Antigen Presentation via MHC Flashcards
1
Q
How is the MHC signal 1 for T cell activation?
A
- Underlying principle of adaptive T cell immunity is specificity of response
- Requires the T cell recognizing and responding to the correct antigens → signal 1
- Interaction between the MHC epitope complex and the TCR of the T cell thus provides specificity
2
Q
What is the function of MHC-I, and what cells express it?
A
- Present peptides from intracellular pathogens (commonly viruses) to cytotoxic CD8+ T cells
- Viruses can infect any nucleated cell, almost all such cells express MHC-I, highest being:
- T cells
- B cells
- Macrophages
- DCs
- Neutrophils
- RBCs do not express MHC, so a RBC is a site where infection can go undetected → malaria
3
Q
What is the function of MHC-II, and what cells express it?
A
- Present peptides from extracellular antigens to CD4+ T cells
- Main function is to activate other effector cells of the immune system, so mainly expressed on:
- B cells
- Macrophages
- DCs
- As reviewed in Kambayashi and Laufer, 2014, as well as APCs, other cell types have been found to express MHC-II:
- Mast cells → could present antigen to CD4+ T cells in vitro, but cant prime naïve T cells
- Basophils → can present antigens to T cells
- Eosinophils → MHC-II expression can be induced. Form clusters with APCs in draining lymph nodes and could restimulate memory
- Innate lymphoid cells → express genes for MHC-II
- LN stromal cells → upregulate MHC-II under inflammatory conditions
- Endothelial cells → Express MHC-II, and evidence that interactions with CD4+ T cells involved in some autoimmune disaeases and graft rejection.
4
Q
How do interferons regulate MHC expression?
A
- IFN-a and IFN-B increase expression of MHC-I
- IFN-y inceases expression of MHC-I and II, and can induce MHC-II on cell types that don’t normally express it
- IFNs also enhance antigen presenting function of MHC-I by inducing key components in the peptide loading machinery
5
Q
What are the problems that must be overcome by MHC?
A
- Individual can become infected with a huge variety of pathogens → MHC must be able to bind to and express each of all pathogen peptides it encounters
- If not, the individual will not be able to mount an adaptive T cell response to many pathogens, leaving them immunocompromised
- MHC must stably bind to and present peptides for recognition by T cells
- Think how infrequently a CD8+ T cell may encounter its cognate peptide
- Peptide exchanges should not occur as this may lead to inappropriate cellular activation, or anergy
6
Q
What are the 2 properties of MHC that make it difficult for a pathogen to evade?
A
- Polygenic → several different MHC-I and MHC-II genes, so every individual possess a set of MHC molecules with different ranges of peptide binding specificities
- Polymorphic → multiple variants, or alleles, of each gene within the population
7
Q
Describe the MHC gene cluster.
A
- In humans, it is AKA the human leukocyte antigen (HLA.
- Span as many as 7 million base pairs, containing over 200 genes.
- 3 class I molecules – HLA-A, HLA-B and HLA-C
- 3 class II molecules – HLA-DR, HLA-DQ and HLA-DP
- In many people, the DR cluster contains an extra beta gene whos product can pair with the DR-alpha chain. This means 3 gets of genes can give rise to 4 types of MHC-II
- Located on chromosome 6 (b-2 microglobulin chromosome 15, invariant chain chromosome 5)
- Genes of the MHC are linked with genes for the TAP and the proteasome, suggesting the entire MHC has been selected during evolution for antigen processing and presentation.
- Treating with IFNs increases expression of the MHC, proteasome and TAP genes.
- IFNs produced early in the viral response
- Thus increases ability of all cells to process viral proteins and present them on the cell surface
8
Q
Talk about MHC polymorphisms
A
- Because of the polygeny of MHC, each person expresses at least 3 MHC-I and 2 (sometimes 4) MHC-II.
- However, the number of different MHC expressed is greater because of polymorphisms → more than 800 alleles for some of the genes.
- Notable exception of the DR-alpha locus, which is functionally monomorphic
- Each allele is relatively frequent in the population, so there is only a small chance that the corresponding gene loci on both homologous chromosomes of an individual will have the same allele – most will be heterozygous.
- The combination of MHC alleles found on a chromosome is called the haplotype
- Expression of MHC alleles is co-dominant.
• For MHC-II, the number of different MHC molecules may be increased further by a combination of alpha and beta chains encoded by different chromosomes
- Each MHC isoform may differ from each other by up to 20 amino acids
- Differences usually localized the peptide binding cleft → many polymorphisms alter the amino acids lining the binding pocket (anchor residues).
- The set of anchor residues is called a sequence motif
- In rare cases, processing of an antigen will not generate a peptide with a suitable sequence motif for binding to any of the MHC molecules expressed by an individual
- Such failures in responsiveness to antigens were first reported in inbred animals, where they were called immune response gene defects.
- The immune response affected by these defects was known to depend on T cells, and early experiments showed that T cells could be activated only by macrophages or B cells that shared MHC aleles with the mouse in which the T cells originated → first evidence that antigen recognition by T cells depends on the presence of specifc MHC molecules (MHC restriction).
- We now know MHC restriction is due to the fact that binding specificity of TCR is not for its peptide antigen alone, but the complex of peptide and MHC
- Obvious important for host defense
• Because most individuals are heterozygous, most matings will produce offspring that receive one of 4 possible combinations of the parent haplotypes → thus siblings are likely to differ in the MHC, only ¼ chance they will be the same.
- MHC polymorphisms seem to have been selected for by evolutionary pressures.
- Effect of section pressure in favour of polymorphisms can be seen in the pattern of point mutations → replacement substitutions occur at a highly frequency relative to the silent substitutions that would be expected, providing evidence that polymorphisms have been actively selected for.
- MHC provides ways a pathogen could evade detection:
- Mutations that eliminated from the pathogen all peptides that can bind the MHC
- Epstein-Barr virus
- 60% population in New Guinea have HLA-A11 allele
- Epstein-Barr virus have mutations in the dominant peptide epitope that bidns to HLA-A11
- Some pathogens can block presentation of their peptides by MHC
- Adenoviruses
- In large, outbred populations, polymorphism means different individuals will differ in combinations of MHC, and makes it unlikely all individuals in a population will be equally susceptible to a pathogen → limits the spread!
- Also, increasing variety of MHC means it is unlikely a pathogen can block presentation of their peptdies by ALL MHC
• Question raised: If having 3 MHC loci is better than one, why aren’t there more? → Each time a distinct MHC molecule is added to the repertoire, all T cells that can respond to self peptide bound to it must be deleted. Number of MHC genes therefore is an optimal balance of increased range of preptide presentation, and minimal loss of T cells from the repertoire
9
Q
What is the structure of the MHC-I?
A
- Heterodimeric glycoprotein
- TM polymorphic alpha chain from chromosome 6, non-covalently associated with the b-2 microglobulin chain (non-polymorphic) from chromosome 15.
- Only the alpha chain spans the membrane
- 4 domains, three from the alpha chain, one from the beta-2 microglobulin
- Alpha-3 domain and beta-2 microglobulin resemble Ig domains
- The alpha-1 and alpha-2 domains form the peptide binding cleft (these are polymorphic and determine the sequence of the peptide that can bind).
- In MHC-I, the cleft is CLOSED
10
Q
Describe peptide binding to MHC-I
A
- Important feature is that binding of peptides to MHC molecules is that they are bound as an integral part of the MHC structure → MHC are unstable when peptides are not bound
- Binding is stabilized at both ends of the cleft by contacts between atoms in the free amino and carboxy termini of the peptide, and invariant tyrosine sites found at each end of the cleft.
- Other residues in the peptide serve as additional anchors
- Peptides that bind are 8-10aa long
- Longer peptides may bind but they are subsequently cleaved by exopeptideases in the ER
- Peptides lie in an elongated conformation
- Variations in peptide length are accommodated by kinking in the peptide backbone
- The MHC polymorphisms give different amino acids in the key peptide-interaction sites.
- Peptides that can bind to an MHC have the same aa residues at two or 3 points along the peptide sequence
- The amino acid side chains of these residues insert into pockets in the MHC linked by polymorphic amino acids
- The peptides involved in this are called anchor residues – they determine binding specificity
- A set of anchor residues is called a sequence motif
- Most MHC-I have a hydrophic anchor residue at the C-terminus
- Binding also depends on the nature of aa’s at other positions on the peptide, and in some cases particular aa’s are preferred in certain positions → these are called secondary anchors.
- Any given MHC-I can theoretically bind any number of peptides as long as they have comparable anchor residues.
11
Q
Describe the 26S proteasome
A
- Typical proteasome composed of one 20S catalytic core and two 19S regulatory caps
- The 20S core is a large, cyclindrical complex of 28 subunits, arranged in 4 stacked rings of 7 subunits
- It is a hollow core lined by active sites of proteolytic subunits
- Proteins are tagged for degradation by ubiquitin → targets them to the 19S cap
- ATPases control the opening of the 20S core chanber
12
Q
Describe the immunoproteasome
A
- The two inner rings of the 20S proteasome core are composed of B1, B2 and B5 subunits
- These are sometimes displaced by alternative subunits called LMP7 → encoded within the MHC near the TAP
- LMP7 is induced by interferons, thus the proteasome can exist in two forms:
- Constitutive 26S proteasome present in all cells
- Immunoproteasome present in cells stimulated with IFNs
- The replacement of the beta subunits with LMP7 alters the enzymatic specificity of the proteasome
- Increased cleavage of polypeptides after hydrophobic residues
- Decreased cleavage after acidic residues
- This produces peptides with carboxy-terminal residues that are preferred anchor residues for MHC-I, and preferred structures for TAP
- The production of peptides of the correct length is increased by a further modification that is induced by IFN-y → binding of the proteasome to the proteasome activator complex PA28.
- Binds to either end of the 20S core in place of the 19S cap
- Acts to increase the rate peptides are rleased
- Translation of self or pathogen derived mRNA in the cytoplasm may generate defected ribosomal products (DRiPs)
- Ensures both self proteins and proteins derived from pathogens generate abundant peptides for eventual presentation by MHC-I
13
Q
What are the TAPs
A
- Members of the ATP binding cassette (ABC) family
- Mediate the ATP-dependent transport of ions, sugars, amino acids and peptides across membranes
- The two ABCs associated with the ER membrane, and the ones that are missing from mutant cells with fewer MHC on the surface, are TAP1 and TAP2.
- Form a heterodimer across the ER membrane
- Prefers to transport proteins 8-16aa long with hydrophobic residues at the C-terminus
14
Q
Describe peptide loading to MHC-I
A
- Partially folded MHC-I alpha chains bind to calnexin until the b2-microglobulin binds
• Calnexin retains MHC-I in a partially folded state - MHC-I a:B2 microglobulin complex is released from calnexin, binds the peptide loading complex (calreticulin, ERp57) and binds to TAP via tapasin
• When B2 microgloulin binds to the alpha chain, the partly folded MHC-I a:B2 microglobulin heterodimer dissociates from calnexin, and now binds to the MHC class I peptide loading complex
• Calreticulin is similar to calnexin
• Tapasin forms a bridge between MHC-I and TAP
• ERp57 forms a stable disulphide link with tapsasin - Cytosolic proteins and DRiPs are degraded to peptide fragments by the proteasome. TAP delivers the peptides to the ER
• Proteasome produces peptides, and chaperones such as TRiC protect the peptides from complete degradation in the cytoplasm.
• Many of the peptides produced are too long to bind to MHC-I, so proteasome cleavage may not be the only mechanism:
• Evidence that the C-terminal ends are produced by proteasome cleavage, but the N terminal may be produced by another mechanism → proteins that are too long can still be transported into the ER, where their amino termini can be trimmed by ERAAPs
• TAP delivers all these peptides to the ER> - A peptide binds the MHC-I and completes its folding. The MHC-I is released from the TAP complex and is exported to the cell membrane.
• Not yet clear whether the PLC actively loads peptides onto the MHC, or whether binding to the PLC simply allows the MHC-I molecule to scan the peptides transported by TAP before they diffuse away
• Most of the peptides transported by TAP will not be bound by MHC, and are rapidly cleared from the ER by the Sec61 complex.
15
Q
How can viruses interfere with MHC-I antigen presentation?
A
- Some viruses evade immune recognition by producing immunoevasins → prevent the appearance of peptide:MHC class I on the infected cell
- Some immunoevasins block peptide entry into the ER by targeting the TAP
- Herpes simplex and cytomegalovirus → bind to surface of TAP or inhibit its ATPase activity
- Viral proteins can also prevent peptide:MHC complexes from reaching the cell surface by retaining MHC-I in the ER
- Adenovirus → contains motif retains the protein complex in the ER
- Several viral proteins catalyse the degradation of the newly synthesized MHC-I by a process known as dislocation – initiates the pathway normally used to degrade misfolded ER proteins by directed them back into the cytosol
- Gamma herpes → direct association with the TAP:Tapsasin complex. Its ubiquitin ligase activity adds ubiquitin to the tails of MHC-I so it is targeted for degradation
