Chikungunya Group, ICMR-National Institute of Virology, Pune 411001, India.
| | - Min Li
- Neuroscience Research Laboratory, Mr. & Mrs. Ko Chi-Ming Centre for Parkinson's Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong, HKSAR, China.
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55
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Rodríguez-Carrio J, López P, Alperi-López M, Caminal-Montero L, Ballina-García FJ, Suárez A. IRF4 and IRGs Delineate Clinically Relevant Gene Expression Signatures in Systemic Lupus Erythematosus and Rheumatoid Arthritis. Front Immunol 2019; 9:3085. [PMID: 30666255 PMCID: PMC6330328 DOI: 10.3389/fimmu.2018.03085] [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: 09/10/2018] [Accepted: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Introduction: Overactivation of the type I interferon (IFN) signature has been observed in several systemic autoimmune conditions, such as Systemic Lupus Erythematosus (SLE) or Rheumatoid Arthritis (RA). Impaired control of Interferon-Responding Genes (IRGs) expression by their regulatory mechanisms, including Interferon Regulatory Factors (IRFs), may underlie these findings and it may explain the heterogeneity observed among these conditions. In the present study we aimed to evaluate the associations between IRF4 gene expression and those of IRGs in SLE and RA patients to gain insight about its links with the IFN signature as well as to explore the potential clinical relevance of these associations. Methods: The gene expression of IRF4 and IRGs (IFI44, IFI44L, IFI6, and MX1) in peripheral blood was analyzed in 75 SLE patients, 98 RA patients, and 28 healthy controls. A group of 13 biological-naïve RA patients was prospectively followed upon TNFα-blockade. The associations among IRF4 and IRGs were evaluated by principal component analyses (PCA), correlations and network analyses. Publicly available datasets were used for replication. Results: A broad activation of IRGs was observed in autoimmune patients, although certain heterogeneity can be distinguished, whereas IRF4 was only upregulated in RA. The differential expression of IRF4 in RA was then confirmed in publicly available gene expression datasets. PCA revealed different associations among IRF4 and IRGs in each condition, which was later confirmed by correlation and network analyses. Cluster analysis identified 3 gene expression signatures on the basis of IRF4 and IRGs expression which were differentially used by SLE and RA patients. Cluster III was associated with markers of disease severity in SLE patients. Cluster II, hallmarked by IRF4 upregulation, was linked to clinical stage and mild disease course in RA. TNFα-blockade led to changes in the association between IRF4 and IRGs, whereas increasing IRF4 expression was associated with a good clinical outcome in RA. Conclusions: The differential expression of IRF4 and IRGs observed in SLE and RA can delineate gene expression signatures associated with clinical features and treatment outcomes. These results support a clinically-relevant phenomenon of shaping of the IFN signature by IRF4 in autoimmune patients.
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Affiliation(s)
- Javier Rodríguez-Carrio
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Bone and Mineral Research Unit, REDinREN del ISCIII, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Patricia López
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Mercedes Alperi-López
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Luis Caminal-Montero
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Internal Medicine, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Francisco J Ballina-García
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Rheumatology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Ana Suárez
- Area of Immunology, Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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56
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Stoltz KP, Jondle CN, Pulakanti K, Sylvester PA, Urrutia R, Rao S, Tarakanova VL. Tumor suppressor Interferon Regulatory Factor 1 selectively blocks expression of endogenous retrovirus. Virology 2019; 526:52-60. [PMID: 30342302 PMCID: PMC6875439 DOI: 10.1016/j.virol.2018.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/01/2018] [Accepted: 10/01/2018] [Indexed: 01/23/2023]
Abstract
Endogenous retroviruses (ERVs) comprise 10% of the genome, with many of these transcriptionally silenced post early embryogenesis. Several stimuli, including exogenous virus infection and cellular transformation can reactivate ERV expression via a poorly understood mechanism. We identified Interferon Regulatory Factor 1 (IRF-1), a tumor suppressor and an antiviral host factor, as a suppressor of ERV expression. IRF-1 decreased expression of a specific mouse ERV in vitro and in vivo. IRF-3, but not IRF-7, also decreased expression of distinct ERV families, suggesting that suppression of ERVs is a relevant biological function of the IRF family. Given the emerging appreciation of the physiological relevance of ERV expression in cancer, IRF-1-mediated suppression of specific ERVs may contribute to the overall tumor suppressor activity of this host factor.
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Affiliation(s)
- K P Stoltz
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - C N Jondle
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - K Pulakanti
- Blood Research Institute, BloodCenter of Wisconsin, a Part of Versiti, 8727 West Watertown Plank Road, Milwaukee, WI 53226, United States
| | - P A Sylvester
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - R Urrutia
- Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - S Rao
- Blood Research Institute, BloodCenter of Wisconsin, a Part of Versiti, 8727 West Watertown Plank Road, Milwaukee, WI 53226, United States.
| | - V L Tarakanova
- Microbiology and Immunology Department, Medical College of Wisconsin, Milwaukee, Wisconsin, United States; Cancer Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States.
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57
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Hamed FN, McDonagh AJG, Almaghrabi S, Bakri Y, Messenger AG, Tazi-Ahnini R. Epigallocatechin-3 Gallate Inhibits STAT-1/JAK2/IRF-1/HLA-DR/HLA-B and Reduces CD8 MKG2D Lymphocytes of Alopecia Areata Patients. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15122882. [PMID: 30558329 PMCID: PMC6313664 DOI: 10.3390/ijerph15122882] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Alopecia areata (AA) is associated with Interferon- γ (IFN-γ) mediated T-lymphocyte dysfunction and increased circulating Interleukine-17 (IL-17) levels. Epigallocatechin-3-gallate (EGCG) specifically inhibits IFN-γ pathways and unlike Janus Kinase 1 and 2 (JAK1/JAK2) inhibitors (tofacitinib, ruxolitinib), EGCG is safer, more cost-effective, and is a topically active agent. Our objective is to test the mode of action of EGCG in vitro and ex vivo using HaCat, Jurkat cell lines, and peripheral blood mononuclear cells (PBMCs) of AA patients and healthy controls (HCs), respectively. METHODS distribution of T helper cells (Th1, Th17), and cytotoxic cells (CD8) in PBMCs isolated from 30 AA patients and 30 HCs was investigated by flowcytomterty. In vitro treatment of HaCat and Jurkat cells with 40 μm EGCG for 48 h was performed to measure the level of phosphorylation of signal transducer and activator of transcription protein STAT1, and replicated in ex vivo model using PBMCs of AA patients. RESULTS Interestingly, 40 μm EGCG is capable of completely inhibiting phosphorylation of STAT1 after 48 h in HaCat and Jurkat cells and ex vivo in PBMCs of AA patients. Based on QPCR data, the action of EGCG on p-STAT1 seems to be mediated via downregulation of the expression of JAK2 but not JAK1 leading to the inhibition of human leukocyte antigens (HLA-DR and HLA-B) expression probably via IRF-1. On the other hand, AA patients have significantly increased levels of Th1, Th17, and CD8 cells and the production of IFN-γ and IL-17 by PBMCs in AA patients was significantly higher compared to HC; p = 0.008 and p = 0.006, respectively. Total numbers of CD8+ cells were not significantly different between treated and untreated samples. However, CD8+ cells with positive Natural killer group 2 member D (NKG2D) transmembrane receptor (CD8+ NKG2D+ subset) was significantly reduced when PBMCs were treated with 20 μm EGCG for 48 h. CONCLUSION These results suggest that EGCG has a synergistic action that inhibits expression of HLA-DR and HLA-B molecules via the IFN-γ pathway to maintain immune privilege in HF; also it reduces CD8+ NKG2D+ subset.
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Affiliation(s)
- Fatma N Hamed
- Department of Infection, Immunity and Cardiovascular disease, The Medical School, University of Sheffield, Sheffield S10 2RX, UK.
| | - Andrew J G McDonagh
- Department of Dermatology, Royal Hallamshire Hospital, Sheffield S10 2JF, UK.
| | - Sarah Almaghrabi
- Department of Infection, Immunity and Cardiovascular disease, The Medical School, University of Sheffield, Sheffield S10 2RX, UK.
| | - Youssef Bakri
- Laboratoire de Biologie de Pathologies Humaines, Faculté des Sciences, Université Mohammed V Rabat, Rabat B.P:8007.N.U, Morocco.
| | - Andrew G Messenger
- Department of Dermatology, Royal Hallamshire Hospital, Sheffield S10 2JF, UK.
| | - Rachid Tazi-Ahnini
- Department of Infection, Immunity and Cardiovascular disease, The Medical School, University of Sheffield, Sheffield S10 2RX, UK.
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58
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Fungal ligands released by innate immune effectors promote inflammasome activation during Aspergillus fumigatus infection. Nat Microbiol 2018; 4:316-327. [PMID: 30510167 DOI: 10.1038/s41564-018-0298-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/22/2018] [Indexed: 01/09/2023]
Abstract
Invasive pulmonary aspergillosis causes substantial mortality in immunocompromised individuals. Recognition of Aspergillus fumigatus by the host immune system leads to activation of the inflammasome, which provides protection against infection. However, regulation of inflammasome activation at the molecular level is poorly understood. Here, we describe two distinct pathways that coordinately control inflammasome activation during A. fumigatus infection. The C-type lectin receptor pathway activates both MAPK and NF-κB signalling, which leads to induction of downstream mediators, such as the transcription factor IRF1, and also primes the inflammasomes. Toll-like receptor signalling through the adaptor molecules MyD88 and TRIF in turn mediates efficient activation of IRF1, which induces IRGB10 expression. IRGB10 targets the fungal cell wall, and the antifungal activity of IRGB10 causes hyphae damage, modifies the A. fumigatus surface and inhibits fungal growth. We also demonstrate that one of the major fungal pathogen-associated molecular patterns, β-glucan, directly triggers inflammasome assembly. Thus, the concerted activation of both Toll-like receptors and C-type lectin receptors is required for IRF1-mediated IRGB10 regulation, which is a key event governing ligand release and inflammasome activation upon A. fumigatus infection.
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59
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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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60
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Lou H, Pickering MC. Extracellular DNA and autoimmune diseases. Cell Mol Immunol 2018; 15:746-755. [PMID: 29553134 PMCID: PMC6141478 DOI: 10.1038/cmi.2017.136] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 10/23/2017] [Accepted: 10/23/2017] [Indexed: 01/02/2023] Open
Abstract
Extracellular DNA is secreted from various sources including apoptotic cells, NETotic neutrophils and bacterial biofilms. Extracellular DNA can stimulate innate immune responses to induce type-I IFN production after being endocytosed. This process is central in antiviral responses but it also plays important role in the pathogenesis of a range of autoimmune diseases such as systemic lupus erythematosus. We discuss the recent advances in the understanding of the role of extracellular DNA, released from apoptotic and NETotic cells, in autoimmunity.
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Affiliation(s)
- Hantao Lou
- Molecular Immunology, Imperial College London, London, UK, W12 0NN.
| | - Matthew C Pickering
- Centre for Complement and Inflammation Research, Imperial College London, London, UK, W12 0NN
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61
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Carlin AF, Plummer EM, Vizcarra EA, Sheets N, Joo Y, Tang W, Day J, Greenbaum J, Glass CK, Diamond MS, Shresta S. An IRF-3-, IRF-5-, and IRF-7-Independent Pathway of Dengue Viral Resistance Utilizes IRF-1 to Stimulate Type I and II Interferon Responses. Cell Rep 2018; 21:1600-1612. [PMID: 29117564 DOI: 10.1016/j.celrep.2017.10.054] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 01/19/2023] Open
Abstract
Interferon-regulatory factors (IRFs) are a family of transcription factors (TFs) that translate viral recognition into antiviral responses, including type I interferon (IFN) production. Dengue virus (DENV) and other clinically important flaviviruses are suppressed by type I IFN. While mice lacking the type I IFN receptor (Ifnar1-/-) succumb to DENV infection, we found that mice deficient in three transcription factors controlling type I IFN production (Irf3-/-Irf5-/-Irf7-/- triple knockout [TKO]) survive DENV challenge. DENV infection of TKO mice resulted in minimal type I IFN production but a robust type II IFN (IFN-γ) response. Using loss-of-function approaches for various molecules, we demonstrate that the IRF-3-, IRF-5-, IRF-7-independent pathway predominantly utilizes IFN-γ and, to a lesser degree, type I IFNs. This pathway signals via IRF-1 to stimulate interleukin-12 (IL-12) production and IFN-γ response. These results reveal a key antiviral role for IRF-1 by activating both type I and II IFN responses during DENV infection.
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Affiliation(s)
- Aaron F Carlin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emily M Plummer
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Edward A Vizcarra
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Nicholas Sheets
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Yunichel Joo
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - William Tang
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Jeremy Day
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Jay Greenbaum
- Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA
| | - Christopher K Glass
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Michael S Diamond
- Departments of Medicine, Pathology and Immunology, and Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sujan Shresta
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA; Division of Inflammation Biology, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
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62
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Karki R, Lee E, Place D, Samir P, Mavuluri J, Sharma BR, Balakrishnan A, Malireddi RKS, Geiger R, Zhu Q, Neale G, Kanneganti TD. IRF8 Regulates Transcription of Naips for NLRC4 Inflammasome Activation. Cell 2018; 173:920-933.e13. [PMID: 29576451 DOI: 10.1016/j.cell.2018.02.055] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/17/2018] [Accepted: 02/21/2018] [Indexed: 02/08/2023]
Abstract
Inflammasome activation is critical for host defenses against various microbial infections. Activation of the NLRC4 inflammasome requires detection of flagellin or type III secretion system (T3SS) components by NLR family apoptosis inhibitory proteins (NAIPs); yet how this pathway is regulated is unknown. Here, we found that interferon regulatory factor 8 (IRF8) is required for optimal activation of the NLRC4 inflammasome in bone-marrow-derived macrophages infected with Salmonella Typhimurium, Burkholderia thailandensis, or Pseudomonas aeruginosa but is dispensable for activation of the canonical and non-canonical NLRP3, AIM2, and Pyrin inflammasomes. IRF8 governs the transcription of Naips to allow detection of flagellin or T3SS proteins to mediate NLRC4 inflammasome activation. Furthermore, we found that IRF8 confers protection against bacterial infection in vivo, owing to its role in inflammasome-dependent cytokine production and pyroptosis. Altogether, our findings suggest that IRF8 is a critical regulator of NAIPs and NLRC4 inflammasome activation for defense against bacterial infection.
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Affiliation(s)
- Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ein Lee
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - David Place
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Parimal Samir
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jayadev Mavuluri
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Arjun Balakrishnan
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Rechel Geiger
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qifan Zhu
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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Khoyratty TE, Udalova IA. Diverse mechanisms of IRF5 action in inflammatory responses. Int J Biochem Cell Biol 2018; 99:38-42. [PMID: 29578052 DOI: 10.1016/j.biocel.2018.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 10/25/2022]
Abstract
Interferon regulatory factor 5 (IRF5) is a key signal-dependent transcription factor in myeloid cells. Its expression is induced by granulocyte-macrophage colony stimulating factor and interferon-gamma. IRF5 protein is further activated in response to stimulation, translocating to the nucleus where it mediates inflammatory responses. IRF5 is capable of both the up-regulation of pro-inflammatory genes and repressing anti-inflammatory mediators, thus polarising macrophages to a pro-inflammatory phenotype. We discuss IRF5 interactions with a wide range of transcriptional regulators that give rise to its diverse effects at the level of chromatin.
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Affiliation(s)
- Tariq E Khoyratty
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, United Kingdom
| | - Irina A Udalova
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, United Kingdom.
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64
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Gun SY, Claser C, Teo TH, Howland SW, Poh CM, Chye RRY, Ng LFP, Rénia L. Interferon regulatory factor 1 is essential for pathogenic CD8+ T cell migration and retention in the brain during experimental cerebral malaria. Cell Microbiol 2018; 20:e12819. [PMID: 29281764 DOI: 10.1111/cmi.12819] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/15/2017] [Accepted: 11/26/2017] [Indexed: 12/22/2022]
Abstract
Host immune response has a key role in controlling the progression of malaria infection. In the well-established murine model of experimental cerebral malaria (ECM) with Plasmodium berghei ANKA infection, proinflammatory Th1 and CD8+ T cell response are essential for disease development. Interferon regulatory factor 1 (IRF1) is a transcription factor that promotes Th1 responses, and its absence was previously shown to protect from ECM death. Yet the exact mechanism of protection remains unknown. Here we demonstrated that IRF1-deficient mice (IRF1 knockout) were protected from ECM death despite displaying early neurological signs. Resistance to ECM death was a result of reduced parasite sequestration and pathogenic CD8+ T cells in the brain. Further analysis revealed that IRF1 deficiency suppress interferon-γ production and delayed CD8+ T cell proliferation. CXCR3 expression was found to be decreased in pathogenic CD8+ T cells, which limited their migration to the brain. In addition, reduced expression of adhesion molecules by brain endothelial cells hampered leucocyte retention in the brain. Taken together, these factors limited sequestration of pathogenic CD8+ T cells and consequently its ability to induce extensive damage to the blood-brain barrier.
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Affiliation(s)
- Sin Yee Gun
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Carla Claser
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Teck Hui Teo
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shanshan W Howland
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chek Meng Poh
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rebecca Ren Ying Chye
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Biological Science, National University of Singapore, Singapore
| | - Lisa F P Ng
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Laurent Rénia
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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65
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Yang MQ, Du Q, Varley PR, Goswami J, Liang Z, Wang R, Li H, Stolz DB, Geller DA. Interferon regulatory factor 1 priming of tumour-derived exosomes enhances the antitumour immune response. Br J Cancer 2018; 118:62-71. [PMID: 29112686 PMCID: PMC5765230 DOI: 10.1038/bjc.2017.389] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/16/2017] [Accepted: 10/04/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tumour-derived exosomes (TEXs) have a potential for application in cancer vaccines. Whether TEXs after induction by interferon regulatory factor 1 (IRF-1) are capable of enhancing the antitumour response remains to be determined. METHODS Exosomes released by tumour cells infected with IRF-1-expressing adenovirus (IRF-1-Exo) or treated with interferon-γ (IFN-Exo) were isolated via ultracentrifugation. The IRF-1 target proteins IL-15Rα and MHC class I (MHC-I) were analysed by western blot. Exosomes along with CpG adjuvant were injected into tumour models to assess the antitumour effects. Tumours were harvested for immunofluorescence staining. Splenocytes from tumour-bearing mice were co-cultured with tumour cells. The IFNγ-positive and granzyme B-positive CD8α+ splenocyte cells were quantified by flow cytometry. RESULTS The IRF-1-Exo or IFN-Exo displayed increased IL-15Rα and MHC-I expression. Injection of IRF-1-Exo or IFN-Exo combined with CpG had improved antitumour effects in mice. This effect may be a result of increased infiltration of tumours by CD4+ and CD8α+ T cells. Antibody-mediated depletion of CD4+ or CD8+ T cells abrogated the antitumour effects. Splenocytes isolated from CpG+IRF-1-Exo-injected Hepa 1-6 tumour mice had increased IFNγ-positive and granzyme B-positive CD8+ cells after co-culturing with Hepa 1-6 cells as compared with MC38 cells. CONCLUSIONS The IRF-1 priming of TEXs enhances antitumour immune response.
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Affiliation(s)
- Mu-qing Yang
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
- Department of General Surgery, Tenth People’s Hospital affiliated to Tongji University, Shanghai 200072, China
| | - Qiang Du
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Patrick R Varley
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Julie Goswami
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Zhihai Liang
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Ronghua Wang
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Hui Li
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
- The Third Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Donna B Stolz
- Center for Biologic Imaging, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - David A Geller
- Thomas E. Starzl Transplantation Institute, Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
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66
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Interferon Regulatory Factor 1 Protects against Chikungunya Virus-Induced Immunopathology by Restricting Infection in Muscle Cells. J Virol 2017; 91:JVI.01419-17. [PMID: 28835505 DOI: 10.1128/jvi.01419-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 08/20/2017] [Indexed: 01/14/2023] Open
Abstract
The innate immune system protects cells against viral pathogens in part through the autocrine and paracrine actions of alpha/beta interferon (IFN-α/β) (type I), IFN-γ (type II), and IFN-λ (type III). The transcription factor interferon regulatory factor 1 (IRF-1) has a demonstrated role in shaping innate and adaptive antiviral immunity by inducing the expression of IFN-stimulated genes (ISGs) and mediating signals downstream of IFN-γ. Although ectopic expression experiments have suggested an inhibitory function of IRF-1 against infection of alphaviruses in cell culture, its role in vivo remains unknown. Here, we infected Irf1 -/- mice with two distantly related arthritogenic alphaviruses, chikungunya virus (CHIKV) and Ross River virus (RRV), and assessed the early antiviral functions of IRF-1 prior to induction of adaptive B and T cell responses. IRF-1 expression limited CHIKV-induced foot swelling in joint-associated tissues and prevented dissemination of CHIKV and RRV at early time points. Virological and histological analyses revealed greater infection of muscle tissues in Irf1 -/- mice than in wild-type mice. The antiviral actions of IRF-1 appeared to be independent of the induction of type I IFN or the effects of type II and III IFNs but were associated with altered local proinflammatory cytokine and chemokine responses and differential infiltration of myeloid cell subsets. Collectively, our in vivo experiments suggest that IRF-1 restricts CHIKV and RRV infection in stromal cells, especially muscle cells, and that this controls local inflammation and joint-associated swelling.IMPORTANCE Interferon regulatory factor 1 (IRF-1) is a transcription factor that regulates the expression of a broad range of antiviral host defense genes. In this study, using Irf1 -/- mice, we investigated the role of IRF-1 in modulating pathogenesis of two related arthritogenic alphaviruses, chikungunya virus and Ross River virus. Our studies show that IRF-1 controlled alphavirus replication and swelling in joint-associated tissues within days of infection. Detailed histopathological and virological analyses revealed that IRF-1 preferentially restricted CHIKV infection in cells of nonhematopoietic lineage, including muscle cells. The antiviral actions of IRF-1 resulted in decreased local inflammatory responses in joint-associated tissues, which prevented immunopathology.
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67
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Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 2017; 45:9244-9259. [PMID: 28934481 PMCID: PMC5716146 DOI: 10.1093/nar/gkx618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/06/2017] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
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Affiliation(s)
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, 08003, Spain
| | - Vera Pancaldi
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain
| | - Felipe Were
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ignacio Martin-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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van der Weyden L, Karp NA, Swiatkowska A, Adams DJ, Speak AO. Genome wide in vivo mouse screen data from studies to assess host regulation of metastatic colonisation. Sci Data 2017; 4:170129. [PMID: 28895944 PMCID: PMC5827107 DOI: 10.1038/sdata.2017.129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/28/2017] [Indexed: 02/02/2023] Open
Abstract
The process of metastasis is a multi-stage cascade with prior studies suggesting that the colonisation of the secondary site is the rate limiting step. This process involves contributions from the tumour cells and also non-tumour intrinsic factors such as the stroma and the haematopoietic system. In this study, we present data from screening 810 genetically-modified mouse lines with the experimental metastasis assay where intravenous delivery of murine metastatic melanoma B16-F10 cells was used to assess the formation of pulmonary metastasic foci. To date, these data have been studied with a two-step process cumulating in an integrative data analysis to identify genes controlling metastatic colonisation. We present the raw data, and a description to support fresh analyses where researchers can look both within and across gene sets to further elucidate process that regulate metastatic colonisation.
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Affiliation(s)
| | - Natasha A Karp
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.,Quantitative Biology, IMED, AstraZeneca, Darwin Building (Unit 310), Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK
| | | | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Anneliese O Speak
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
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69
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Zhao B, Lu Q, Cheng Y, Belcher JM, Siew ED, Leaf DE, Body SC, Fox AA, Waikar SS, Collard CD, Thiessen-Philbrook H, Ikizler TA, Ware LB, Edelstein CL, Garg AX, Choi M, Schaub JA, Zhao H, Lifton RP, Parikh CR. A Genome-Wide Association Study to Identify Single-Nucleotide Polymorphisms for Acute Kidney Injury. Am J Respir Crit Care Med 2017; 195:482-490. [PMID: 27576016 DOI: 10.1164/rccm.201603-0518oc] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Acute kidney injury is a common and severe complication of critical illness and cardiac surgery. Despite significant attempts at developing treatments, therapeutic advances to attenuate acute kidney injury and expedite recovery have largely failed. OBJECTIVES Identifying genetic loci associated with increased risk of acute kidney injury may reveal novel pathways for therapeutic development. METHODS We conducted an exploratory genome-wide association study to identify single-nucleotide polymorphisms associated with genetic susceptibility to in-hospital acute kidney injury. MEASUREMENTS AND MAIN RESULTS We genotyped 609,508 single-nucleotide polymorphisms and performed genotype imputation in 760 acute kidney injury cases and 669 controls. We then evaluated polymorphisms that showed the strongest association with acute kidney injury in a replication patient population containing 206 cases with 1,406 controls. We observed an association between acute kidney injury and four single-nucleotide polymorphisms at two independent loci on metaanalysis of discovery and replication populations. These include rs62341639 (metaanalysis P = 2.48 × 10-7; odds ratio [OR], 0.64; 95% confidence interval [CI], 0.55-0.76) and rs62341657 (P = 3.26 × 10-7; OR, 0.65; 95% CI, 0.55-0.76) on chromosome 4 near APOL1-regulator IRF2, and rs9617814 (metaanalysis P = 3.81 × 10-6; OR, 0.70; 95% CI, 0.60-0.81) and rs10854554 (P = 6.53 × 10-7; OR, 0.67; 95% CI, 0.57-0.79) on chromosome 22 near acute kidney injury-related gene TBX1. CONCLUSIONS Our findings reveal two genetic loci that are associated with acute kidney injury. Additional studies should be conducted to functionally evaluate these loci and to identify other common genetic variants contributing to acute kidney injury.
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Affiliation(s)
- Bixiao Zhao
- 1 Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | - Qiongshi Lu
- 2 Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Yuwei Cheng
- 3 Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
| | - Justin M Belcher
- 4 Program of Applied Translational Research and.,5 Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut.,6 Clinical Epidemiology Research Center, Veterans Affairs Medical Center, West Haven, Connecticut
| | - Edward D Siew
- 7 Division of Nephrology and Hypertension and.,8 Vanderbilt Center for Kidney Disease, and.,9 Vanderbilt Integrated Program for Acute Kidney Injury Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Simon C Body
- 11 Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Amanda A Fox
- 12 Department of Anesthesiology and Pain Management and.,13 McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Charles D Collard
- 14 Department of Anesthesiology, Baylor St. Luke's Medical Center and the Texas Heart Institute, Houston, Texas
| | - Heather Thiessen-Philbrook
- 4 Program of Applied Translational Research and.,5 Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut.,15 Lilibeth Caberto Kidney Clinical Research Unit, London Health Sciences Centre, London, Ontario, Canada
| | - T Alp Ikizler
- 7 Division of Nephrology and Hypertension and.,8 Vanderbilt Center for Kidney Disease, and.,9 Vanderbilt Integrated Program for Acute Kidney Injury Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lorraine B Ware
- 16 Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine
| | | | - Amit X Garg
- 15 Lilibeth Caberto Kidney Clinical Research Unit, London Health Sciences Centre, London, Ontario, Canada.,18 Division of Nephrology, Department of Medicine and Department of Epidemiology and Biostatistics, Western University, London, Ontario, Canada.,19 Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada; and
| | - Murim Choi
- 1 Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
| | | | - Hongyu Zhao
- 1 Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,2 Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Richard P Lifton
- 1 Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,20 Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut
| | - Chirag R Parikh
- 4 Program of Applied Translational Research and.,5 Section of Nephrology, Yale University School of Medicine, New Haven, Connecticut.,6 Clinical Epidemiology Research Center, Veterans Affairs Medical Center, West Haven, Connecticut
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Triad of human cellular proteins, IRF2, FAM111A, and RFC3, restrict replication of orthopoxvirus SPI-1 host-range mutants. Proc Natl Acad Sci U S A 2017; 114:3720-3725. [PMID: 28320935 PMCID: PMC5389286 DOI: 10.1073/pnas.1700678114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Viruses and their hosts can reach balanced states of evolution ensuring mutual survival, which makes it difficult to appreciate the underlying dynamics. To uncover hidden interactions, virus mutants that have lost defense genes may be used. Deletion of the gene that encodes serine protease inhibitor 1 (SPI-1) of rabbitpox virus and vaccinia virus, two closely related orthopoxviruses, prevents their efficient replication in human cells, whereas certain other mammalian cells remain fully permissive. Our high-throughput genome-wide siRNA screen identified host factors that prevent reproduction and spread of the mutant viruses in human cells. More than 20,000 genes were interrogated with individual siRNAs and those that prominently increased replication of the SPI-1 deletion mutant were subjected to a secondary screen. The top hits based on the combined data-replication factor C3 (RFC3), FAM111A, and interferon regulatory factor 2 (IRF2)-were confirmed by custom assays. The siRNAs to RFC1, RFC2, RFC4, and RFC5 mRNAs also enhanced spread of the mutant virus, strengthening the biological significance of the RFC complex as a host restriction factor for poxviruses. Whereas association with proliferating cell nuclear antigen and participation in processive genome replication are common features of FAM111A and RFC, IRF2 is a transcriptional regulator. Microarray analysis, quantitative RT-PCR, and immunoblotting revealed that IRF2 regulated the basal level expression of FAM111A, suggesting that the enhancing effect of depleting IRF2 on replication of the SPI-1 mutant was indirect. Thus, the viral SPI-1 protein and the host IRF2, FAM111A, and RFC complex likely form an interaction network that influences the ability of poxviruses to replicate in human cells.
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71
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Elias HK, Bryder D, Park CY. Molecular mechanisms underlying lineage bias in aging hematopoiesis. Semin Hematol 2017; 54:4-11. [DOI: 10.1053/j.seminhematol.2016.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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72
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Interferon Regulatory Factor 1 and Type I Interferon Cooperate To Control Acute Gammaherpesvirus Infection. J Virol 2016; 91:JVI.01444-16. [PMID: 27795415 DOI: 10.1128/jvi.01444-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/18/2016] [Indexed: 12/20/2022] Open
Abstract
Gammaherpesviruses are ubiquitous pathogens that establish lifelong infection in >95% of adults worldwide and are associated with a variety of malignancies. Coevolution of gammaherpesviruses with their hosts has resulted in an intricate relationship between the virus and the host immune system, and perturbation of the virus-host balance results in pathology. Interferon regulatory factor 1 (IRF-1) is a tumor suppressor that is also involved in the regulation of innate and adaptive immune responses. Here, we show that type I interferon (IFN) and IRF-1 cooperate to control acute gammaherpesvirus infection. Specifically, we demonstrate that a combination of IRF-1 and type I IFN signaling ensures host survival during acute gammaherpesvirus infection and supports IFN gamma-mediated suppression of viral replication. Thus, our studies reveal an intriguing cross talk between IRF-1 and type I and II IFNs in the induction of the antiviral state during acute gammaherpesvirus infection. IMPORTANCE Gammaherpesviruses establish chronic infection in a majority of adults, and this long-term infection is associated with virus-driven development of a range of malignancies. In contrast, a brief period of active gammaherpesvirus replication during acute infection of a naive host is subclinical in most individuals. Here, we discovered that a combination of type I interferon (IFN) signaling and interferon regulatory factor 1 (IRF-1) expression is required to ensure survival of a gammaherpesvirus-infected host past the first 8 days of infection. Specifically, both type I IFN receptor and IRF-1 expression potentiated antiviral effects of type II IFN to restrict gammaherpesvirus replication in vivo, in the lungs, and in vitro, in primary macrophage cultures.
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Li MMH, Bozzacco L, Hoffmann HH, Breton G, Loschko J, Xiao JW, Monette S, Rice CM, MacDonald MR. Interferon regulatory factor 2 protects mice from lethal viral neuroinvasion. J Exp Med 2016; 213:2931-2947. [PMID: 27899441 PMCID: PMC5154937 DOI: 10.1084/jem.20160303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 09/09/2016] [Accepted: 11/01/2016] [Indexed: 01/08/2023] Open
Abstract
Li et al. describe a novel role for IRF2, previously known as a negative regulator of type I IFN signaling, in protection of mice from lethal viral neuroinvasion by facilitating the proper localization of B cells and antibodies to the central nervous system. The host responds to virus infection by activating type I interferon (IFN) signaling leading to expression of IFN-stimulated genes (ISGs). Dysregulation of the IFN response results in inflammatory diseases and chronic infections. In this study, we demonstrate that IFN regulatory factor 2 (IRF2), an ISG and a negative regulator of IFN signaling, influences alphavirus neuroinvasion and pathogenesis. A Sindbis virus strain that in wild-type (WT) mice only causes disease when injected into the brain leads to lethal encephalitis in Irf2−/− mice after peripheral inoculation. Irf2−/− mice fail to control virus replication and recruit immune infiltrates into the brain. Reduced B cells and virus-specific IgG are observed in the Irf2−/− mouse brains despite the presence of peripheral neutralizing antibodies, suggesting a defect in B cell trafficking to the central nervous system (CNS). B cell–deficient μMT mice are significantly more susceptible to viral infection, yet WT B cells and serum are unable to rescue the Irf2−/− mice. Collectively, our data demonstrate that proper localization of B cells and local production of antibodies in the CNS are required for protection. The work advances our understanding of host mechanisms that affect viral neuroinvasion and their contribution to immunity against CNS infections.
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Affiliation(s)
- Melody M H Li
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Leonia Bozzacco
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jakob Loschko
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Jing W Xiao
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Sébastien Monette
- Tri-Institutional Laboratory of Comparative Pathology, Memorial Sloan-Kettering Cancer Center, The Rockefeller University, Weill Cornell Medical College, New York, NY 10065
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065
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Nhu QM, Cuesta N, Vogel SN. Transcriptional regulation of lipopolysaccharide (LPS)-induced Toll-like receptor (TLR) expression in murine macrophages: role of interferon regulatory factors 1 (IRF-1) and 2 (IRF-2). ACTA ACUST UNITED AC 2016. [DOI: 10.1177/09680519060120050401] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Activation of TLRs is most closely associated with induction of pro-inflammatory gene expression; however, expression of many other genes, including the TLR genes themselves, has also been shown to be modulated following TLR engagement. A large family of nuclear transcription factors, the interferon regulatory factors (IRFs), have been implicated in TLR signaling leading to pro-inflammatory gene expression. Given that IRF-1 and IRF-2 counter-regulate the transcriptional activity of many genes, we hypothesized that IRF-1 and IRF-2 might also regulate TLR gene expression following LPS stimulation of murine macrophages. mRNA derived from medium- or LPS-treated primary peritoneal macrophages was analyzed for TLR gene expression using quantitative real-time PCR. In wild-type macrophages, LPS up-regulated expression of TLRs 1—3 and 6—9 steady-state mRNA, while TLR4 mRNA was modestly downregulated. IRF-2—/ — macrophages responded to LPS with dysregulated expression of TLR3, TLR4, and TLR5 mRNA, whereas IRF-1 deficiency dampened LPS-induced mRNA expression for TLR3, TLR6, and TLR9. Functional studies revealed aberrant TLR3 signaling in IRF-2—/ — macrophages. Collectively, these findings reveal an additional level of complexity associated with TLR transcriptional regulation and suggest that the trans-acting factors, IRF-1 and IRF-2, contribute to the innate immune response to infections by regulating TLR gene expression.
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Affiliation(s)
- Quan M. Nhu
- Department of Microbiology and Immunology, University of Maryland, Baltimore (UMB), School of Medicine, Baltimore, Maryland, USA
| | - Natalia Cuesta
- Department of Microbiology and Immunology, University of Maryland, Baltimore (UMB), School of Medicine, Baltimore, Maryland, USA
| | - Stefanie N. Vogel
- Department of Microbiology and Immunology, University of Maryland, Baltimore (UMB), School of Medicine, Baltimore, Maryland, USA,
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Barber S, Salkowski C, Fultz M, Perera PY, McNally R, Vogel S. Regulation of gene expression and nitric oxide production in murine macrophages by the serine/threonine phosphatase inhibitor okadaic acid. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/096805199600300103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
LPS-stimulated macrophages produce cytokines which, at appropriate levels, direct successful immune responses against harmful pathogens. However, excessive cytokine production, as seen in endotoxemia, results in pathophysiological damage to the host. Therefore, understanding mechanisms of cytokine regulation may aid the development of strategies designed to control cytokine production during an ongoing immune response. We have examined the role of okadaic acid-sensitive phosphatases in the production of cytokines and nitric oxide by macrophages. Okadaic acid induces TNFα, IL-1β, IL-6, IFN-β, and IP-10, but not IL-10 or IL-12 (p40) mRNA. Okadaic acid differentially regulates the expression of LPS-inducible IL-10 and IL-12 (p40) mRNA. These findings suggest that okadaic acid-sensitive phosphatases are key regulators of cytokine production in unstimulated and immune-activated macrophages. Finally, okadaic acid inhibits iNOS mRNA and nitric oxide production by macrophages activated by LPS and IFN-γ.
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Affiliation(s)
- S.A. Barber
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - C.A. Salkowski
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - M.J. Fultz
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - P-Y. Perera
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - R. McNally
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - S.N. Vogel
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
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76
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Han X, Wang Y, Zhang X, Qin Y, Qu B, Wu L, Ma J, Zhou Z, Qian J, Dai M, Tang Y, Chan EKL, Harley JB, Zhou S, Shen N. MicroRNA-130b Ameliorates Murine Lupus Nephritis Through Targeting the Type I Interferon Pathway on Renal Mesangial Cells. Arthritis Rheumatol 2016; 68:2232-43. [PMID: 27111096 DOI: 10.1002/art.39725] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/14/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Xiao Han
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Yan Wang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Xiaoyan Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Yuting Qin
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Bo Qu
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Lingling Wu
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Jianyang Ma
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Zhenyuan Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Jie Qian
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Min Dai
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | | | - John B. Harley
- Cincinnati Children's Hospital Medical Center and Cincinnati VA Medical Center; Cincinnati Ohio
| | - Shiyu Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, and Shanghai Jiao Tong University School of Medicine; Shanghai China
| | - Nan Shen
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Institute of Rheumatology, Shanghai Cancer Institute, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, and Shanghai Jiao Tong University School of Medicine, Shanghai, China, and Cincinnati Children's Hospital Medical Center; Cincinnati Ohio
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77
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IRF1 Downregulation by Ras/MEK Is Independent of Translational Control of IRF1 mRNA. PLoS One 2016; 11:e0160529. [PMID: 27508303 PMCID: PMC4980046 DOI: 10.1371/journal.pone.0160529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/19/2016] [Indexed: 01/09/2023] Open
Abstract
Oncogenic activation of Ras/MEK downregulates the expression of interferon regulatory factor 1 (IRF1), which is a prerequisite for oncolytic viruses to replicate in cancer cells [1]. Moreover, restoration of IRF1 expression is essential to induce apoptosis of cancer cells treated with a MEK inhibitor [2]. However, the molecular mechanisms that underlie IRF1 downregulation by Ras/MEK remain unclear. In this study, we determined whether Ras/MEK activation modulates IRF1 expression at its translational level. MEK inhibition increased the activity of IRF1 promoter construct in Ras transformed NIH3T3 cells and wild type MEF, but not in IRF1 deficient MEF, indicating that IRF1 protein is required for the transcriptional activation of IRF1. By conducting reporter analysis using IRF1 5’- and 3’- UTR constructs, we determined that cis elements on 5’- and 3’-UTR of IRF1 mRNA are not involved in the IRF1 regulation by Ras/MEK. We further compared the recruitment of ribosomes to IRF1 mRNA in RasV12 cells treated with or without the MEK inhibitor by conducting polysome analysis. No difference was observed in the polysomal distribution of IRF1 mRNA between RasV12 cells treated with and without the MEK inhibitor. These results suggest that regulation of IRF1 translation is independent of IRF1 downregulation by Ras/MEK.
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78
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Zhan FB, Liu H, Lai RF, Jakovlić I, Wang WB, Wang WM. Molecular identification and functional characterisation of the interferon regulatory factor 1 in the blunt snout bream (Megalobrama amblycephala). FISH & SHELLFISH IMMUNOLOGY 2016; 54:456-465. [PMID: 27150048 DOI: 10.1016/j.fsi.2016.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 06/05/2023]
Abstract
Interferon regulatory factors (IRFs) play a key role in mediating the host response against pathogen infection and other important biological processes. This is the first report of an IRF family member in blunt snout bream Megalobrama amblycephala. The complete cDNA of M. amblycephala (Ma) IRF1 gene has 1422 nucleotides (nt.), with an open reading frame of 858 nt, encoding a polypeptide of 285 amino acids. The putative MaIRF1 polypeptide shared significant structural homology with known IRF1 homologs: a conserved IRF domain was found at the N-terminal and an IRF association domain 2 at the C-terminal. Phylogenetic analysis showed that MaIRF1 amino acid sequence clustered with other teleost IRF1s, with a grass carp ortholog exhibiting the highest similarity. MaIRF1 mRNA expression patterns were studied using quantitative real-time PCR in healthy fish tissues and after a challenge with Aeromonas hydrophila bacterium. It was constitutively expressed in all examined tissues: the highest in blood, the lowest in muscle. The expression after A. hydrophila challenge was up-regulated in liver, spleen and kidney, but down-regulated in intestine and gills. At the protein level, similar expression patterns were observed in liver and gills. Patterns differed in intestine (up-regulation), spleen (down-regulation) and kidney (expression mostly unchanged). This study indicates that MaIRF1 gene plays an important role in the blunt snout bream immune system, hence providing an important base for further studies.
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Affiliation(s)
- Fan-Bin Zhan
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Han Liu
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Rui-Fang Lai
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Ivan Jakovlić
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Bin Wang
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 41500, China
| | - Wei-Min Wang
- College of Fisheries, Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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79
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Langlais D, Barreiro LB, Gros P. The macrophage IRF8/IRF1 regulome is required for protection against infections and is associated with chronic inflammation. J Exp Med 2016; 213:585-603. [PMID: 27001747 PMCID: PMC4821649 DOI: 10.1084/jem.20151764] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/10/2016] [Indexed: 12/26/2022] Open
Abstract
IRF8 and IRF1 are transcriptional regulators that play critical roles in the development and function of myeloid cells, including activation of macrophages by proinflammatory signals such as interferon-γ (IFN-γ). Loss of IRF8 or IRF1 function causes severe susceptibility to infections in mice and in humans. We used chromatin immunoprecipitation sequencing and RNA sequencing in wild type and inIRF8andIRF1mutant primary macrophages to systematically catalog all of the genes bound by (cistromes) and transcriptionally activated by (regulomes) IRF8, IRF1, PU.1, and STAT1, including modulation of epigenetic histone marks. Of the seven binding combinations identified, two (cluster 1 [IRF8/IRF1/STAT1/PU.1] and cluster 5 [IRF1/STAT1/PU.1]) were found to have a major role in controlling macrophage transcriptional programs both at the basal level and after IFN-γ activation. They direct the expression of a set of genes, the IRF8/IRF1 regulome, that play critical roles in host inflammatory and antimicrobial defenses in mouse models of neuroinflammation and of pulmonary tuberculosis, respectively. In addition, this IRF8/IRF1 regulome is enriched for genes mutated in human primary immunodeficiencies and with loci associated with several inflammatory diseases in humans.
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Affiliation(s)
- David Langlais
- Department of Biochemistry, McGill University, H3G 0B1 Montreal, Quebec, Canada Complex Traits Group, McGill University, H3G 0B1 Montreal, Quebec, Canada
| | - Luis B Barreiro
- Sainte Justine Hospital Research Centre, H3T 1C5 Montreal, Quebec, Canada Department of Pediatrics, Faculty of Medicine, University of Montreal, H3T 1J4 Montreal, Quebec, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, H3G 0B1 Montreal, Quebec, Canada Complex Traits Group, McGill University, H3G 0B1 Montreal, Quebec, Canada
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80
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Suprunenko T, Hofer MJ. The emerging role of interferon regulatory factor 9 in the antiviral host response and beyond. Cytokine Growth Factor Rev 2016; 29:35-43. [PMID: 26987614 DOI: 10.1016/j.cytogfr.2016.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/01/2016] [Indexed: 12/24/2022]
Abstract
The host response to viral infections relies on tightly regulated and intricate signaling pathways involving type I interferons (IFN-Is). The IFN-Is mediate their antiviral effects predominantly through a signaling factor complex that comprises the transcription factors, interferon regulatory factor 9 (IRF9) and the signal transducers and activators of transcription (STAT) 1 and STAT2. While STAT1 and STAT2 have been studied extensively, the biological significance of IRF9 is only beginning to emerge. Recent studies have revealed a unique role for IRF9 as a conductor of the cellular responses to IFN-Is. Intriguingly, novel roles for IRF9 outside of the antiviral response are also being identified. Thus IRF9 may have a more extensive influence on cellular processes than previously recognized, ranging from antiviral immune responses to oncogenesis and gut homeostasis. In this review, we will focus on the distinct and emerging roles of IRF9 in the antiviral host response and beyond.
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Affiliation(s)
- Tamara Suprunenko
- School of Life and Environmental Sciences, The Charles Perkins Centre and the Bosch Institute, Maze Crescent G08, The University of Sydney, NSW 2006, Australia.
| | - Markus J Hofer
- School of Life and Environmental Sciences, The Charles Perkins Centre and the Bosch Institute, Maze Crescent G08, The University of Sydney, NSW 2006, Australia.
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81
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Tumor Suppressor Interferon-Regulatory Factor 1 Counteracts the Germinal Center Reaction Driven by a Cancer-Associated Gammaherpesvirus. J Virol 2015; 90:2818-29. [PMID: 26719266 DOI: 10.1128/jvi.02774-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/18/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Gammaherpesviruses are ubiquitous pathogens that are associated with the development of B cell lymphomas. Gammaherpesviruses employ multiple mechanisms to transiently stimulate a broad, polyclonal germinal center reaction, an inherently mutagenic stage of B cell differentiation that is thought to be the primary target of malignant transformation in virus-driven lymphomagenesis. We found that this gammaherpesvirus-driven germinal center expansion was exaggerated and lost its transient nature in the absence of interferon-regulatory factor 1 (IRF-1), a transcription factor with antiviral and tumor suppressor functions. Uncontrolled and persistent expansion of germinal center B cells led to pathological changes in the spleens of chronically infected IRF-1-deficient animals. Additionally, we found decreased IRF-1 expression in cases of human posttransplant lymphoproliferative disorder, a malignant condition associated with gammaherpesvirus infection. The results of our study define an unappreciated role for IRF-1 in B cell biology and provide insight into the potential mechanism of gammaherpesvirus-driven lymphomagenesis. IMPORTANCE Gammaherpesviruses establish lifelong infection in most adults and are associated with B cell lymphomas. While the infection is asymptomatic in many hosts, it is critical to identify individuals who may be at an increased risk of virus-induced cancer. Such identification is currently impossible, as the host risk factors that predispose individuals toward viral lymphomagenesis are poorly understood. The current study identifies interferon-regulatory factor 1 (IRF-1) to be one of such candidate host factors. Specifically, we found that IRF-1 enforces long-term suppression of an inherently mutagenic stage of B cell differentiation that gammaherpesviruses are thought to target for transformation. Correspondingly, in the absence of IRF-1, chronic gammaherpesvirus infection induced pathological changes in the spleens of infected animals. Further, we found decreased IRF-1 expression in human gammaherpesvirus-induced B cell malignancies.
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82
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Enhancer repertoires are reshaped independently of early priming and heterochromatin dynamics during B cell differentiation. Nat Commun 2015; 6:8324. [PMID: 26477271 PMCID: PMC4633987 DOI: 10.1038/ncomms9324] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 08/11/2015] [Indexed: 02/06/2023] Open
Abstract
A widely accepted model posits that activation of enhancers during differentiation goes through a priming step prior to lineage commitment. To investigate the chronology of enhancer repertoire establishment during hematopoiesis, we monitored epigenome dynamics during three developmental stages representing hematopoietic stem cells, B-cell progenitors and mature B-cells. We find that only a minority of enhancers primed in stem cells or progenitors become active at later stages. Furthermore, most enhancers active in differentiated cells were not primed in earlier stages. Thus, the enhancer repertoire is reshaped dynamically during B-cell differentiation and enhancer priming in early stages does not appear to be an obligate step for enhancer activation. Furthermore, our data reveal that heterochromatin and Polycomb-mediated silencing have only a minor contribution in shaping enhancer repertoires during cell differentiation. Together, our data revisit the prevalent model about epigenetic reprogramming during hematopoiesis and give insights into the formation of gene regulatory networks. Enhancers in differentiated haematopoietic cells are generally believed to be primed prior to lineage commitment. Here, the authors show that early priming and Polycomb group mediated silencing have minor roles in shaping the enhancer repertoire in differentiated B cells and that most active enhancers are generated de novo.
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83
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Control of pathogenic effector T-cell activities in situ by PD-L1 expression on respiratory inflammatory dendritic cells during respiratory syncytial virus infection. Mucosal Immunol 2015; 8:746-59. [PMID: 25465101 PMCID: PMC4632244 DOI: 10.1038/mi.2014.106] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/21/2014] [Indexed: 02/04/2023]
Abstract
Respiratory syncytial virus (RSV) infection is a leading cause of severe lower respiratory tract illness in young infants, the elderly and immunocompromised individuals. We demonstrate here that the co-inhibitory molecule programmed cell death 1 (PD-1) is selectively upregulated on T cells within the respiratory tract during both murine and human RSV infection. Importantly, the interaction of PD-1 with its ligand PD-L1 is vital to restrict the pro-inflammatory activities of lung effector T cells in situ, thereby inhibiting the development of excessive pulmonary inflammation and injury during RSV infection. We further identify that PD-L1 expression on lung inflammatory dendritic cells is critical to suppress inflammatory T-cell activities, and an interferon-STAT1-IRF1 axis is responsible for increased PD-L1 expression on lung inflammatory dendritic cells. Our findings suggest a potentially critical role of PD-L1 and PD-1 interactions in the lung for controlling host inflammatory responses and disease progression in clinical RSV infection.
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84
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Zhang XJ, Zhang P, Li H. Interferon regulatory factor signalings in cardiometabolic diseases. Hypertension 2015; 66:222-47. [PMID: 26077571 DOI: 10.1161/hypertensionaha.115.04898] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/14/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Xiao-Jing Zhang
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.)
| | - Peng Zhang
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.)
| | - Hongliang Li
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.).
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85
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Man SM, Karki R, Malireddi RS, Neale G, Vogel P, Yamamoto M, Lamkanfi M, Kanneganti TD. The transcription factor IRF1 and guanylate-binding proteins target activation of the AIM2 inflammasome by Francisella infection. Nat Immunol 2015; 16:467-75. [PMID: 25774715 PMCID: PMC4406811 DOI: 10.1038/ni.3118] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/05/2015] [Indexed: 12/17/2022]
Abstract
Inflammasomes are critical for mounting host defense against pathogens. The molecular mechanisms that control activation of the AIM2 inflammasome in response to different cytosolic pathogens remain unclear. Here we found that the transcription factor IRF1 was required for activation of the AIM2 inflammasome during infection with the Francisella tularensis subspecies novicida (F. novicida), whereas engagement of the AIM2 inflammasome by mouse cytomegalovirus (MCMV) or transfected double-stranded DNA did not require IRF1. Infection of F. novicida detected by the DNA sensor cGAS and its adaptor STING induced type I interferon-dependent expression of IRF1, which drove the expression of guanylate-binding proteins (GBPs); this led to intracellular killing of bacteria and DNA release. Our results reveal a specific requirement for IRF1 and GBPs in the liberation of DNA for sensing by AIM2 depending on the pathogen encountered by the cell.
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Affiliation(s)
- Si Ming Man
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, NSW, Australia
| | - Rajendra Karki
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | | | - Geoffrey Neale
- Hartwell Center for Bioinformatics & Biotechnology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Peter Vogel
- Animal Resources Center and the Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Masahiro Yamamoto
- Department of Microbiology and Immunology, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mohamed Lamkanfi
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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86
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Ren G, Cui K, Zhang Z, Zhao K. Division of labor between IRF1 and IRF2 in regulating different stages of transcriptional activation in cellular antiviral activities. Cell Biosci 2015; 5:17. [PMID: 25960866 PMCID: PMC4424430 DOI: 10.1186/s13578-015-0007-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 03/27/2015] [Indexed: 12/21/2022] Open
Abstract
Background Cellular antiviral activities are critically controlled by transcriptional activation of interferon-inducible genes, involving interferon regulatory factors (IRFs). Previous data suggested that IRF1 is an activator and IRF2 is a repressor, which functionally antagonize each other in transcriptional regulation. However, it is not clear how these two factors function to regulate cellular antiviral activities. Results We show that IRF2 is critically required for the induction of the TLR3 and other interferon-inducible genes in a chromatin environment. While both IRF1 and IRF2 directly interact with the BAF chromatin remodeling complex, IRF2 is associated with the TLR3 promoter in the unstimulated state and IRF1 binding to the promoter is strongly induced by stimulation with interferon, suggesting that these two factors may function at different stages of gene induction in the recruitment of the BAF complex. IRF2 acts to maintain the basal level expression, an open chromatin structure, and active histone modification marks (H3K9, K14 acetylation and H3K4 tri-methylation) of the TLR3 promoter in the unstimulated state, while IRF1 serves to rapidly activate the promoter upon stimulation. Conclusions IRF1 and IRF2 of the IRF family of transcription factors play distinct roles in cellular response to viral infection. IRF2 binds to TLR3 and other IFN-inducible gene promoters and maintains an active chromatin structure in the unstimulated state, which is required for their induction, while IRF1 binding to these promoters activates their transcription upon viral infection. Thus, the division of labor between the IRF transcription factor family members plays a pivotal role in coordinating the transcriptional activation in the cellular antiviral response.
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Affiliation(s)
- Gang Ren
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 PR China.,Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Kairong Cui
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100 PR China
| | - Keji Zhao
- Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892 USA
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87
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Porritt RA, Hertzog PJ. Dynamic control of type I IFN signalling by an integrated network of negative regulators. Trends Immunol 2015; 36:150-60. [DOI: 10.1016/j.it.2015.02.002] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 01/08/2023]
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Abstract
Natural killer (NK) cells are innate lymphocytes that survey the environment and protect the host from infected and cancerous cells. As their name implies, NK cells represent an early line of defense during pathogen invasion by directly killing infected cells and secreting inflammatory cytokines. Although the function of NK cells was first described more than four decades ago, the development of this cytotoxic lineage is not well understood. In recent years, we have begun to identify specific transcription factors that control each stage of development and maturation, from ontogeny of the NK cell progenitor to the effector functions of activated NK cells in peripheral organs. This chapter highlights the transcription factors that are unique to NK cells, or shared between NK cells and other hematopoietic cell lineages, but govern the biology of this cytolytic lymphocyte.
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Affiliation(s)
- Joseph C Sun
- Memorial Sloan Kettering Cancer Center, Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, 408 East 69th Street, ZRC-1402, New York, NY, 10065, USA.
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89
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Mishra A, Sullivan L, Caligiuri MA. Molecular pathways: interleukin-15 signaling in health and in cancer. Clin Cancer Res 2014; 20:2044-50. [PMID: 24737791 DOI: 10.1158/1078-0432.ccr-12-3603] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Interleukin-15 (IL-15) is a proinflammatory cytokine involved in the development, survival, proliferation, and activation of multiple lymphocyte lineages utilizing a variety of signaling pathways. IL-15 utilizes three distinct receptor chains in at least two different combinations to signal and exert its effects on the immune system. The binding of IL-15 to its receptor complex activates an "immune-enhancing" signaling cascade in natural killer cells and subsets of T cells, as well as the induction of a number of proto-oncogenes. Additional studies have explored the role of IL-15 in the development and progression of cancer, notably leukemia of large granular lymphocytes, cutaneous T-cell lymphoma, and multiple myeloma. This review provides an overview of the molecular events in the IL-15 signaling pathway and the aberrancies in its regulation that are associated with chronic inflammation and cancer. We briefly explore the potential therapeutic opportunities that have arisen as a result of these studies to further the treatment of cancer. These involve both targeting the disruption of IL-15 signaling as well as IL-15-mediated enhancement of innate and antigen-specific immunity.
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Affiliation(s)
- Anjali Mishra
- Authors' Affiliation: The Divisions of Dermatology and Hematology, Department of Internal Medicine, The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
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90
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Maruyama S, Kanoh M, Matsumoto A, Kuwahara M, Yamashita M, Asano Y. A novel function of interferon regulatory factor-1: inhibition of Th2 cells by down-regulating the Il4 gene during Listeria infection. Int Immunol 2014; 27:143-52. [PMID: 25280793 DOI: 10.1093/intimm/dxu092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infection with certain pathogens induces a shift of the Th subset balance to a Th1 dominant state. This, in turn, results in the suppression of Th2 responses. We focused on the involvement of interferon regulatory factor-1 (IRF-1) in the suppression of Th2 cells during Listeria infection. We found that the inhibition of IL-4 production by Th2 cells is mediated by a soluble factor (LmSN) produced by Listeria-infected antigen-presenting cells. The inhibition is not observed with T cells from Irf1 gene-targeted mice. IRF-1 suppresses transcription of the Il4 gene in Th2 cells. Under the influence of the LmSN, IRF-1 binds to the 3' untranslated region (UTR) region of the Il4 gene and down-regulates Il4 gene transcription. Finally, we identified IL-1α and IL-1β as the mediator of the LmSN activity. Signaling through IL-1R induces the stabilization and/or nuclear translocation of IRF-1. We propose that IRF-1 functions to induce the T-cell subset shift via a novel mechanism. Under the influence of IL-1, IRF-1 translocates into the nucleus and acts on the 3'UTR region of the Il4 gene, thus inhibiting its transcription in Th2 cells. As a result, the immune system shifts predominantly to a Th1 response during Listeria infection, resulting in effective protection of the host.
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Affiliation(s)
- Saho Maruyama
- Department of Immunology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Makoto Kanoh
- Department of Infection and Host Defenses, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Akira Matsumoto
- Department of Infection and Host Defenses, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Makoto Kuwahara
- Department of Immunology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan Translational Research Center, Ehime University Hospital, Toon, Ehime 791-0295, Japan
| | - Masakatsu Yamashita
- Department of Immunology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan Department of Infection and Host Defenses, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yoshihiro Asano
- Department of Immunology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan Department of Infection and Host Defenses, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
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91
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Interferon regulatory factor 1 restricts gammaherpesvirus replication in primary immune cells. J Virol 2014; 88:6993-7004. [PMID: 24719409 DOI: 10.1128/jvi.00638-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Gammaherpesviruses are ubiquitous pathogens that establish a lifelong infection and are associated with cancer. In spite of the high seroprevalence of infection, the risk factors that predispose the host toward gammaherpesvirus-induced malignancies are still poorly understood. Interferon (IFN) regulatory factor 1 (IRF-1) is a tumor suppressor that is also involved in the regulation of innate and adaptive immune responses. On the basis of its biology, IRF-1 represents a plausible host factor to attenuate gammaherpesvirus infection and tumorigenesis. In this study, we show that IRF-1 restricts gammaherpesvirus replication in primary macrophages, a physiologically relevant immune cell type. In spite of the known role of IRF-1 in stimulating type I IFN expression, induction of a global type I IFN response was similar in IRF-1-deficient and -proficient macrophages during gammaherpesvirus infection. However, IRF-1 was required for optimal expression of cholesterol-25-hydroxylase, a host enzyme that restricted gammaherpesvirus replication in primary macrophages and contributed to the antiviral effects of IRF-1. In summary, the current study provides an insight into the mechanism by which IRF-1 attenuates gammaherpesvirus replication in primary immune cells, a mechanism that is likely to contribute to the antiviral effects of IRF-1 in other virus systems. IMPORTANCE Interferon regulatory factor 1 (IRF-1) is a transcription factor that regulates innate and adaptive immune responses and functions as a tumor suppressor. IRF-1 restricts the replication of diverse viruses; however, the mechanisms responsible for the antiviral effects of IRF-1 are still poorly understood. Gammaherpesviruses are ubiquitous pathogens that are associated with the induction of several malignancies. Here we show that IRF-1 expression attenuates gammaherpesvirus replication in primary macrophages, in part by increasing expression of cholesterol-25-hydroxylase (CH25H). CH25H and its product, 25-hydroxycholesterol, restrict replication of diverse virus families. Thus, our findings offer an insight into the mechanism by which IRF-1 attenuates the replication of gammaherpesviruses, a mechanism that is likely to be applicable to other virus systems.
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92
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Fairfax BP, Humburg P, Makino S, Naranbhai V, Wong D, Lau E, Jostins L, Plant K, Andrews R, McGee C, Knight JC. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 2014; 343:1246949. [PMID: 24604202 PMCID: PMC4064786 DOI: 10.1126/science.1246949] [Citation(s) in RCA: 546] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-γ (IFN-γ) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-β cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.
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Affiliation(s)
- Benjamin P. Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Seiko Makino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Evelyn Lau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katharine Plant
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Robert Andrews
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton CB10 1SA, UK
| | - Chris McGee
- Wellcome Trust Sanger Institute, University of Cambridge, Hinxton CB10 1SA, UK
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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93
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Gene cloning and expression analysis of IRF1 in half-smooth tongue sole (Cynoglossus semilaevis). Mol Biol Rep 2014; 41:4093-101. [DOI: 10.1007/s11033-014-3279-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 02/13/2014] [Indexed: 12/23/2022]
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94
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Abstract
Constitutive expression of interferons (IFNs) and activation of their signaling pathways have pivotal roles in host responses to malignant cells in the tumor microenvironment. IFNs are induced by the innate immune system and in tumors through stimulation of Toll-like receptors (TLRs) and through other signaling pathways in response to specific cytokines. Although in the oncologic context IFNs have been thought of more as exogenous pharmaceuticals, the autocrine and paracrine actions of endogenous IFNs probably have even more critical effects on neoplastic disease outcomes. Through high-affinity cell surface receptors, IFNs modulate transcriptional signaling, leading to regulation of more than 2,000 genes with varying patterns of temporal expression. Induction of the gene products by both unphosphorylated and phosphorylated STAT1 after ligand binding results in alterations in tumor cell survival, inhibition of angiogenesis, and augmentation of actions of T, natural killer (NK), and dendritic cells. The interferon-stimulated gene (ISG) signature can be a favorable biomarker of immune response but, in a seemingly paradoxical finding, a specific subset of the full ISG signature indicates an unfavorable response to DNA-damaging interventions such as radiation. IFNs in the tumor microenvironment thus can alter the emergence, progression, and regression of malignancies.
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Affiliation(s)
- Hyeonjoo Cheon
- Lerner Research Institute, Taussig Cancer Institute, and Case Comprehensive Cancer Center, Cleveland, OH.
| | - Ernest C Borden
- Lerner Research Institute, Taussig Cancer Institute, and Case Comprehensive Cancer Center, Cleveland, OH
| | - George R Stark
- Lerner Research Institute, Taussig Cancer Institute, and Case Comprehensive Cancer Center, Cleveland, OH
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95
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Kidane D, Chae WJ, Czochor J, Eckert KA, Glazer PM, Bothwell ALM, Sweasy JB. Interplay between DNA repair and inflammation, and the link to cancer. Crit Rev Biochem Mol Biol 2014; 49:116-39. [PMID: 24410153 DOI: 10.3109/10409238.2013.875514] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA damage and repair are linked to cancer. DNA damage that is induced endogenously or from exogenous sources has the potential to result in mutations and genomic instability if not properly repaired, eventually leading to cancer. Inflammation is also linked to cancer. Reactive oxygen and nitrogen species (RONs) produced by inflammatory cells at sites of infection can induce DNA damage. RONs can also amplify inflammatory responses, leading to increased DNA damage. Here, we focus on the links between DNA damage, repair, and inflammation, as they relate to cancer. We examine the interplay between chronic inflammation, DNA damage and repair and review recent findings in this rapidly emerging field, including the links between DNA damage and the innate immune system, and the roles of inflammation in altering the microbiome, which subsequently leads to the induction of DNA damage in the colon. Mouse models of defective DNA repair and inflammatory control are extensively reviewed, including treatment of mouse models with pathogens, which leads to DNA damage. The roles of microRNAs in regulating inflammation and DNA repair are discussed. Importantly, DNA repair and inflammation are linked in many important ways, and in some cases balance each other to maintain homeostasis. The failure to repair DNA damage or to control inflammatory responses has the potential to lead to cancer.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics
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96
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Gupta M, Rath PC. Interferon regulatory factor-1 (IRF-1) interacts with regulated in development and DNA damage response 2 (REDD2) in the cytoplasm of mouse bone marrow cells. Int J Biol Macromol 2014; 65:41-50. [PMID: 24412152 DOI: 10.1016/j.ijbiomac.2014.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/12/2013] [Accepted: 01/02/2014] [Indexed: 01/07/2023]
Abstract
IRF-1 is a critical hematopoietic transcription factor, which regulates cell growth, development of immune cells, immune response, tumor suppression, apoptosis and autophagy in mammalian cells. Protein-protein interactions of IRF-1 in mouse bone marrow cells (BMCs) by GST-IRF-1 pull-down followed by mass spectrometry, coimmunoprecipitation, immunoblotting and colocalization show that regulated in development and DNA damage response 2 (REDD2) is an IRF-1-interacting protein. REDD2 is a highly conserved mammalian regulatory protein of the TSC2/mTOR pathway. It is structurally similar to REDD1 but has a distinct loop region. Cellular IRF-1 and REDD2 complex is present in the cytoplasm of BMCs as distinct speckles in punctate pattern. In vitro interaction of recombinant IRF-1 and REDD2 shows their physical interaction. Taken together, our results suggest that IRF-1 physically interacts with REDD2 in the large cytoplasmic protein complex, which may function as cellular signaling proteins for 'cross-talk' of mTOR and cytokine pathways during regulation of cell growth/proliferation, apoptosis and autophagy of mammalian bone marrow cells during health and disease.
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Affiliation(s)
- Manish Gupta
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Pramod C Rath
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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97
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Yang H, Lee SM, Gao B, Zhang J, Fang D. Histone deacetylase sirtuin 1 deacetylates IRF1 protein and programs dendritic cells to control Th17 protein differentiation during autoimmune inflammation. J Biol Chem 2013; 288:37256-66. [PMID: 24214980 DOI: 10.1074/jbc.m113.527531] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The type III histone deacetylase Sirt1 has recently emerged as a critical immune regulator by suppressing T cell immunity and macrophage activation during inflammation, but its role in dendritic cells (DCs) remains unknown. Here, we show that mice with genetic Sirt1 deletion specifically in DCs are resistant to MOG-induced experimental autoimmune encephalomyelitis. Loss of Sirt1 functions in DCs enhances their ability to produce IL-27 and interferon β (IFN-β). Co-cultivation of Sirt1-null DCs with CD4(+) T cells inhibited Th17 differentiation, which is reversed by anti-IL27 and anti-IFN-β neutralization antibodies. Sirt1 antagonizes acetylation of IRF1, a transcription factor that drives IL-27 production. Genetic deletion of IRF1 in Sirt1-null DCs abolishes IL-27 production and suppresses Th17 differentiation. Our results show that the histone deacetylase Sirt1 programs DCs to regulate Th17 differentiation during inflammation.
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Affiliation(s)
- Heeyoung Yang
- From the Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611 and
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98
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Lucas-Hourani M, Dauzonne D, Jorda P, Cousin G, Lupan A, Helynck O, Caignard G, Janvier G, André-Leroux G, Khiar S, Escriou N, Desprès P, Jacob Y, Munier-Lehmann H, Tangy F, Vidalain PO. Inhibition of pyrimidine biosynthesis pathway suppresses viral growth through innate immunity. PLoS Pathog 2013; 9:e1003678. [PMID: 24098125 PMCID: PMC3789760 DOI: 10.1371/journal.ppat.1003678] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/16/2013] [Indexed: 12/19/2022] Open
Abstract
Searching for stimulators of the innate antiviral response is an appealing approach to develop novel therapeutics against viral infections. Here, we established a cell-based reporter assay to identify compounds stimulating expression of interferon-inducible antiviral genes. DD264 was selected out of 41,353 compounds for both its immuno-stimulatory and antiviral properties. While searching for its mode of action, we identified DD264 as an inhibitor of pyrimidine biosynthesis pathway. This metabolic pathway was recently identified as a prime target of broad-spectrum antiviral molecules, but our data unraveled a yet unsuspected link with innate immunity. Indeed, we showed that DD264 or brequinar, a well-known inhibitor of pyrimidine biosynthesis pathway, both enhanced the expression of antiviral genes in human cells. Furthermore, antiviral activity of DD264 or brequinar was found strictly dependent on cellular gene transcription, nuclear export machinery, and required IRF1 transcription factor. In conclusion, the antiviral property of pyrimidine biosynthesis inhibitors is not a direct consequence of pyrimidine deprivation on the virus machinery, but rather involves the induction of cellular immune response. Our therapeutic arsenal to treat viral diseases is extremely limited, and there is a critical need for molecules that could be used against multiple viruses. Among possible strategies, there is a growing interest for molecules stimulating cellular defense mechanisms. We recently developed a functional assay to identify stimulators of antiviral genes, and selected compound DD264 from a chemical library using this approach. While searching for its mode of action, we identified this molecule as an inhibitor of pyrimidine biosynthesis, a metabolic pathway that fuels the cell with pyrimidine nucleobases for both DNA and RNA synthesis. Interestingly, it was recently shown that inhibitors of this metabolic pathway prevent the replication of RNA viruses. Here, we established a functional link between pyrimidine biosynthesis pathway and the induction of antiviral genes, and demonstrated that pyrimidine biosynthesis inhibitors like DD264 or brequinar critically rely on cellular immune response to inhibit virus growth. Thus, pyrimidine deprivation is not directly responsible for the antiviral activity of pyrimidine biosynthesis inhibitors, which rather involves the induction of a metabolic stress and subsequent triggering of cellular defense mechanisms.
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Affiliation(s)
- Marianne Lucas-Hourani
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Daniel Dauzonne
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Pierre Jorda
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Gaëlle Cousin
- Institut Curie, Centre de Recherche, Paris, France
- CNRS, UMR176, Paris, France
| | - Alexandru Lupan
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
| | - Olivier Helynck
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
| | - Grégory Caignard
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Geneviève Janvier
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Gwénaëlle André-Leroux
- Institut Pasteur, Unité de Biochimie Structurale, Paris, France
- CNRS, UMR 3528, Paris, France
| | - Samira Khiar
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Nicolas Escriou
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
| | - Philippe Desprès
- Institut Pasteur, Unité Interactions moléculaires Flavivirus-Hôtes, Paris, France
| | - Yves Jacob
- CNRS, UMR3569, Paris, France
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Paris, France
- Dana-Farber Cancer Institute, Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Boston, Massachusetts, United States of America
| | - Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Paris, France
- CNRS, UMR3523, Paris, France
- * E-mail: (HML); (FT); (POV)
| | - Frédéric Tangy
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
- * E-mail: (HML); (FT); (POV)
| | - Pierre-Olivier Vidalain
- Institut Pasteur, Unité de Génomique Virale et Vaccination, Paris, France
- CNRS, UMR3569, Paris, France
- * E-mail: (HML); (FT); (POV)
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99
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Completion of the entire hepatitis C virus life cycle in genetically humanized mice. Nature 2013; 501:237-41. [PMID: 23903655 PMCID: PMC3858853 DOI: 10.1038/nature12427] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 07/02/2013] [Indexed: 12/12/2022]
Abstract
More than 130 million people worldwide chronically infected with hepatitis C virus (HCV) are at risk of developing severe liver disease. Antiviral treatments are only partially effective against HCV infection, and a vaccine is not available. Development of more efficient therapies has been hampered by the lack of a small animal model. Building on the observation that CD81 and occludin (OCLN) comprise the minimal set of human factors required to render mouse cells permissive to HCV entry, we previously showed that transient expression of these two human genes is sufficient to allow viral uptake into fully immunocompetent inbred mice. Here we demonstrate that transgenic mice stably expressing human CD81 and OCLN also support HCV entry, but innate and adaptive immune responses restrict HCV infection in vivo. Blunting antiviral immunity in genetically humanized mice infected with HCV results in measurable viraemia over several weeks. In mice lacking the essential cellular co-factor cyclophilin A (CypA), HCV RNA replication is markedly diminished, providing genetic evidence that this process is faithfully recapitulated. Using a cell-based fluorescent reporter activated by the NS3-4A protease we visualize HCV infection in single hepatocytes in vivo. Persistently infected mice produce de novo infectious particles, which can be inhibited with directly acting antiviral drug treatment, thereby providing evidence for the completion of the entire HCV life cycle in inbred mice. This genetically humanized mouse model opens new opportunities to dissect genetically HCV infection in vivo and provides an important preclinical platform for testing and prioritizing drug candidates and may also have utility for evaluating vaccine efficacy.
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100
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Berghout J, Langlais D, Radovanovic I, Tam M, MacMicking JD, Stevenson MM, Gros P. Irf8-regulated genomic responses drive pathological inflammation during cerebral malaria. PLoS Pathog 2013; 9:e1003491. [PMID: 23853600 PMCID: PMC3708918 DOI: 10.1371/journal.ppat.1003491] [Citation(s) in RCA: 40] [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: 12/07/2012] [Accepted: 05/28/2013] [Indexed: 02/07/2023] Open
Abstract
Interferon Regulatory Factor 8 (IRF8) is required for development, maturation and expression of anti-microbial defenses of myeloid cells. BXH2 mice harbor a severely hypomorphic allele at Irf8 (Irf8R294C) that causes susceptibility to infection with intracellular pathogens including Mycobacterium tuberculosis. We report that BXH2 are completely resistant to the development of cerebral malaria (ECM) following Plasmodium berghei ANKA infection. Comparative transcriptional profiling of brain RNA as well as chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq) was used to identify IRF8-regulated genes whose expression is associated with pathological acute neuroinflammation. Genes increased by infection were strongly enriched for IRF8 binding sites, suggesting that IRF8 acts as a transcriptional activator in inflammatory programs. These lists were enriched for myeloid-specific pathways, including interferon responses, antigen presentation and Th1 polarizing cytokines. We show that inactivation of several of these downstream target genes (including the Irf8 transcription partner Irf1) confers protection against ECM. ECM-resistance in Irf8 and Irf1 mutants is associated with impaired myeloid and lymphoid cells function, including production of IL12p40 and IFNγ. We note strong overlap between genes bound and regulated by IRF8 during ECM and genes regulated in the lungs of M. tuberculosis infected mice. This IRF8-dependent network contains several genes recently identified as risk factors in acute and chronic human inflammatory conditions. We report a common core of IRF8-bound genes forming a critical inflammatory host-response network. Cerebral malaria is a severe and often lethal complication from infection with Plasmodium falciparum which is driven in part by pathological host inflammatory response to parasitized red cells′ adherence in the brain microvasculature. However, the pathways that initiate and amplify this pathological neuroinflammation are not well understood. As susceptibility to cerebral malaria is variable and has been shown to be partially heritable, we have studied this from a genetic perspective using a mouse model of infection with P. berghei which induces experimental cerebral malaria (ECM). Here we show that mice bearing mutations in the myeloid transcription factor IRF8 and its heterodimerization partner IRF1 are completely resistant to ECM. We have identified the genes and associated networks that are activated by IRF8 during ECM. Loss-of-function mutations of several IRF8 targets are also shown to be protective. Parallel analysis of lungs infected with Mycobacterium tuberculosis show that IRF8-associated core pathways are also engaged during tuberculosis where they play a protective role. This contrast illustrates the balancing act required by the immune system to respond to pathogens and highlights a lynchpin role for IRF8 in both. Finally, several genes in these networks have been individually associated with chronic or acute inflammatory conditions in humans.
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Affiliation(s)
- Joanne Berghout
- Department of Biochemistry and Complex Traits Group, McGill University, Montreal, Quebec, Canada
| | - David Langlais
- Department of Biochemistry and Complex Traits Group, McGill University, Montreal, Quebec, Canada
| | - Irena Radovanovic
- Department of Biochemistry and Complex Traits Group, McGill University, Montreal, Quebec, Canada
| | - Mifong Tam
- McGill University Health Centre, Montreal, Quebec, Canada
| | - John D. MacMicking
- Section of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | | | - Philippe Gros
- Department of Biochemistry and Complex Traits Group, McGill University, Montreal, Quebec, Canada
- * E-mail:
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