Infection and Immunity Lecture 24 - Viral Evasion PDF

INFECTION AND IMMUNITY - PANM22041 LECTURE 24 Viral Evasion of the Innate Immune Response Professor Andrew Davidson E46 Biomedical Sciences Building [email protected] 19/11/24  Overview Interfero...

INFECTION AND IMMUNITY - PANM22041 LECTURE 24 Viral Evasion of the Innate Immune Response Professor Andrew Davidson E46 Biomedical Sciences Building [email protected] 19/11/24  Overview Interferons involved in the innate immune response The type I interferon response Induction of interferons Induction of interferon responsive genes The antiviral state (PKR, RNase L and 2′-5′ oligo(A) synthetase, and Mx proteins) Evasion of the interferon response  Intended Learning Outcomes Describe the different types of interferons and their role in host defence. Provide an overview of the type I interferon (IFN) response. Describe how viral pathogens are sensed and induce IFN production. Understand how binding of IFNs to their receptors triggers the activation of “interferon sensitive gene (ISG)” expression. Understand the role of ISG products in establishing an “antiviral state”, providing some well-studied examples. Describe how viruses have evolved to perturb and evade all arms of the IFN response and understand the implications on the viral host interaction.  The innate response is the first line of immune defense. The innate immune response functions continually in a normal host without any prior exposure to the invading virus. Innate defense systems are encoded by germ-line cells and arose early in the evolution of multicellular organisms. Viruses have evolved to survive in the harsh world of multicellular, genetically outbred hosts that possess powerful innate and adaptive defense mechanisms.  The innate immune response. The innate (or non-specific) immune response discriminates self from non-self by the recognition of biochemical characteristics common to or induced by viruses including: – unusual polymers on virus particles, – distinctive cell surface components – high concentrations of double-stranded RNA (a common intermediate of RNA virus replication) The innate immune response is accompanied by the inflammatory response. The inflammatory response is invoked by ”unnatural“ cell damage (i.e. necrosis as opposed to apoptosis), which is often associated with virus infection. The induction of interferons in cells that have been exposed to virus. Three different types of interferon are induced: Interferon Interferon Producer cells Target cells Inducers Type Type I IFN-α Most, if not all nucleated Most, if not all Viral infection, cells; dendritic cells nucleated cells dsRNA major producers IFN-β Most, if not all nucleated Most, if not all Viral infection, cells; dendritic cells nucleated cells dsRNA major producers Type II IFN-γ T cells, NK cells Most, if not all Antigens, nucleated cells mitogens, IL-2, IL-12 Type III IFN-λ Most, if not all nucleated Largely Viral infection, cells; dendritic cells restricted to dsRNA major producers epithelial cells The three interferon types. The interferon system. sensing signalling antiviral state Katze et al., (2008) Nat Rev Immunol, 8:644-654  The interferon system. Stage 1 (Sensing) The induction of interferons in cells that have been exposed to virus (TLRs, intracellular RLRs.) Stage 2 (Signalling) The induced interferons are secreted and bind to their cognate receptors on adjacent cells. Signal transduction pathways are activated and a set of interferon-inducible genes are expressed. Stage 3 (Antiviral state) The expression of interferon-inducible gene products induces an “antiviral state“, i.e. the cells are no longer able to support virus replication.  Stage 1 - sensing. The signals that trigger the synthesis of interferons are not yet fully understood. Important signals are thought to be mediated by: The recognition of virus components by cell surface receptors (Toll like receptors – TLRs) The recognition of the intracellular production of viral RNA /dsRNA (RIG-I like receptors, RLRS). The recognition of intracellular viral/cellular DNA (cGAS/STING) These signals are collectively known as Pathogen-Associated Molecular Patterns (PAMPs). The molecules that recognize PAMPs are collectively known as Pattern Recognition Receptors (PRRs). Toll-like receptors (TLRs).  TLRs involved in viral recognition TLR molecule Ligands (organism of origin) TLR2 specific virus proteins (ie measles virus HA protein) TLR3 Double-stranded RNA (virus) TLR4 Envelope protein (specific viruses) specific viral proteins (ie dengue virus NS1) HSP60, HSP70, HSPgp96 (host) TLR7 Single-stranded RNA (virus) TLR8 Single-stranded RNA (virus) TLR9 Hypomethylated CpG DNA (virus, bacteria) Chromatin-IgG complexes (host) TLR molecule Expression TLR3 macrophages, dendritic and B cells, intestinal epithelium TLR4 macrophages, dendritic, endothelial and mast cells TLR7 macrophages, B and plasmacytoid dendritic cells TLR8 macrophages, neutrophils TLR9 macrophages, plasmacytoid dendritic cells, B, NK and microglial cells,  RIG-I-like receptors (RLRs). RIG-I MDA5 There are also TLR- IPS-1 independent pathways / MAVS for the recognition of intracellular viral replication.  RIG-I-like receptors (RLRs). Cells express the cytoplasmic RNA helicases RIG-I (retinoic acid- inducible gene) and MDA5 (melanoma differentiation-associated antigen 5). – RIG-I: dsRNA and 5’-triphosphate ssRNA – MDA5: dsRNA RIG-I and MDA5 contain “CARD” like domains that are required for signalling. The CARD domains recognising a CARD domain on the adapter MAVS (mitochondrial antiviral signalling protein; also known as IPS-I or VISA) that is localised to the mitochondrial membrane. The interaction initiates intracellular signalling pathways leading to IRF3, NF-B and AP-1 signalling. Fig 3.3: Flint et al., (2015) Principles of Virology 4th Edn. The cGAS/Sting axis in innate immunity.  The cGAS/Sting axis in innate immunity. Viral or cellular DNA (nuclear/mitochondrial) is detected by cyclic GMP-AMP (cGAMP) synthetase (cGAS). Activated cGAS produces cGAMP(2′-5′) using ATP and GTP. cGAMP(2′-5′) binds to STING (stimulator of interferon genes). Activated STING moves to the Golgi and activates TBK1 which leads to IRF3 and NF-B signalling. Type I INF and proinflammatory cytokine gene transcription. Interferon induction in most cells is biphasic Interferon induction in pDC cells is monophasic (constitutive IRF7 expression) The interferon system. sensing signalling antiviral state Katze et al., (2008) Nat Rev Immunol, 8:644-654  The induced interferons are Stage 2 - Signalling. secreted and bind to their cognate receptors on adjacent cells Jak I and Tyk 2 Tyrosine kinases Stat I and Stat 2 "signal transduction and activators of Signal transduction transcription“ pathways are proteins activated Isgf 3 Interferon stimulated gene factor Irf 9 Interferon regulatory factor ISRE Interferon-stimulated response element Induction of > 300 INF sensitive genes  Stage 3 – The antiviral state. The antiviral state is complex There are, at least, three levels to the antiviral state. 1. Mechanisms to specifically prevent virus replication. 2. Mechanisms to kill the cell if it becomes infected. 3. Mechanisms to kill uninifected cells in the vicinity of infection. Targets for interferon (IFN)-stimulated proteins within viral life cycles. Three “classic” antiviral mechanisms. Protein kinase, RNA activated (PKR) Pkr is a serine-threonine protein kinase composed of an N terminal regulatory domain and a C terminal catalytic domain. Small quantities of PKR are present in uninfected cells but transcription of its gene is induced 10-fold by interferon. Pkr is activated by binding of dsRNA to two motifs at the N terminus of the protein. Activation is accompanied by autophosphorylation. Activated Pkr can also phosphorylate many other substrates. Model of activation of PKR Substate interaction dimerization dsRNA binding Downstream effects  PKR-mediated inhibition of translation When eIF2 is phosphorylated on the alpha-subunit, it binds irreversibly to eIF2B  RNase L and 2′-5′ oligo(A) synthetase RNase L is a nuclease that can degrade most cellular and viral RNA species. Its concentration increases 10 to 1000-fold in response to IFN but the protein remains inactive unless a second enzyme is synthesized. This enzyme, 2′-5′ oligo(A) synthetase (OAS), makes oligomers of adenylic acid but only when activated by dsRNA. These unusual nucleotide oligomers then induce formation of active RNase L. RNase L also has a role in the induction of apoptosis. RNase L and 2′-5′ oligo(A) synthetase One potential action of MxA  Mx proteins Unlike the broad spectrum antiviral effects of PKR and RNase L, Mx proteins are directed against specific viruses. Humans have two genes, termed mxA and mxB. Both protein products, MxA and MxB, reside in the cytoplasm. The MxA protein is able to prevent the replication of influenza virus, VSV, measles virus, human parainfluenza virus type 23 and some bunyaviruses. The mechanism of interference seems to be different for each virus. In the case of bunyaviruses, MxA interfers with the transport of the viral nucleocapsid to the site of virus assembly. In the case of influenza virus, MxA prevents the incoming viral nucleocapsids from being transported to the nucleus, the site of virus transcription and replication. Viruses inhibit distinct aspects of the antiviral response (sensing). The paramyxovirus V protein is able to block the interaction of activated MDA-5 with MAVS, the first downstream partner in the sensing cascade. Viruses inhibit distinct aspects of the antiviral response (signalling). The Hepatitis C virus NS5A protein is able to block the formation of ISGF3 and STAT dimers. It also blocks the action of PKR, as does the virus structural protein E2 Viruses inhibit distinct aspects of the antiviral response (the antiviral state). Influenza virus NS1 protein is able to suppress the interferon response at many levels: binds to dsRNA preventing the activation of PKR and the 2-5 oligoadenylate synthetase- RNase L system. binds directly to PKR and prevents the phosphorylation of eIF2. blocks the nuclear export of polyadenylated cellular transcripts, including interferon response gene transcripts. There is hardly any arm of the interferon response that is not attacked by viruses.  Why is interferon not a wonder-drug to combat all virus infections? In addition to its antiviral activities, interferon has marked effects on uninfected cells. it blocks cell proliferation, alters transcription and induces the expression of many deleterious gene products. The continued production (or administration) of interferon in large amounts has dramatic physiological (side) effects. Interferon acts as a localized “firebreak“ to infection. Therapeutic use of interferon can be effective eg. the treatment of some persistent infections such as hepatitis B and hepatitis C) but it will never be a remedy for the common cold.  Summary The production of type I (best studied) and III interferons is a key component of the innate immune response against viruses. The type I interferon (IFN) response consists of: pathogen sensing and IFN production; IFN signalling and the induction of antiviral state. TLRs, RLRs and cGAS/STING are important for the detection of virus components and replication intermediates and recognition results in the activation of IRF3, IRF7, NF-B and AP-1, leading to the transcription of type I and III IFN genes. IFN is secreted and binds to an IFN receptor on neighbouring cells, leading to JAK-STAT signalling and the transcription of > 300 ISGs. Well characterised ISGs include PKR, 2′-5′ OAS and Mx. Production of the corresponding proteins leads to both broad action and specific antiviral effects. Viruses have evolved to encode proteins that can antagonise all aspects of the IFN response, leading to a delicate balance between induction of the antiviral state and viral inhibition.  Further reading Books: Principles of Virology. Volume II Chapter 3 “Secreted mediators of the innate immune response”. 5th Edn Eds. S.J. Flint et al. Published by ASM Press (2020) – available as eBook – UoB electronic resources Garcia-Sastre (2017). Ten strategies of interferon evasion by viruses. Cell Host and Microbe, v22 p176-184 Cann’s Principles of Molecular Virology. Chapter 6 (7th edition) Rybicki and Cann. Academic Press. 2023 – available as eBook – UoB electronic resources