A type I interferon response defines a conserved microglial state required for effective phagocytosis

Microglia, the innate immune cells of the brain, are exquisitely sensitive to dynamic changes in the brain environment. We used single cell RNA sequencing to define glial responses in the early postnatal somatosensory cortex after partial whisker lesion, revealing transcriptomic shifts in both astrocytes and microglia during the resulting topographic remapping. The most distinct change was the emergence of a type I interferon (IFN-I) responsive microglia population that was rare in the resting cortex but expanded 20-fold after whisker deprivation. The top gene candidate in this cluster, Ifitm3, marked a conserved but transient subset of microglia that were in the process of phagocytosing whole cells. IFITM3 protein identified this subset in vivo, where it was enriched in early microglial phagosomes. Loss of canonical IFN-I signaling in Ifnar1-/- animals resulted in abnormal 'bubble' microglia with deficient phagolysosomal processing. In a meta-analysis of transcriptomes, we identified the IFN-I signature in microglia across a range of pathologies. We identified phagocytic IFITM3+ microglia in two murine disease models: SARS-CoV-2 infection and Alzheimer's Disease. These data reveal the potential of transcriptional profiling after defined perturbation to elicit transient microglial states, and identify a novel role for IFN-I signaling in regulating microglial phagocytosis.

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The brain parenchyma has a type I interferon response that can limit virus spread

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1618157114 ◽

2016 ◽

Vol 114 (1) ◽

pp. E95-E104 ◽

Cited By ~ 25

Author(s):

Eugene Drokhlyansky ◽

Didem Göz Aytürk ◽

Timothy K. Soh ◽

Ryan Chrenek ◽

Elaine O’Loughlin ◽

...

Keyword(s):

Immune Response ◽

Innate Immune Response ◽

Type I Interferon ◽

Brain Parenchyma ◽

Innate Immune ◽

Interferon Response ◽

Type I ◽

Virus Spread ◽

Viral Spread ◽

The Brain

The brain has a tightly regulated environment that protects neurons and limits inflammation, designated “immune privilege.” However, there is not an absolute lack of an immune response. We tested the ability of the brain to initiate an innate immune response to a virus, which was directly injected into the brain parenchyma, and to determine whether this response could limit viral spread. We injected vesicular stomatitis virus (VSV), a transsynaptic tracer, or naturally occurring VSV-derived defective interfering particles (DIPs), into the caudate–putamen (CP) and scored for an innate immune response and inhibition of virus spread. We found that the brain parenchyma has a functional type I interferon (IFN) response that can limit VSV spread at both the inoculation site and among synaptically connected neurons. Furthermore, we characterized the response of microglia to VSV infection and found that infected microglia produced type I IFN and uninfected microglia induced an innate immune response following virus injection.

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The Type I Interferon Response Determines Differences in Choroid Plexus Susceptibility between Newborns and Adults in Herpes Simplex Virus Encephalitis

mBio ◽

10.1128/mbio.00437-16 ◽

2016 ◽

Vol 7 (2) ◽

Cited By ~ 19

Author(s):

Douglas R. Wilcox ◽

Stephen S. Folmsbee ◽

William J. Muller ◽

Richard Longnecker

Keyword(s):

Choroid Plexus ◽

Type I Interferon ◽

Adult Brain ◽

Interferon Response ◽

Type I ◽

Β Receptor ◽

Simplex Virus ◽

The Brain ◽

Hsv 1

ABSTRACTNewborns are significantly more susceptible to severe viral encephalitis than adults, with differences in the host response to infection implicated as a major factor. However, the specific host signaling pathways responsible for differences in susceptibility and neurologic morbidity have remained unknown. In a murine model of HSV encephalitis, we demonstrated that the choroid plexus (CP) is susceptible to herpes simplex virus 1 (HSV-1) early in infection of the newborn but not the adult brain. We confirmed susceptibility of the CP to HSV infection in a human case of newborn HSV encephalitis. We investigated components of the type I interferon (IFN) response in the murine brain that might account for differences in cell susceptibility and found that newborns have a dampened interferon response and significantly lower basal levels of the alpha/beta interferon (IFN-α/β) receptor (IFNAR) than do adults. To test the contribution of IFNAR to restricting infection from the CP, we infected IFNAR knockout (KO) adult mice, which showed restored CP susceptibility to HSV-1 infection in the adult. Furthermore, reduced IFNAR levels did not account for differences we found in the basal levels of several other innate signaling proteins in the wild-type newborn and the adult, including protein kinase R (PKR), that suggested specific regulation of innate immunity in the developing brain. Viral targeting of the CP, a region of the brain that plays a critical role in neurodevelopment, provides a link between newborn susceptibility to HSV and long-term neurologic morbidity among survivors of newborn HSV encephalitis.IMPORTANCECompared to adults, newborns are significantly more susceptible to severe disease following HSV infection. Over half of newborn HSV infections result in disseminated disease or encephalitis, with long-term neurologic morbidity in 2/3 of encephalitis survivors. We investigated differences in host cell susceptibility between newborns and adults that contribute to severe central nervous system disease in the newborn. We found that, unlike the adult brain, the newborn choroid plexus (CP) was susceptible early in HSV-1 infection. We demonstrated that IFN-α/β receptor levels are lower in the newborn brain than in the adult brain and that deletion of this receptor restores susceptibility of the CP in the adult brain. The CP serves as a barrier between the blood and the cerebrospinal fluid and plays a role in proper neurodevelopment. Susceptibility of the newborn choroid plexus to HSV-1 has important implications in viral spread to the brain and, also, in the neurologic morbidity following HSV encephalitis.

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Viperin binds STING and enhances the type-I interferon response following dsDNA detection

10.1101/493098 ◽

2018 ◽

Cited By ~ 3

Author(s):

Keaton M. Crosse ◽

Ebony A. Monson ◽

Arti B. Dumbrepatil ◽

Monique Smith ◽

Yeu-Yang Tseng ◽

...

Keyword(s):

Type I Interferon ◽

Innate Immune ◽

Signalling Pathway ◽

Interferon Response ◽

Type I ◽

Viral Pathogens ◽

Radical Sam ◽

Signalling Molecules ◽

Inducible Protein ◽

Interferon Inducible Protein

AbstractViperin is an interferon-inducible protein that is pivotal for eliciting an effective immune response against an array of diverse viral pathogens. Here we describe a mechanism of viperin’s broad antiviral activity by demonstrating the protein’s ability to synergistically enhance the innate immune dsDNA signalling pathway to limit viral infection. Viperin co-localised with the key signalling molecules of the innate immune dsDNA sensing pathway, STING and TBK1; binding directly to STING and inducing enhanced K63-linked polyubiquitination of TBK1. Subsequent analysis identified viperin’s necessity to bind the cytosolic iron-sulphur assembly component 2A, to prolong its enhancement of the type-I interferon response to aberrant dsDNA. Here we show that viperin facilitates the formation of a signalling enhanceosome, to coordinate efficient signal transduction following activation of the dsDNA signalling pathway; which results in an enhanced antiviral state. We also provide evidence for viperin’s radical SAM enzymatic activity to self-limit its immunomodulatory functions. This data further defines viperin’s role as a positive regulator of innate immune signalling, offering a mechanism of viperin’s broad antiviral capacity.

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Molecular Insight Into the IRE1α-Mediated Type I Interferon Response Induced by Proteasome Impairment in Myeloid Cells of the Brain

Frontiers in Immunology ◽

10.3389/fimmu.2019.02900 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 3

Author(s):

Maja Studencka-Turski ◽

Gonca Çetin ◽

Heike Junker ◽

Frédéric Ebstein ◽

Elke Krüger

Keyword(s):

Type I Interferon ◽

Myeloid Cells ◽

Interferon Response ◽

Type I ◽

The Brain ◽

Insight Into

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Type I interferon–mediated monogenic autoinflammation: The type I interferonopathies, a conceptual overview

Journal of Experimental Medicine ◽

10.1084/jem.20161596 ◽

2016 ◽

Vol 213 (12) ◽

pp. 2527-2538 ◽

Cited By ~ 174

Author(s):

Mathieu P. Rodero ◽

Yanick J. Crow

Keyword(s):

Lupus Erythematosus ◽

Clinical Medicine ◽

Type I Interferon ◽

Treatment Options ◽

Clinical Importance ◽

Innate Immune ◽

Interferon Response ◽

Type I ◽

Monogenic Diseases ◽

Type I Interferonopathies

Type I interferon is a potent substance. As such, the induction, transmission, and resolution of the type I interferon–mediated immune response are tightly regulated. As defined, the type I interferonopathies represent discrete examples of a disturbance of the homeostatic control of this system caused by Mendelian mutations. Considering the complexity of the interferon response, the identification of further monogenic diseases belonging to this disease grouping seems likely, with the recognition of type I interferonopathies becoming of increasing clinical importance as treatment options are developed based on an understanding of disease pathology and innate immune signaling. Definition of the type I interferonopathies indicates that autoinflammation can be both interferon and noninterferon related, and that a primary disturbance of the innate immune system can “spill over” into autoimmunity in some cases. Indeed, that several non-Mendelian disorders, most particularly systemic lupus erythematosus and dermatomyositis, are also characterized by an up-regulation of type I interferon signaling suggests the possibility that insights derived from this work will have relevance to a broader field of clinical medicine.

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Type I Interferon Response Limits Astrovirus Replication and Protects against Increased Barrier PermeabilityIn VitroandIn Vivo

Journal of Virology ◽

10.1128/jvi.02367-15 ◽

2015 ◽

Vol 90 (4) ◽

pp. 1988-1996 ◽

Cited By ~ 26

Author(s):

Shauna A. Marvin ◽

C. Theodore Huerta ◽

Bridgett Sharp ◽

Pamela Freiden ◽

Troy D. Cline ◽

...

Keyword(s):

Type I Interferon ◽

Interferon Response ◽

Type I ◽

Barrier Permeability ◽

Type I Ifns ◽

Human Astroviruses ◽

Human Astrovirus ◽

New Evidence

ABSTRACTLittle is known about intrinsic epithelial cell responses against astrovirus infection. Here we show that human astrovirus type 1 (HAstV-1) infection induces type I interferon (beta interferon [IFN-β]) production in differentiated Caco2 cells, which not only inhibits viral replication by blocking positive-strand viral RNA and capsid protein synthesis but also protects against HAstV-1-increased barrier permeability. Excitingly, we found similar resultsin vivousing a murine astrovirus (MuAstV) model, providing new evidence that virus-induced type I IFNs may protect against astrovirus replication and pathogenesisin vivo.IMPORTANCEHuman astroviruses are a major cause of pediatric diarrhea, yet little is known about the immune response. Here we show that type I interferon limits astrovirus infection and preserves barrier permeability bothin vitroandin vivo. Importantly, we characterized a new mouse model for studying astrovirus replication and pathogenesis.

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A Human 3D neural assembloid model for SARS-CoV-2 infection

10.1101/2021.02.09.430349 ◽

2021 ◽

Author(s):

Lu Wang ◽

David Sievert ◽

Alex E. Clark ◽

Hannah Federman ◽

Benjamin D. Gastfriend ◽

...

Keyword(s):

Clinical Evidence ◽

Type I Interferon ◽

Type I ◽

Transcriptional Responses ◽

The Central Nervous System ◽

Membrane Components ◽

Virus Spreading ◽

The Brain ◽

Basement Membrane Components

AbstractClinical evidence suggests the central nervous system (CNS) is frequently impacted by SARS-CoV-2 infection, either directly or indirectly, although mechanisms remain unclear. Pericytes are perivascular cells within the brain that are proposed as SARS-CoV-2 infection points1. Here we show that pericyte-like cells (PLCs), when integrated into a cortical organoid, are capable of infection with authentic SARS-CoV-2. Prior to infection, PLCs elicited astrocytic maturation and production of basement membrane components, features attributed to pericyte functions in vivo. While traditional cortical organoids showed little evidence of infection, PLCs within cortical organoids served as viral ‘replication hubs’, with virus spreading to astrocytes and mediating inflammatory type I interferon transcriptional responses. Therefore, PLC-containing cortical organoids (PCCOs) represent a new ‘assembloid’ model2 that supports SARS-CoV-2 entry and replication in neural tissue, and PCCOs serve as an experimental model for neural infection.

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Activation of RIG-I-mediated antiviral signaling triggers autophagy through the MAVS-TRAF6-Beclin-1 signaling axis

10.1101/340323 ◽

2018 ◽

Cited By ~ 1

Author(s):

Na-Rae Lee ◽

Junsu Ban ◽

Noh-Jin Lee ◽

Chae-Min Yi ◽

Jiyoon Choi ◽

...

Keyword(s):

Type I Interferon ◽

Sendai Virus ◽

Feedback Mechanism ◽

Innate Immune ◽

Beclin 1 ◽

Interferon Response ◽

Type I ◽

Interferon Signaling ◽

Negative Feedback Mechanism ◽

Signaling Axis

AbstractAutophagy has been implicated in innate immune responses against various intracellular pathogens. Recent studies have reported that autophagy can be triggered by pathogen recognizing sensors, including Toll-like receptors and cyclic guanosine monophosphate-adenosine monophosphate synthase, to participate in innate immunity. In the present study, we examined whether the RIG-I signaling pathway, which detects viral infections by recognizing viral RNA, triggers the autophagic process. The introduction of polyI:C into the cytoplasm, or Sendai virus infection, significantly induced autophagy in normal cells but not in RIG-I-deficient cells. PolyI:C transfection or Sendai virus infection induced autophagy in the cells lacking type-I interferon signaling. This demonstrated that the effect was not due to interferon signaling. RIG-I-mediated autophagy diminished by the deficiency of mitochondrial antiviral signaling protein (MAVS) or tumor necrosis factor receptor-associated factor (TRAF)6, showing that the RIG-I-MAVS-TRAF6 signaling axis was critical for RIG-I-mediated autophagy. We also found that Beclin-1 was translocated to the mitochondria, and it interacted with TRAF6 upon RIG-I activation. Furthermore, Beclin-1 underwent K63-polyubiquitination upon RIG-I activation, and the ubiquitination decreased in TRAF6-deficient cells. This suggests that the RIG-I-MAVS-TRAF6 axis induced K63-linked polyubiquitination of Beclin-1, which has been implicated in triggering autophagy. Collectively, the results of this study show that the recognition of viral infection by RIG-I is capable of inducing autophagy to control viral replication. As deficient autophagy increases the type-I interferon response, the induction of autophagy by the RIG-I pathway might also contribute to preventing an excessive interferon response as a negative-feedback mechanism.ImportanceMammalian cells utilize various innate immune sensors to detect pathogens. Among those sensors, RIG-I recognizes viral RNA to detect intracellular viral replication. Although cells experience diverse physiological changes upon viral infection, studies to understand the role of RIG-I signaling have focused on the induction of type-I interferon. Autophagy is a process that sequesters cytosolic regions and degrades the contents to maintain cellular homeostasis. Autophagy participates in the immune system, and has been known to be triggered by some innate immune sensors, such as TLR4 and cGAS. We demonstrated that autophagy can be triggered by the activation of RIG-I. In addition, we also proved that MAVS-TRAF6 downstream signaling is crucial for the process. Beclin-1, a key molecule in autophagy, is translocated to mitochondria, where it undergoes K63-ubiquitination in a TRAF6-dependent manner upon RIG-I activation. As autophagy negatively regulates RIG-I-mediated signaling, the RIG-I-mediated activation of autophagy may function as a negative-feedback mechanism.

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Pinpointing of cysteine oxidation sites in vivo by high-resolution proteomics reveals mechanism of redox-dependent inhibition of STING

10.1101/2020.03.25.008920 ◽

2020 ◽

Cited By ~ 1

Author(s):

Natalia Zamorano Cuervo ◽

Audray Fortin ◽

Elise Caron ◽

Stéfany Chartier ◽

Nathalie Grandvaux

Keyword(s):

Redox Regulation ◽

Type I Interferon ◽

Cellular Responses ◽

Innate Immune ◽

Type I ◽

Post Translational Modifications ◽

Inhibitory Function ◽

Host Interaction ◽

Interferon Pathway

AbstractProtein function is regulated by post-translational modifications, among which reversible oxidation of Cys (Cys ox-PTM) emerged as a key regulatory mechanism of cellular responses. The redox regulation of virus-host interactions is well documented, but in most cases, proteins subjected to Cys ox-PTM remain unknown. The identification of Cys ox-PTM sites in vivo is essential to underpin our understanding of the mechanisms of the redox regulation. In this study, we present a proteome-wide identification of reversible Cys ox-PTM sites in vivo during stimulation by oxidants using a maleimide-based bioswitch method coupled to mass spectrometry. We identified 2720 unique Cys ox-PTM sites encompassing 1473 proteins with distinct abundance, location and functions. Label-free quantification (LFQ)-based analysis revealed the enrichment of ox-PTM in numerous pathways, many relevant to virus-host interaction. Here, we focused on the oxidation of STING, the central adaptor of the innate immune type I interferon pathway induced upon detection of cytosolic DNA. We provide the first in vivo demonstration of reversible oxidation of Cys148 and Cys206 of STING. Molecular analyses led us to establish a new model in which Cys148 oxidation is constitutive, while Cys206 oxidation is inducible by oxidative stress or by the natural ligand 2’3’-cGAMP. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation through the constraint of a conformational change associated with the formation of inactive polymers containing intermolecular disulfide bonds. This provides new ground for the design of therapies targeting STING relevant to autoinflammatory disorders, immunotherapies and vaccines.Brief summary of the main resultsThe function of proteins is regulated by post-translational modifications, among which reversible oxidation of Cys recently emerged as a key component. Comprehension of redox regulation of cellular responses requires identification of specific oxidation sites in vivo. Using a bioswitch method to specifically label Cys subjected to reversible oxidation coupled to mass spectrometry, we identified thousands of novel oxidation sites. Many are relevant to virus-host interaction pathways. Here, we focused on the oxidation of STING, an adaptor critical for activating the innate immune type I interferon pathway engaged upon cytosolic DNA sensing. Molecular studies led us to establish a new model in which STING Cys148 is oxidized at basal levels, while Cys206 oxidation is induced by oxidative stress and ligand binding. We show that oxidation of Cys206 has an inhibitory function to prevent STING hyperactivation. This study provides ground for novel research avenues aimed at designing therapeutics that target this pathway.

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Inhibiting DDX3X Triggers Tumor-Intrinsic Type I Interferon Response and Enhances Anti-Tumor Immunity

10.21203/rs.3.rs-60342/v1 ◽

2020 ◽

Author(s):

Hyeongjwa Choi ◽

Juntae Kwon ◽

Jiafang Sun ◽

Min Soon Cho ◽

Yifan Sun ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Cells ◽

Breast Cancer Cells ◽

Rna Binding ◽

Type I Interferon ◽

Cytotoxic T Cells ◽

Immune Checkpoint Blockade ◽

Innate Immune ◽

Interferon Response ◽

Type I

Abstract Accumulating evidence has shown that cellular double-stranded RNAs (dsRNAs) induce antiviral innate immune responses in human normal and malignant cancer cells. However, it is not fully understood how endogenous ‘self’ dsRNA homeostasis is regulated in the cell. Here, we show that an RNA-binding protein, DEAD-box RNA helicase 3X (DDX3X), prevents the aberrant accumulation of cellular dsRNAs. Loss of DDX3X induces dsRNA sensor-mediated type I interferon signaling and innate immune response in breast cancer cells due to abnormal cytoplasmic accumulation of dsRNAs. Dual depletion of DDX3X and a dsRNA-editing protein, ADAR1 synergistically activates the cytosolic dsRNA pathway in the breast cancer cells. Moreover, inhibiting DDX3X enhances the antitumor activity by increasing tumor intrinsic-type I interferon response, antigen presentation, and tumor-infiltration of cytotoxic T cells as well as dendritic cells in breast tumors, which may lead to the development of breast cancer therapy by targeting DDX3X in combination with immune checkpoint blockade.

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