MHC and antigen presentation Flashcards
What does MHC stand for?
MHC stands for Major Histocompatibility complex, a group of proteins consisting of three classes, class I, II and III, encoded by the MHC locus. Class I and II are structurally similar while class III are a group of unrelated proteins that do not share structural similarity or function with class I and II.
Describe the function of MCH class I and II.
Class I and II are membrane-bound glycoproteins that function as highly specialized antigen-presenting molecules with grooves that form unusually stable complexes with peptide ligands, displaying them on the cell surface for recognition via T-cell receptor (TCR) engagement
Describe the structure of MHC class I proteins
Even though MHC I and II have a similar quaternary structure, they have differing composition. MHC I consists of one membrane-anchored heavy-chain glycoprotein that consists of a cytoplasmic anchor segment, a transmembrane domain and three extracellular domains, α1, α2 and α3. α1 and 2 make up the peptide binding groove (membrane distal domains) and α3 is associated (non-covalently) with a small protein light-chain called β2-microglobulin are the membrane proximal domain. The α1 and α2 domains interact to form a floor of eight antiparallel β strands rimmed by two long α helices, that can hold a peptide of between 8-10 amino acids (most are 9 aa, aka nonamers) through non-covalent interactions. The α3 domain is highly conserved, especially in a sequence that interacts strongly with CD8 surface markers on Tc cells.
Describe the structure of MHC class II proteins.
MHC class II proteins consists of two non-identical but similarly sized glycoprotein chains α and β, associated by non-covalent interactions. Both chains are anchored in the membrane and consists of a cytoplasmic domain, a transmembrane domain and two extracellular domains, α1 and 2 and β1 and 2 respectively. The α1 and β1 are membrane distal and make up the peptide binding groove, that can hold a peptide of 13-18 amino acids.
Compare the MHC I and II proteins in terms of similarities and differences.
Similarities:
- Similar quaternary structure and function, the ability to bind antigen and present it to T cells
- both have membrane distal domains that make up the peptide binding groove
- both have membrane proximal domains that share similarities with immunoglobulins, and thus belonging to the Ig superfamily of proteins.
- all interactions are non-covalent
Differences:
- MHC I consists of one membrane bound glycoprotein chain while MHC II consists of two.
- The peptide-binding groove in class I molecules is blocked at both ends, whereas the ends of the groove are open in class II molecules, resulting in differing size of peptides fit in the grooves, 8-10 in class I and 13-18 in class II.
- recognized by different T cell surface receptors.
- presents peptides from different sources, MHC I - intracellular while MHC II extracellular.
MHC class I and II molecules exhibit polymorphism, explain what this means.
With polymorphism, we mean that many alternative forms of each gene, or alleles, exist within the population. There are several hundred different allelic variants of class I and II molecules in humans, differing specifically in the peptide-binding region.
How many different class I and II molecules can be expressed by a person maximum?
Up to 6 class I & 12 class II molecules expressed per person.
With only a limited set of MHC molecules, how is it possible to present thousands of different peptides to T cells?
A given MHC molecule can bind numerous different peptides, and some
peptides can bind to several different MHC molecules. The peptide - MHC binding is promiscuous, way less specific than that of antigen - T/BCR.
What is the source of the peptide presented on MHC class I molecules?
The source of peptide for class I is intracellular peptides (could be both self peptides to show healthy status or peptides from intracellular pathogens to show infected status) that is presented to CD8+ T cells.
What determines the peptide specificity of MHC class I molecules?
The peptides binding to MHC class I molecules are usually nonamers (9 aa long) and specific amino acids on the second, sometimes third and ninth position act as anchors that anchor the peptide into the groove leaving the rest of the amino acids to bulge out, available to interact with a TCR. These anchor residues can vary depending on the allelic variant, but for a given set of MHC, these anchor amino acids are the determinant of whether a peptide can bind or not.
Which cells express MHC class I molecules?
All nucleated cells express the set of MHC class I molecules (not red blood cells). Each nucleated cell expresses approx. 10^5 copies of each MHC I molecule so many peptides will be presented simultaneously, but not identical peptide presentation between individuals!
What is the source of the peptide presented on MHC class II molecules?
Class II MHC present antigen peptides derived from extracellular/exogenous sources to CD4+ T cells.
What determines the peptide specificity of MHC class II molecules?
The peptide specificity of MHC class II generally shows less restricted amino acid sequence preferences because of the structure of the peptide binding groove. It also have less conserved sequences in the peptide binding site and thus have greater variability of sequence (and length) than class I. The open ends and shape of the groove maintain a roughly constant elevation on the floor of the binding groove and hydrogen bonds between the backbone of the peptide and the class II molecule are distributed throughout the binding site rather than being clustered predominantly at the ends of the site, like class I.
Which cells express MHC class II molecules?
MHC class II proteins show a more limited tissue distribution and more varied expression levels. In general, class II molecules are primarily found on the surface of professional APCs (dendritic cells, macrophages and B-cells), cells with the unique capacity to alert T cells to the presence of a specific antigen. Also by non-professional APCs like epithelial cells too.
What is the MHC gene cluster referred to in humans and mice?
The MHC is referred to as the human leukocyte antigen (HLA) complex in humans and as the H2 complex in mice.
The MHC locus encodes three major classes of molecules, which?
– Class I MHC genes
– Class II MHC genes
– Class III MHC genes (Complement and inflammation proteins)
Note, there are both classical MHC genes and non-classical MHC genes in the MHC locus.
Explain the structure of the HLA/MHC genes in humans.
The major histocompatibility complex is a collection of genes arrayed within a long continuous stretch of DNA on chromosome 6 in humans.
- The three class I genes are located downstream (B, C, A - all α). β -Microglobulin is encoded outside the MHC locus, on a separate chromosome altogether (chromosome 15 in humans).
- Class II genes are located first (DP, DQ and DR - all α & β)
- Class III in the middle but have no role in antigen presentation. These genes encode for for example the complement components C4, C2, and factor B, as well as several inflammatory cytokines, such as the tumor necrosis factor proteins.
Note: In mice, the MHC class I genes are interrupted by class II and III, so H2-K first, class II and III, then H2-D and H2-L.
Explain the inheritance of HLA genes for class I and II.
Allelic forms of MHC genes are inherited in linked groups called haplotypes, you get one set/haplotype from each parent. Both maternal and paternal MHC genes are expressed in offspring cells - co-dominant expression.
- The class I genes, HLA B, C and A all encode for the α chain, so 6 different ones are possible.
- The class II genes, HLA DP, DQ and DR all encode for an α & β chain, which are inherited separately and from each parent, so 12 different are possible.
In different regions of the world, some allelic variants of the MHC genes are more common, so you can get the same from both parent, that’s why we say that you can have maximum 6 different class I genes and 12 different class II genes. With inbreeding, the offspring can get homozygous, expressing identical MHC molecules because the maternal and paternal haplotypes are identical (useful in mouse models).
There are some non classical MHC genes, where are they encoded? Give one example of a function of these genes.
The non-classical MHC genes are encoded in the class II and I gene stretches. The non-classical MCH genes have a more restricted tissue expression, less diversity, and more varied roles in immunity. One example of a role of these are the DM genes, which are involved in peptide loading of MHC class II, and HLA-G is involved in self/nonself discrimination.
The MHC region is polygenic, what is meant by that?
The MHC locus is polygenic which means that it contains multiple genes that encode for proteins with slightly different structure but same function.
The haplotypes of MHC molecules are the basis of finding matches for organ/tissue transplants. Who is more likely a good match, a parent or a sibling?
A sibling is more likely a good match since you only share half of your MHC molecules with each parent. A sibling can in theory have the same haplotypes from each parent.
Note, some class I and II molecules are more important, e. g. A, B class I and DR class II, so even if someone isn’t a perfect match, a difference in a less important MHC molecule can still make for a good match.
Also note, recombination during meiosis can occur, which can lead to even more diversity.
Differences between allelic variants of MHC tend to be clustered at amino acid locations within the peptide binding sites, why? What are the consequences of this?
If the areas outside the grooves were changed too much, the new conformation might bind nothing, so the non peptide binding sites are highly conserved. This provides opportunity of being better equipped to handle new pathogens and also ensures that not everyone dies from the same disease.
The consequences of this variability is that some allelic variants are linked to higher risk of certain autoimmune diseases, e.g HLA–B27 is linked to a 90 times higher risk of developing ankylosing spondytisis. On a brighter side some allelic variants are linked to being better equipped to handle diseases, e.g. HLA-B57 linked to slower progression of AIDS.
There are five main functions of the MHC molecules, which?
The main functions of MHC molecules are:
- To display self-MHC class I and self-peptide to demonstrate that the cell is healthy
- To display a foreign peptide in class I to show that the cell is infected and to engage with TC cells
- To display a foreign peptide in class II to show the body is infected and activate TH cells
- To display a self-peptide in class I and II to test developing T cells for autoreactivity (in primary lymphoid organs)
- To display a self-peptide in class I and II to maintain tolerance to self-proteins (in secondary lymphoid organs)
It is also important to note that the cell type, tissue location, and timing of expression vary for each
of these situations.
MHC expression can differ during certain conditions, give three examples of regulation/conditions that can influence MHC expression.
MCH expression can be changed under the following conditions:
- During infection certain transcription factors can be used to drive up MHC II expression, e.g. CIITA (class II MHC complex transactivator) that bind promoters to MHC class II genes.
- Cytokine mediated upregulation in pAPCs can occur during infection, e.g. interferons and TNF.
- Viruses can interfere with MHC class I expression to evade recognition and destruction of CD8+ T cells. e.g. by decreasing TAP (transporter) expression involved in MHC peptide loading.
What problems arise with the fact that MHC molecules have a role in autoreactivity testing?
– Determinant selection model: different Class II molecules differ in peptide binding. Still, some peptides may be more crucial to be able to eliminate the
pathogen than others -> we respond differently!
– Holes-in repertoire model: T-cells bearing receptors recognizing antigens too similar to self, are eliminated (to avoid autoimmunity) – will leave holes in the repertoire!
Note: both can be true, not mutually exclusive.
T cells exhibit self-MHC restriction, what does this mean?
CD8+/CD4+ T cells can only recognize peptides presented by MHC class I/II, respectively. The MHC haplotype of the presenting cell must match the haplotype of the T cell to activate them. Thus, you can’t use APCs from another person/haplotype to activate T cells.
Classic experiment, page 558 - read through and understand.
Describe an experiment that show that antigen presentation is a metabolic process.
Three treatments:
- fix APCs, incubate with antigen, remove antigen and incubate APCs with Th cells –> no activation of Th cells
- Incubate APCs with antigen, fix the APCs and remove antigen, incubate APCs with Th cells –> activation of Th
- Fix APCs, incubate the fixed APCs with antigen derived peptides, remove and incubate APCs with Th cells –> activation of Th!
This clearly shows that in order for antigen presentation to occur, the APCs must be metabolically active to process the antigen into peptides that can be presented.
The processing and presentation pathways differ between class I and II in one major way connected to the source of antigen, what?
Since the peptides have different source, MHC I - intracellular and MHC II extracellular, the MHC I pathway requires live virus/pathogen that can enter the cell. The MHC II pathway can either use live or dead (pieces) of virus to be used in antigen presentation.
Explain the intracellular/endogenous pathway of antigen presentation step-by-step.
MHC I (endogenous) pathway:
- Protein degradation: Intracellular proteins are degraded in the proteasome (often by ubiquitin targeting) or immunoproteasome (present in pAPCs), forming short peptides that can be both endogenous (self) or for example from a virus. The immunoproteasomes is a modified version of the constitutive proteasome but “spits out” peptides of the perfect length for MHC I binding and presentation.
- Peptide transport into RER: The peptides are transported into the rough ER by TAP (transporter associated with antigen processing - a dimer with ATP binding - ATP hydrolysis needed), where newly formed MHC I molecules sit waiting to be loaded with peptides.
- Peptide loading onto MHC I: The loading of the peptides requires chaperones, first, calnexin promotes folding of the MHC I and recruitment of the β-microglobulin, second, calreticulin and tapasin joins to bring the MHC i too the TAP to get loaded, third, the peptide gets trimmed to fit into the MHCI groove, is loaded and the chaperones dissociate.
- The peptide loaded MHC molecule exits the ER through the secretory system ( →golgi, →exocytosis vesicle) to be transported to the outer membrane where it can present the ag to CD8+ Tc cells.
Explain the extracellular/exogenous pathway of antigen presentation step-by-step.
MHC II (exogenous) pathway:
- Internalization by endocytosis: The antigen source is internalized (often by receptor mediated endocytosis) and go through the endocytic processing pathway. Degradation in endosomes: The endocytic vesicles (endosomes) are fused with lysosomes and the contents are degraded, generating peptides. Antigen-presenting cells have a unique form of late endosome, the MHC class II–containing compartment (MIIC), in which final protein degradation and peptide loading into MHC class II proteins occurs.
- The invariant chain: The invariant chain (CD74) guides transport of class II MHC molecules to endocytic vesicles, it binds in the groove preventing peptides from binding to the groove too early in the ER. It also uses sorting signals in its cytoplasmic tail to direct MHC class II molecule–containing vesicles to peptide-containing endocytic
compartments. - CLIP - antigen exchange: The assembly of the peptides and MHC II involves CLIP (class II–associated invariant chain peptide) which is a part of the localization sequence for the endosome of the invariant chain. CLIP occupies the peptide binding groove to prevent premature binding, and is exchanged for the peptide by HLA-DM (a nonclassical MHC class II molecule) which catalyzes the exchange.
- Once the peptide is bound to the MHC II the MCHII-peptide is transported to the outer membrane to present antigens to CD4+ Th cells. The rest of the invariant chain is digested.
What is cross-presentation?
Cross presentation is when APCs have engulfed antigens and thus are not infected themselves, but still need to activate/prime CD8+ T-cell responses.
During cross presentation, APCs divert exogenous antigens (which would normally go through the exogenous pathway to be presented on MHC II to Th cells) to be processed in the endogenous pathway instead, leading to class I MHC loading and presentation to Tc cells, priming them for destroying other virally infected target cells that express this same peptide-MHC combination.
Which cell type is primarily performing cross presentation? What is needed for them to do this?
Dendritic cells are the primary cross-presenting cell type as far as we know. But to do this they need “licencing” by Th cells.
How does licencing for cross presentation work?
If DC can present foreign antigen to CD4+ helper T cell, it
gets “license” to redirect exogenous Ag into the endogenous pathway, the “License” might be back/forth cytokine signal between the APC/helper T cell indicating situation is right for cross-presentation. Although, the actual redirection method is unclear.
All the examples of MHC mediated antigen presentation are peptides, can only peptides be presented?
No, some none-classic MHC molecules can present non-protein antigens that can be recognized by small subgroups of T cells, that can recognize different non-peptide antigens.
The CD1 family of non-classical class I molecules can present lipids, very little polymorphisms are displayed in these MHC molecules.
