Interferons and how viruses evade them Flashcards
What is the most common cause of sporadic encephalitis in the western world?
Herpes simplex encephalitis (HSE)
When is herpes simplex encephalitis most common?
In childhood, affecting previously healthy individuals on primary infection with HSV-1
What does HSE impair?
The CNS’ intrinsic interferon alpha/beta response to HSV infection so the virus replicates to a much higher extent
What is an interferon?
A transferable factor produced when cells are exposed to virus
What do interferons do?
They bind to specific receptors and signals the activation of de novo transcription of hundreds of interferon stimulated genes (ISG)- these put the cells into an anti-viral state
What are type I interferons?
Polypeptides secreted from infected cells
What are the three major functions of type I interferons?
Induce antimicrobial state in infected and neighbouring cells
Modulate innate response to promote antigen presentation and NK cells but inhibit pro inflammation
Activate the adaptive immune response
In terms of type I interferons, what happens when cells sense a viral infection?
They will make an interferon response that will result in the synthesis of new copies of IFN-beta (first interferon to be made)
What happens when IFN-beta is secreted?
It can diffuse and interact with receptors on neighbouring cells. This will lead to the switching on of genes in neighbouring cells to switch them into an anti-viral state
What are plasmacytoid dendritic cells (PDCs)?
Specialised cells that are very good at making interferon (in particular, IFN-alpha)- express high levels of IRF-7 constitutively
How does secretion of type I interferon amount to an adaptive immune response?
It will recruit APCs and adaptive immune cells
Name the type I interferons?
IFN-alpha
IFN-beta
Which cells secrete IFN-beta?
All cells
Where is the IFNAR receptor found?
It is present on all tissues
What triggers IFNbeta induction?
IRF-3
What type of interferons are the first to get made?
Type I
How many genes are there for IFNbeta and alpha?
IFN-beta- one gene
IFN-alpha- 13/14 isotopes
What is a type II interferon?
IFN-gamma
How is IFN-gamma different to IFN-alpha and IFN-beta?
It is a much more specialist immune signalling molecule
It is produced by immune cells- activated T cells and NK cells
It signals through a different receptor- IFNGR
What is a type III interferon?
IFN-lambda
What receptors does IFN lambda signal through?
IL28 receptor and IL10beta
Where are the IL28 and IL10beta receptors mainly present?
On epithelial surfaces
What is IFN-lambda thought to be important for?
Protecting the barriers of your body e.g. respiratory epithelium and gut
It’s very important in the liver as well because polymorphisms are associated with different outcomes from liver viruses
Response to antiviral therapy
What are PAMPs?
Pathogen associated molecular patterns
What are PRRs?
Pattern recognition receptors
Which receptors sense the presence of viruses?
RLRs- cytoplasmic RIG-I like receptors
TLRs- endosomal toll like receptors
NLRs- Cytoplasmic nucleotide oligomerisation domain receptors
What are TLRs?
Membrane proteins- found on the plasma membrane and on endosomal membranes
How do RLRs work?
They sense viruses in the cytoplasm and they signal through a mitochondrial located pathway
What is the most important DNA sensor and what does it do?
cGAS- this signals to a molecule called STING found on the endoplasmic reticulum
Describe the process of interferon induction?
PRRs (e.g. RIG1) will detect PAMPs like single stranded RNA in cytoplasm of the cell, it will then signal through Mavs (on the mitochondrion) which will trigger signalling through various pathways that result in translocation of molecules from cytoplasm to nucleus
These transcription factors will become phosphorylated, they will bind to the promoter regions of target genes (IFN beta) and generate IFN beta transcripts
The IFN beta will then be released from these cells and will travel to neighbouring cells to induce anti-viral state
This is a way of the host controlling the amount of virus in the body
In a normal healthy cell, what shouldn’t be in the endosome?
Any nucleic acids
What senses nucleic acids in the endosome?
TLRs
What happens when TLRs detect nucleic acids in the endosome?
They will signal to a molecule outside the endosome that will then send various transcription factors to the nucleus of the cdll
It will result in the switching on of expression of IFN-alpha
Give an example of a PAMP?
Single stranded RNA
What is the main way that DNA viruses are sensed?
cGAS
What is cGAS?
An enzyme that binds to dsDNA in the cytoplasm and it synthesises a second messenger- cGAMP
What happens to cGAMP after its formation?
It will diffuse to a protein called STING which is found on the endoplasmic reticulum
What does STING do?
Triggers the phosphorylation of same sets of signalling molecules and transcription factors that RNA viruses were triggering- It is a central player in IFN induction through cGAS
What sort of proteins are IFNs?
Soluble proteins
What are the IFN receptors?
Heterodimers of IFNAR1 and IFNAR2
What happens when interferons bind to the cell surface receptor?
The interferon will activate Jak and Tyk which then goes on to phosphorylate the STAT molecules- these then dimerise and combine with IRF9 which goes on and signals to the nucleus to switch on the transcription of a whole set of interferon stimulated signals
Where is the IFN receptor found?
On surface of all cells in body
What is the IFN receptor capable of sensing?
IFN-alpha and IFN-beta
What is IFITM3 and what does it do?
Interferon induced transmembrane protein 3
It restricts virus entry through endosomes
Where are IFITM3 proteins found?
These proteins sit on the membrane of endosomes, in cells that have been previously stimulated with interferon
If a cell doesn’t have IFITM3 when it comes into contact with flu or dengue virus, what happens?
It will enter the cell by passing through the endosomal pathway and fuse its membrane with the endosomal membrane and release its contents into the cytoplasm
If a cell has IFITM3 when it comes into contact with flu or dengue virus, what happens?
The virus gets trapped in the endosome because the IFITM3 modifies the membrane of the endosome and prevents the virus from being able to fuse with the endosomal membrane and release its genome into the cell
What are antiviral mediators?
GTPase with a homology to dynamin
It can form multimers that wrap around the nucleocapsids of incoming viruses
What are the two types of antiviral mediators?
Mx1= inhibits influenza Mx2= inhibits HIV
What does protein kinase R (PKR) do?
It phosphorylates the alpha subunit of eIF2 which is important in translation
What happens if you permanently phosphorylate the alpha subunit of eIF2?
It means that the ribosomes can’t bind onto the mRNA and translate any new genes- when PKR is activated in a cell, no new genes will be translated
What does PKR also phosphorylate as well as the alpha subunit of eIF2?
It also phosphorylates NFkB which is an important transcription factor that is part of the interferon and inflammatory response
Why is switching on PKR an extremely toxic thing to do?
It has such an intricate control mechanism because the cell can’t tolerate making these gene products all the time
When do cells express PKR?
When they have no choice- if they don’t switch on these genes, the cells will be infected by the virus and the virus could kill the cell
How long does the antiviral state last?
Only several hours- SOCS genes suppress the cytokine signalling and turn off the response- if SOCS genes are then switched on, even if the IFN is bound to the receptor the signals won’t get through and no new PKR will be made
How do viruses evade IFN response?
Avoid detection by hiding the PAMP
Interfere globally with host cell gene expression and/or protein synthesis
Block IFN induction cascades by destroying or binding
Inhibit IFN signalling
Block the action of individual IFN induced antiviral enzymes
Activate SOCS
Replication strategy that is insensitive to IFN
What is NS3/4?
A protease that acts as an antagonist to interferon induction by cleaving MAVS
What is MAVS important for?
Detecting Hep C through the RIG-1 pathway- NS3/4 destroys this sensor system
What would happen normally when Hep C enters a cell?
It will be detected by RIG-1 receptors- this will then signal to MAVS which will then switch on the IFN response
What happens when Hep C rapidly synthesises NS3/4?
It cleaves MAVS away from the mitochondrion and prevents the signal from getting through
What is NS1?
An antagonist to interferon induction by binding to the RIG-I/TRIM25/RNA complex and preventing activation of the signalling pathway- acts an early stage
It also prevents nuclear processing of newly induced genes
What would happen in a normal cell with influenza?
The influenza will be triggering RIG-1 via the production of viral RNA in the cytoplasm which would normally signal to MAVS
How does NS1 affect the normal cells response to influenza?
The NS1 in the influenza binds to the RIG/Trim25 complex which is detecting the viral RNA, and stops it from triggering this pathway
The NS1 also migrates to the nucleus where it prevents the export of newly synthesised genes
What do pox viruses do?
Prevent the signal from getting through
What sort of viruses and pox and herpes viruses?
Large DNA viruses
What is more than half of the pox virus genome comprised of?
Accessory genes that modify the immune response
What do pox viruses encode?
Soluble cytokine receptors which mops up IFN and prevents it from ever reaching its receptor
What could the pox virus function of encoding for soluble cytokine receptors be useful for?
In some autoimmune and inflammatory conditions, IFN and other cytokines are produced in abundance and contribute to the pathology of the condition
How does HIV deal with restriction factors?
Using accessory factors
Vif targets APOBEC
Vpu targets tetherin
What is APOBEC3G?
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide like 3G
What is APOBEC3G involved in?
Innate immune resistance to retroviruses and hepadnaviruses
What does reverse transcriptase produce?
DNA from RNA
What is reverse transcriptase able to do in the presence of APOBEC3G?
It is able to modify some of the nucleotides and make them into the wrong version
What does APOBEC3G do?
It dominates dC to dU in the minus strand viral cDNA during reverse transcription which results in G to A hypermutation leading to error catastrophe
What is Vif?
Virus infectivity factor- a small accessory protein encoded for by HIV virus
What does Vif do?
Counteracts the activity of the host innate protection factor APOBEC
What would happen if you didn’t have any Vif in the infected cell?
The APOBEC would be able to modify the reverse transcript o the viral genome and induce hypermutation so the virus doesn’t propagate
What does Vif target?
The APOBEC enzyme for degradation so there is not enough APOBEC to be incorporated into the virus particle and interfere with reverse transcription
What do HIV Vpu, Env and Nef target?
Tetherin
What is tetherin and where is it found?
It sits on the cell surface of virus infected cells and as the virus tries to escape to go and infect other cells, the tethering grabs hold of the virus and prevents it from being released from the infected cell- limits viral infection
What does Vpu do?
Pulls tethering back from the cell surface and targets it for degradation and gets rid of it
What two proteins does ebola code for that helps it counteract the immune response?
VP35- inhibits the RIG-I pathway
VP24- stops the signal from getting through from the IFN beta receptor to the nucleus
What are the consequences of innate immunity in terms of viral pathology?
A combination of damage of infected cells by the virus and damage of infected and bystander cells by the immune response.
Why do viruses modulate the immune response?
Increase they own replication and transmission which can result in inadvertent pathology
How can the effect of interferons change?
It can vary from protective to immunopathologic (making too much of it) - it depends on how much is made- 100 times more IFN is required for IL-6 induction than for Mx
What is used to look at the skewing of IFN response by different viruses?
Transcriptomimics- way of measuring how much mRNAs get switched up
What do proteomics reveal?
Viral control of protein expression- a method of counting proteins that get made from various transcripts
What is the cytokine storm?
The virus replicates and induces high levels of IFN accompanied by massive release of TNF alpha and other cytokines
What is the cytokine storm typical of?
Dengue haemorrhagic fever, severe influenza infections and ebola
What does cytokine storm lead to?
Pulmonary fibrosis which is caused by the accumulation of immune cells in the lung spaces
Why are interferons not used as a broad spectrum antiviral?
They produced several unpleasant side effects- it stimulated the production of several cytokines which made patients feel pretty awful
What type of interferons could be used as an influenza therapeutic?
IFN lambda as it is active on receptors present on epithelial cells but it can’t signal through receptors present on immune cells so no side effects
How are IFNs being used in cancer therapy?
Oncolytic viruses are being engineered that can uniquely replicate inside cancer cells due to the IFN deficient state and kill them
Why are cancer cells IFN deficient?
As cancer cells accumulate mutations, they acquire mutations that lead to loss of pathways in their IFN system
Cancer cells are deficient in their ability to mount a proper interferon response
