2. Antigen Presentation Flashcards
What is MHC?
- A set of molecules the immune system uses to identify self and non-self and tell the difference between them.
- Class 1 and 2
- Human Leukocyte Antigen in humans.
- Important in Adaptive and antigen specific responses.
What is the biggest immunological problem?
How does the body what is self and what is not.
How do we know adaptive immunity if evolutionarily successful?
Everything has an immune system.
How does the structure of proteins allow for specific recognition in immunity?
- They can be broken down into small chains of 13-20 amino acids.
- There are 20 different amino acids possible for each position in the chain.
- Therefore huge numbers of unique amino acid chains that can be used to identify foreign bodies.
How was the MHC’s role in antigen restricted killing proved?
- In 1973, a Nobel prize-winning paper looked at restriction in mouse MHC molecules.
- They used a chromium assay to show the point of cell death (chromium is released on death).
- Only a certain cell type was killed by the immune cells showing restricted killing of cells.
- This paper showed that MHC stimulated or delivered something to the cells to enable killing.
What made identifying MHC structure possible?
improved scientific techniques to identify crystal structures.
What does MHC do?
Present different peptides to a TCR on a naive T cell
What antigens are presented on MHC1?
- Intracellular antigens processed in the cytosol
- presented to CD8+ T cells
What antigens are presented on MHC2?
- Extracellular antigens that are endocytosed and degraded in an endosome.
- Presented to CD4+ T cells
How many peptides do APC present?
Many different peptides on many different MHC molecules
How many peptides can bind a TCR?
1 unique peptide
What educates the immune system?
The peptidome displayed in the thymus during clonal selection and central tolerance.
How does the T cell repertoire arise?
- All the T cells are produced and mature in the thymus.
- The peptidome of the individual is displayed in the thymus determines the thymocytes that survive.
- This means every immune system is different with different T cells.
When is the immune system active?
- It is always active and surveying the antigens displayed but it is not fully active when self peptides are expressed as the immune system has learnt to recognise and tolerate yourself.
- It is fully activated when a foreign antigen is detected on an MHC.
What information does all the MHC molecules carry?
A map of all the self peptides in the body.
What is the immunological advantage of being able to define self?
The immune system can identify novel antigens/pathogens that have never existed before due to MHC presentation.
What is the peptidome?
All the peptides that are meant to be in the body.
What is the function of the peptidome?
To keep the T cells recognising and tolerating self peptides in-order for them to be able to distinguish foreign antigens
Important components of MHC1 processing: Proteases
- They break down large proteins into small peptides that can be presented as antigens.
- work in the proteasome
Important components of MHC1 processing: Adjacent proteins
- These allow or aid the binding of the peptide into the MHC.
- Chaperones like calnexin and calreticulin
- Transporter proteins like TAP
- Membrane loading complexes
What cells express MHC1?
All nucleated cells all of the time
What is the process of peptide loading into MHC1?
- The protein is tagged for degradation by ubiquitin.
- Degraded by protease activity.
- The peptide is exported to the ER.
- The peptide is loaded in the MHC1 with the aid of TAP.
- The peptide-MHC complex is transported to the cell surface in a vesicle.
Important components of MHC2 processing: HLA-DO and HLA-DM
These are chaperones that keep the MHC ready to receive peptides.
Important components of MHC2 processing: Invariant chain
This keeps the binding groove available and ready for a peptide. This is the CLIP.
Important components of MHC2 processing: proteolytic enzymes
These degrade the protein to peptides to provide substrate for MHC2
What is the process of peptide loading into MHC2?
- Occurs in an antigen processing compartment.
- HLA-DO regulates HLA-DM function which inhibits the exchange of Invariant chain for a peptide.
- The invariant chain is sequentially protealysed.
- The residual fragment, the CLIP, is retained in the peptide binding groove.
- HLA-DM binds MHC2 and displaces the CLIP allowing peptides to bind
- The peptide MHC2 complex is transported to the cell surface
What is an antigen processing compartment?
- A subcellular compartment.
- There can be many throughout the cell.
- They contain all the proteins needed for MHC loading.
- They are defined by enzymes present in them.
When and where are MHC2 expressed?
All the time but only on antigen-presenting cells.
What are professional antigen presenting cells?
- B cells that then become specialised to secrete different antibodies
- Dendritic cells: type 1 + 2 and plasmocytoid
- Macrophages type 1 and 2
When can some other cell types present MHC2?
- Under the pressure of inflammation MHC2 can be expressed on tissues that don’t normally.
- This is especially relevant on endothelial cells.
- It is driven by type 1 and type 2 interferons.
- This causes CD4+ activation where you don’t want it.
How are peptides for presentation produced?
MHC1: by the proteosome and associated enzymes.
MHC2: in the late endosome and lysosome enzymes
What shapes the peptides that can be presented?
The specific cutting patterns of the proteases.
Why are peptides edited before MHC loading?
To ensure high affinity binding in order to present the peptide falling off in circulation.
What edits peptides for MHC1?
- Tapasin
- It competes with low affinity peptides for binding to MHC
- It is displaced by higher affinity peptides.
What edits peptides for MHC2?
- HLA-DM
- Edits the repertoire in favour of high affinity and stable binding
- This alters CD4+ T cell selection
What can expand the peptide repertoire?
- Damaged or mutated proteins.
- This changes the antigens presented in the thymus therefore changes the T cell selection and repertoire.
- Due to altered T cell selection, this makes people more prone to autoimmunity.
Where does MHC1 acquire antigens?
from the cytosol
How does MHC2 acquire antigens?
- Clathrin-mediated endocytosis
- Phagocytosis
- Pinocytosis
MHC2 antigen acquisition: Clathrin-mediated endocytosis
- Specific uptake of material bound to receptors on APC.
- Receptors include - BCR, FcR, Lectin receptor, complement receptor
- Material enters through clathrin-coated vesicles and enters an antigen processing compartment.
- B cells rely almost exclusively on this method
MHC2 antigen acquisition: Phagocytosis
- Done by Dendritic cells and macrophages.
- Takes things up from the environment.
- Receptors - FcR, complement receptor and scavenging receptors.
- Used for bigger molecules.
- Phagosomes are not very proteolytic so fuse with lysosomes to make phagolysosomes
- This uses lots of energy and membrane.
MHC2 antigen acquisition: Macropinocytosis
- Non-specific uptake of environmental material.
- Large material including bacteria.
- Plasma membrane ruffles entrap external material.
- Very common in immature dendritic cells, and common in DC and macrophages
What is cross presentation?
The presentation of exogenous antigens on MHC1 so this occurs on APC.
How was cross presentation identified?
Due to organ transplantation and rejection. Donor peptides were recognised on host dendritic cells.
What is the benefit of cross presentation?
- Helps with the detection of bacteria and viruses that replicate in the endosome.
- Also helps with tumours
- Activates naive CD8 T cells against these targets.
Pathways of cross-presentation: Cytosolic pathway
- Exogenous antigens are endocytosed and exported into the cytosol by channels or transporters or a ruptured vesicle.
- Degraded by proteasome.
- Endosomal loading where cytosolic peptides are imported to a phagosome via TAP and loaded onto MHC1.
- ER loading using TAP (not a lot of evidence for this)
MHC1 antigen acquisition in cross presentation: Vacuolar pathway
- Similar to Class 2 loading
- Exogenous antigen endocytosed.
- Antigen degraded in the phagosome
- Peptides loaded onto MHC1 in the endosome
- Independent of ER transporters and loading machinery.
How do the MHC1 end up in an endosome for cross presentation?
- Don’t really know
- Newly-synthesised MHC1 transported to endosomes
- Pre-existing MHC1 is recycled from the membrane into endosomes then the peptide is exchanged.
How can MHC2 acquire intracellular antigens?
- Not cross presentation but autophagy
- 20-30% of MHC2 peptides
- done by autophagy
- deficiency in autophagy disrupts thymic selection due to lack of MHC2 expression
What is the change of state of antigen processing?
- Antigen presentation changes from the basal state to stimulated during infection.
- Stimulation increases MHC1+2 expression and alters the peptidome.
- This process is driven by TLR signalling and type 1 interferons and the presence of inflammation.
- This encourages antigen specific responses.
Change of state of antigen processing: Peptide production
MHC1: Remodelling of the proteasome 20S subunit by IFNy to form immunoproteasome.
MHC2: GILT reduces intramolecular disulphide bonds, increasing proteolysis
Both these increase peptide production
What is GILT?
IFN-g induced lysosomal thiol reductase
Change of state of antigen processing: Dendritic cells
Immature DC: MHC2 turnover is very rapid and regulated by ubiquitin.
Stimulated DC by TLR signalling:
1. Increased proteolysis for a limited time
2. Fill up MHC2
3. Push lots of MHC2 onto the surface membrane and stay there.
4. Takes cell to the lymph node
5. Increases half life of MHC massively to over 100 hours
6. This presents a snapshot of the cell in inflammation in order to activate the adaptive response
Change of state of antigen processing: Macrophages
- Up regulation of MHC and co stimulatory molecules
- More efficient antigen presentation
- This is regulated by MARCH1
What controls the MHC up regulation in dendritic cells?
- Burst of CDC42 and actin regulated macropinocytosis
- Increased proton pump activity = acidification
What is MARCH1?
- An E3 ubiquitin ligase
- It is down regulated in infection to stabilise and extend MHC half life.
Change of state of antigen processing: B cells
co-localisation of MHC2 and BCR associated antigen in the same compartment for efficient loading.
How many T cells per antigen are there?
For 60 million naive T cells in a mouse there were:
20 to 200 naive CD4+ cells per antigen
80 to 1200 naive CD8+ cells per antigen
How can you measure how many T cells per antigen?
using a MHC tetramer surrounding a fluorophore core
How are the interactions between APCs and relevant T cells optimised?
- Constrain immunosurveillance to secondary lymphoid organs, concentrating dendritic and T cells.
- Upregulate blood and lymph flow on innate immune signalling, to increase the rate of naive T cell entry and the retention time through upregulation of CD69
- Optimise lymphocyte searching to favour detection of rare populations, switching between a scanning phase and a motion phase.
- Drive co-localisation of different rare cell types by chemokine and chemokine receptor expression.
- High sensitivity T cells can respond to fewer than 10 agonistic pMHC per APC.
