Microbiology 2 - Interferons and how viruses evade them

Question 1

What is the most common cause of sporadic encephalitis in the western world?

Answer 1

Herpes Simplex Encephalitis (HSE) - most common in childhood

Affects healthy individuals on primary infection with HSV-1

Question 2

HSE is associated with inborn errors in genes - give some examples and what do they do

Answer 2

e.g. TLR3, UNC93B1, TRIF, TRAF3, TBK1, IRF3

These genes are all linked by a common pathway

Errors in these genes impair intrinsic CNS IFN a/B response to HSV infection

Question 3

What do ZAP and CpG do?

Answer 3

ZAP determines if Nucleic Acid is ours or viruses - if there are too many C=G nucleotides, ZAP targets and degrades the Nucleic acid

Question 4

What is an interferon

Answer 4

Transferable, soluble cytokine, that binds to specific repeaters and signals activation of de novo transcription of Interferon Stimulated Genes (ISGs) - these are antiviral

Also has SEs like fever and inflammation

Question 5

Type 1 IFNs are secreted from infected cells. List 3 of their functions

Answer 5

1. Induce antimicrobial state in infected and neighbouring cells
2. Modulate innate response to promote Ag presentation and NK
3. Activate adaptive immune response

Question 6

What are the main producers of Type 1 IFNs

Answer 6

Plasmacytoid Dendritic Cells (PDCs)

Question 7

What are the type 1 IFNs

Answer 7

IFN alpha and beta

IFNb secreted by all cells

IFNAR receptors on ALL tissues

Question 8

Which regulatory factor triggers production of IFNb

Answer 8

IRF-3

Question 9

Which regulatory factor is important for IFN-a secretion

Answer 9

IRF-7

Question 10

What is a difference between IFN a vs IFN b

Answer 10

There is only 1 IFN-b, but 13-14 isotopes of IFN-a

Question 11

What type of IFN is IFN-gamma and what produces it

Answer 11

It is a type 2 IFN

It is produced by activated T cells and NK cells - signalled through receptor IFNGR

Question 12

What type of IFN is IFN-lambda and where is it mainly present?

What is it signalled by?

Answer 12

Type 3 IFN - signalled by IL28R and IL10-b

Mainly present on epithelial cells - so it doesn’t work on immune cells

Question 13

Polymorphisms in IFN-lambda are associated with improved outcome from which viruses?

Answer 13

HCV and HBV

Question 14

How do cells differentiate self from non-self

Answer 14

They have PRRs that recognise PAMPs

Often sensing foreign nucleic acid

Question 15

Name 3 types of PRRs

Answer 15

1. Cytoplasmic RIG-1 like receptors (RLRs)
2. Endosomal Toll like receptors (TLRs)
3. Cytoplasmic nucleotide oligomerization domain receptors NLRs

Question 16

Where are TLRs located

Answer 16

Membrane proteins - on the membrane

They can be on the cell surface or endosomal

Question 17

Where are RLRs and DNA sensors (e.g. cGAS) located

Answer 17

Cytoplasm

Question 18

Explain how the RIG-I pathway can induce IFN-b

TLR works in a similar way but not through MAVS

Answer 18

1. Viral RNA recognised by RIG-I
2. Receptor changes shape and interacts with MAVS (sits on mitochondria)
3. MAVS activates path that phosphorylates IRF-3
4. IRF-3 enters nucleus and stimulates promotor of IFN-b gene

Question 19

RNA is recognised by which PRRs?

Answer 19

TLR and RIG-I

Question 20

Explain how viral DNA is sensed and pathways triggered as a result

Answer 20

1. Any DNA in the cytoplasm is aberrant and a PAMP, which is sensed by cGAS
2. Causes production of cGAMP
3. This is detected by STING and binds to it (STING sits on organelle membrane)
4. Phosphorylation and dimerisation of IRF-3
5. IFN-b promoted

Question 21

How do IFNs induce antiviral actions

Answer 21

1. They are secreted by the infected cell
2. They then bind receptors on neighbours (paracrine) or same cell (autocrine) - IFNAR-1 and dimerisation occurs due to phosphorylation events
3. This activates ISGs
4. Giving off antiviral signals

Question 22

Name 7 Interferon Stimulated Genes (ISGs) and how they work

Answer 22

1. PKR - inhibits translation by reducing ribosome recycling
2. 2’5OAS - activates RNAse L that destroys ss RNA (including cells own RNA)
3. Mx - inhibit incoming viral genomes - GTPase with homology to dynamin
4. ADAR - induces errors during viral replication
5. Serpine - activates proteases
6. Viperin - inhibits viral budding
7. IFITM3 - restricts viral entry via endosomes - makes endosomal membrane very rigid (lack of IFITM3 = higher risk of influenza)

Question 23

What is Mx. How many forms are there and what is special about it

Answer 23

Mx = ISG

Mx 1 + 2 (cytoplasm) form multimers - wrap around nucleocapsids of incoming viruses (then inhibit transcription, replication, nuclear entry)

Mx 1 - inhibits influenza

Mx 2- inhibits HIV

Question 24

Why does the antiviral state not last

Answer 24

It is only maintained for a few hours - the ability to respond to IFN is lost (negative regulation) - due to SOCS (suppressor of cytokine signalling) genes

Cytokines cause inflammation and also cause collateral damage

Question 25

7 ways in which viruses can evade the IFN response

Answer 25

1. Avoid detection by hiding the PAMP
2. Interfere globally with host cells gene expression and/or protein synthesis
3. Block IFN induction cascades by destroying or binding
4. Block action of individual IFN induced enzymes
5. Inhibit IFN signalling
6. Activate SOCS
7. Replicate in ways that are insensitive to IFN

Question 26

2 ways in which viruses controlling/stopping IFN activation

Answer 26

1. Hep. C virus (HCV) - NS3/4 protease cleaves MAVS so less/no IFN
2. Influenza - NS1 binds to RIG-I/TRIM23/RNA complex which prevents activation of the signalling pathway - also preventing nuclear processing of newly induced genes (e.g. IFN-b)

Question 27

What type of viruses are POX and herpes viruses

Answer 27

Large DNA viruses

Question 28

How do Pox viruses prevent the signal getting through?

The technique is being researched to treat RA in future

Answer 28

More than half the genome of Pox Is accessory genes used to modify the immune response

They encode soluble cytokine receptors that are false –> bind to cytokines so cytokines don’t bind to the proper receptors

Question 29

What immune evasion mechanisms does the Ebola virus have

Answer 29

Ebola virus encodes VP35 and 24

VP35 - blocks RLR signalling

VP24 - blocks IFN-R signalling on neighbour cells - ISGs not stimulated

Question 30

How can viruses cause immunopathology

Answer 30

They modulate an immune response but excess IFN production causes inadvertent pathology (e.g. cytokine storm)

Too much IFN can be immunopathologic (e.g. 100x more IFN needed for IL-6 than Mx -> IL-6 has more inflammatory effects on the body)

Question 31

Explain the features of a cytokine storm

Answer 31

Uncontrolled viral replication

Induces large IFN, TNFa and IL-1/6

(Clinical outcome depends on vigour of innate immune system - i.e. worse in young people)

Question 32

Which viral infections is cytokine storm typical of

Answer 32

Dengue haemorrhagic fever, severe influenza infections, ebole

Question 33

What are the effects of a cytokine storm

Answer 33

Endothelial dysfunction

Inflammatory responses

Pulmonary fibrosis

Question 34

Give an example of IFN use as an antiviral

Answer 34

Used for HCV (not anymore - Pegylated IFN often used with ribavirin)

Not used as associated with unpleasant SEs

Question 35

How can viruses be used as oncolytic treatment

Answer 35

1. Viruses deficient in IFN control attenuated with IFN competent cells
2. Viruses therefore induce high IFN levels (IFN acts as an adjuvant to recruit useful immune cells)
3. Cancer cells are naturally IFN deficient - so they will not be able to survive when the virus is injected

Essentially, viruses that can’t control IFN can be used as a new type of live attenuated vaccine