IMI 7: Immune Responses to Intracellular Pathogens Flashcards
Observe the learning outcomes of this session
What are intracellular microbes able to do that obligate extracellular pathogens cannot?
- intracellular microbes have evolved to take advantage of the environment inside cells
- obligate extracellular pathogens lack strategies to enter and/or survive in human cells
Describe the two main classes of intracellular microbes
-
Obligate intracellular pathogens cannot reproduce outside the host cell.
- Typically, they require the cells’ metabolic energy and biosynthetic processes for their proliferation.
- For instance, all known viruses require the host cell’s ribosomes to translate their mRNAs.
- Since they still need to leave the cell to spread, they typically have a distinct - often inactive - extracellular form to survive in the outside environment, such as virus particles, bacterial spores, or encapsulated cells. -
Facultative intracellular pathogens can survive and proliferate in the extracellular environment, but they can also invade host cells.
- For instance, this might allow the bacterium or parasite to cross a cell (e.g. by traversing gut cells to enter the body) or to survive in the phagosomes.
Are intracellular pathogens equipped to survive the extracellular environment?
- Remember that intracellular pathogens do still need strategies to survive the extracellular environment that they must face when they spread within and transmit between their hosts.
- They are typically equipped to gain access to human tissues without the need for a scratch or abrasion, and have specific mechanisms to enter cells.
What are the two phases required for dealing with an intracellular pathogen?
- Detecting that a pathogen is there
- Destroying, inactivating or incapacitating the pathogen once it has been found
What are the three elements that almost all virus particles (virions) have?
- A genome, made of DNA or RNA (or sometimes a bit of both)
- A protein that packages the genome, either like beads on a string (nucleoprotein), or in a protein shell (capsid).
- A protein on the virion surface that binds specifically to a cell surface molecule, allowing the virus to enter the cell.
Therefore, these are universal features (potential PAMPs) that our immune system tries to spot, but equally are features that the virus can adapt to avoid immune detection and elimination
What are the three main characteristics that vary between viruses?
How does this reflect in the immune response?
- What nucleic acid their genome is made of: DNA or RNA; single or double stranded
- Whether or not they have a lipid envelope surrounding their packaged genome.
- Whether they replicate their genome in the cytoplasm or the nucleus
The variation between viruses is defines what immune response will be effectibe at sensing and/or targeting the virus
Observe how viruses can vary according to the three charactersitics that vary
Describe the virus lifecycle in a cell in general
- Entry
- Genome transport
- Transcription and translation of gene products
- Genome replication
- Packaging
- Exit
image is an example of a herpes virus
What are the differences between how different viruses manage their life cycle?
How does this affect what the immune system might do to detect and act against them?
- Entry might be fusion at the cell membrane (where an enveloped virus will leave remnants of its membrane on the surface), or by endocytosis where the virus might hide in a vesicle while it travels about the cell.
- The genome may be transported to the nucleus, or may move to a (often membrane-rich) region of the cytoplasm for its replication.
- A virus might execute a short lived and rapidly cleared (acute infection) but highly productive reproduction process, or might invade and set out for a long stay (persistent/chronic infection), quietly manipulating its host cell, or even shutting down all its protein production (latent infection) until it can re-emerge at a later time or different place.
Why do some viruses cause immense damage to the host, while others we barely notice?
The pathogens that are successful at infecting our bodies are the ones that have evolved to disable or avoid (the technical term is ‘evade’) our immune system’s defences.
- The constant arms race between pathogen and immune system means that many pathogens have evolved to be effective at surviving and spreading in relatively small group of host species.
- This is why in the example in IMI5, it took the generation of an adaptive immune response to rid our body if the influenza virus.
What are the most broadly important PRRs for identifying virus infection?
What are the challenges faced by the immune system?
- those that recognise viral genomes
- the challenge is to distinguish between the nucleic acids making up virus genomes from the DNA or RNA molecules that are part of normal cell biology that do us no harm
When is it easiest to recognise nucleic acids?
Give an example
- when they are in a location that they should no be
- e.g. in a healthy interphase cell, DNA should be retained within the nucleus and mitochondria
- therefore, any sensing DNA in the cytoplasm should ring cellular alarm bells that something has gone wrong
Give an example of a key sensor of cytoplasmic DNA
Explain how it works
- cyclic GMP/AMP synthase (cGAS)
1. cGAS binds to DNA in the cytoplasm
2. cGAS generates cGAMP - once activated by DNA binding, cGAS, catalyses the formation of a small cyclic dinucleotide made from ATP and GTP that can freely diffuse in the cell as a second messenger
3. Bacterial cyclic dinucleotides - as part of their natural processes, many bacteria produce cyclic dinucleotides that are not normally produced in eukaryotic cells
- these can be sensed as PAMPs, indicating a bacterial infection of the cell
4. Cyclic dinucleotides bind to STING - cyclic dinucleotides can diffuse through the cytosol and bind to STING (stimulator of interferon genes) and activate its functions by recruiting the protein kinase TBK1 (also involved in TLR signalling)
5. TBK1 phosphorylates IRF3 - TBK1 phosphorylates IRF3, which then migrates into the nucleus
6. NKfB activation - TBK1 phosphorylates IKK, which then liberates NFkB, allowing it to migrate into the nucleus
7. Gene activation: - IRF3 and NFkB migrate to the nucleus and bind to the promoters of immune genes, resulting in the transcription of (most importantly) type I interferons and also various cytokines
Apart from virus infection, what is the cGAS/STING pathway also important in?
- Since the discovery of the cGAS/STING pathway in the context of virus infection, this mechanism of DNA sensing has been shown to be important in other processes that relate to the cell’s health, such as mitochondrial integrity, DNA damage and errors in cell division.
- As a result, the function of cGAS and STING in cancer biology is a highly active and exciting area of research right now.
Give an example of another group of DNA sensors that is not cGAS
- AIM2-like receptors (ALRs)
- this family of related DNA-binding proteins contains pyrin domains
What biological process is mediated by pyrin domains?
- pyrin domains facilitate the formation of inflammasomes
- And just like the NLRs (IMI4), the ALRs AIM2 and IFI16 can form multimers (in this case dependent on binding long DNA molecules) that recruit caspases to assemble an inflammasome that activates pro-inflammatory cytokines like IL-1β.
Why is sensing viral DNA in the nucleus trickier?
- in an environment full of DNA, how can the cell tell viral from cellular DNA?
- This remains an open research question.
- There are known protein complexes that can suppress the transcription of viral DNA in the nucleus, but how these systems identify viral DNA as foreign remains unresolved.
How is endosomal DNA sensed?
- endosomes represent that twilight zone that is neither the external nor intracellular environment: they are like a bubble of the external environment held within the cell.
- Cytosolic sensors do not penetrate this space, so we are reliant on the endosomal TLRs (3, 7, 8 & 9) for sensing in endosomes, described in IMI1.
- In IMI1, you encountered TLR9, which detects DNA whose CpG dinucleotides are unmethylated.
- Since the vast majority of CpG dinucleotides in genomic DNA are methylated, this is particularly important for APCs to sense bacterial or viral genomes that have been released after degradation of phagocytosed pathogens.
- Similarly, TLR3 is important for sensing RNA released from degraded cells, or viruses with RNA genomes.
How is foreign RNA sensed?
- in contrast to DNA, it is very common to find RNA in the cytoplasm and nucleus
- e.g. mRNA in the cytoplasm and pre-mRNA in the nucleus
- therefore, intracellular PRRs that sense viral RNAs cannot rely on RNA location
- instead they recognise features of viral RNAs that are not shared by cellular RNAs
- so, we consider the biology of RNA viruses
- they rely on their RNA-dependent RNA polymerase to transcribe RNA from RNA, which is unnatural to a eukaryotic cell
- therefore, RNA sensors recognise features that are specific to this process, but not other present in our cells
Give examples of RNA sensors and what in foreign RNA do they sense?
- Detecting uncapped RNA: by RIG-I, which senses shortish RNAs
- Sensing double stranded RNA:
e. g. MDA5: senses long (>2000 nucleotide) double stranded RNA (dsRNA)
- This dsRNA is an unavoidable consequence of synthesising RNA on an RNA template, so it will always be produced during RNA virus replication or transcription.
Describe the signalling cascade triggered when RIG-I-like receptors (RLR) bind to RNA?
Both RIG-I and MDA5 are members of the RIG-I-like receptor (RLR) family, that was briefly introduced in IMI1. When RLRs bind to RNA, they activate a signalling cascade by causing the multimerisation of the mitochondrial protein MAVS:
- RIG-I assembly on foreign RNA:
- RIG-I binds and assembles on foreign RNA
- and they can slide along, allow the multimerisation of its CARD domain - Activation of MAVS signalling complex:
- the CARD domains of RIG-I bind to the CARD domains of MAVs
- resulting in a clustering of the MAVs protein on the mitochondrial membrane
- this clustering activates MAVs - Activation of transcription factors:
- like other sensors, MAVS uses TBK1 and TRAFs to induce phosphorylation events that activate transcription factors:
- Interferon Regulator Factor 3 and 7 (IRF 3/7)
- NFkB - Activation of interferon and inflammatory genes
- these transcription factors then activate immune genes, particularly type I interferons (by IRFs) and pro-inflammatory genes (by NFkB)
How do viruses evade nucleotide sensing?
- In order to successfully infect and thrive in us, viruses have evolved gene products that evade genome sensing by the cell.
- This will typically take the form of binding and inhibiting, or ubiquitinating and degrading components of these innate immune responses.
- Examples include:
- blocking RNA sensing pathways
- cap snatching
- inhibition of DNA sensors
- do not need to memorise these but the explanations are in the e-module
What are the three classes of IFNs?
- Type I IFNs (including all twelve IFN-α subtypes and IFN-β) are produced in response to pathogen-induced signals in the infected cells
- It signals to nearby cells of all types (as we will see shortly).
- Type II IFN (which includes just IFN-γ) is produced by activated immune cells.
- It mainly signals to modulate the responses of other immune cells.
- Type III IFNs (three IFN-λ subtypes) are structurally related to IL-10 but – like type I IFNs – lead to an antiviral state in cells infected with a virus.
What triggers the antiviral state?
- The binding of IFN to its receptor leads to a signalling cascade that triggers the transcription of a large number of ISGs – genes that code for proteins that help fight viruses.
- Signaling in response to IFNs thus triggers an antiviral state.
Which of the following cells benefit from the release of interferon by virus-infected cells?
- nearby infected cells
- antigen-presenting cells
The effects of interferon are mainly local, and they perform both regular cytokine-like functions (activating immune cells associated with combating intracellular infection) and induce the antiviral state, which increases a cell’s innate defence against infection.
Cells that are infected are already doomed, so will not benefit from the release of interferons: the virus will kill them before the infected cell has time to transcribe and translate the ISGs.
Match the PRR to the associated PAMP
Which of the following lead to Interferon production?
- RNA detection in endosomes by TLR3
- sensing DNA in the cytoplasm
- sensing uncapped RNAs in the cytoplasm
As you have learned in IMI4, the inflammasome is an entity that specifically catalyses the cleavage and activation of pro-inflammatory cytokines, so does not directly lead to IFN production. All these other stimuli do.
In fact, interferons are produced in response to PRR signalling triggered by a wide range of PAMPs, but the role of IFNs in response to these diverse pathogens is not as clearly understood as it is for viruses.
Nor are the distinct roles of the many different type I and type III interferons understood.
How do dendritic cells present proteins to a cytotoxic T cell?
- Exactly how this happens is unclear, but in principle, antigens delivered from other APCs are internalised by DCs, shifted to the cytoplasm, cut up into peptides, and mounted on MHC class I molecules.
- Depending on the co-stimulatory signals and cytokine environment, this can either activate the CTLs, or – if there are no danger signals – can induce tolerance (so-called ‘cross tolerance’) for self antigens
Describe in detail how NK cells are activated and deactivated
- The activity of NK cells is defined by the balance of inhibitory and activating receptors.
- Having more inhibitory receptors means that the NK cell tolerates the signal, and does not let loose its destructive weaponry.
- Ligation of inhibitory receptors to MHC class I on a healthy cell is an important inhibitory signal, resulting in NK cell tolerance (left).
- The NK cell becomes activated to kill a target cell as soon as MHC class I molecules go missing, as for example on tumour cells, or by a virus attempting to avoid detection.
- This is called ‘missing self’ recognition (middle).
- Alternatively, signals of intracellular stress, or intracellular infection can upregulate activating receptors to levels that overwhelm the inhibitory signals (right).
- When the activating signals to NK cells outnumber the inhibitory ones, then the NK cell goes into action and destroys the offending cell
NK cells are strongly inhibited by MHC class I so they will need a very strong activating signal to make them kill cells with MHC class I on their surface.
However, they will much more easily kill cells whose MHC class I cells are missing.
Why is this a good anti-viral (and anti-cancer) strategy?
- The answer is a classic example of how the innate and adaptive immune systems complement each other.
- As shown in the cartoon, a cell with MHC class I molecules allows any infections (or mutations in cancer) to be detected so the cell is destroyed by cytotoxic T cells.
- Viruses and cancer cells therefore have a strong interest in down-regulating MHC class I on the cell surface, so they do not present antigenic peptides to T cells.
- Indeed, many viruses have evolved mechanisms to down regulate MHC class I to avoid T cell killing.
- However, because NK cells use MHC class I as an inhibitory ligand, removing MHC class I makes the infected cell vulnerable to NK cell killing, needing far fewer activating receptors to trigger NK cell activation.
What specific antigen does an NK cell need to recognise to be activated?
- NK cells don’t recognise antigen
- The lack of requirement for antigen is is why they are called natural killer cells.
- NK cells have inhibitory receptors, such as those that bind to MHC class I loaded with (any) peptide.
- MHC Class I is not an ‘antigen’ and in any case is not correct because it has an inhibitory effect on NK cells, regardless of whether it contains antigen.
- The decision to act comes from the sum of activating signals triggered by intracellular immune responses, counteracted by negative signals such as that triggered by the presence of MHC class I.
Describe virus latency
- Rather than rapidly spreading and changing, some pathogens have taken the slow road, establishing a persistent infection whose strategy allows it to hide from surveillance by CD8 T cells (eg virus latency).
An example is given below to help you understand this idea, but you will not be expected to know the details.
Which four of these immunological processes, molecules or cells are most important for controlling infection by intracellular pathogens?
- MHC Class I antigen presentation
- natural killer cells
- cytotoxic T cells
- intracellular PRRs
How does the transcriptional strategy of latency (shutting down transcription of viral protein-coding genes) evade immune surveillance?
What is the mechanism by which the virus evades this?
- CD8+ T cells cannot detect viral antigens
- the virus makes no proteins to be presented on MHC Class I
For what reason(s) might inhibiting complement help an enveloped virus?
- To prevent opsonisation of the virus or infected cell
- To prevent the formation of a membrane attack complex destroying the virus particle
Complement does not attract antibody (though antibody can attract complement).
Any surface complement will not enter a cell, as the viral membrane is left at the cell surface, so an intracellular complement receptor (if such a thing existed) could only affect non-enveloped viruses.
However, it could play a role in opsonising the cell as well as the virus, and if complement facilitated MAC formation, it could destroy infectious virus particles.
Summarise the mechanism cells use to handle intracellular responses
Summarise the ways pathogens can counter these activities
