Immunology - Chapter 7 the major histocompatibility complex and antigen presentation

what are the 5 reasons why MHC peptide molecules on the surface of a cell is important?

Although the presentation of foreign antigen to T cells by MHC molecules garners much attention, most MHC molecules spend their lives presenting self-peptides. There are several reasons why an MHC-peptide molecule on the surface of a cell is important. In general, these include the following: 1. To display self-MHC class I and self-peptide to demonstrate that the cell is healthy 2. To display a foreign peptide in class I to show that the cell is infected and to engage with TC cells 3. To display a foreign peptide in class II to show the body is infected and activate TH cells 4. To display a self-peptide in class I and II to test developing T cells for autoreactivity (in primary lymphoid organs) 5. To display a self-peptide in class I and II to maintain tolerance to self-proteins (in secondary lymphoid organs) Finally, please remember that MHC class I expression is found throughout the body (essentially on all nucleated cells), while MHC class II is primarily restricted to antigen-presenting cells, macrophages (activated), B cells (constitutively low levels), and dendritic cells (constitutive).

Why is codominant expression an advantage?

Because it gives the best chance for an organism to have SOME capability of presenting all the possible antigen peptides it encounters. This can also make transplantation somewhat difficult, as humans are heterozygous at each locus and nonmatching MHC patterns will result in rejection of transplanted tissues.

what are the three major classes of molecules that MHC locus encodes for?

Every vertebrate species studied to date possesses the tightly linked cluster of genes that constitute the major histocompatibility complex. The MHC is a collection of genes arrayed within a long continuous stretch of DNA on chromosome 6 in humans and on chromosome 17 in mice. The MHC is also 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: Class I MHC genes encode glycoproteins expressed on the surface of nearly all nucleated cells; the major function of the class I gene products is presentation of endogenous (cytosolic) peptide antigens to CD8+ T cells. Class II MHC genes encode glycoproteins expressed predominantly on APCs (macrophages, dendritic cells, and B cells), where they primarily present exogenous (extracellular) peptide antigens to CD4+ T cells. Class III MHC genes encode a diverse set of proteins, some of which have immune functions, but that do not play a direct role in presenting antigen to T cells (e.g. TNF, C2, C4, factor B). The MHC region is thus said to be polygenic because it contains multiple genes with the same function but with slightly different structures.

Genes that reside within the MHC locus are _________ ___________

Genes that reside within the MHC locus are highly polymorphic; that is, many alternative forms of each gene, or alleles, exist within the population. This polymorphism clusters in the DNA regions that encode amino acids likely to lie in the antigen-binding groove and therefore likely to come into contact with peptide. The genes are also tightly linked so that the set of alleles within the entire MHC locus is generally passed down as one unit; one such linked set of MHC alleles inherited from a parent is called a haplotype. In outbred populations, such as humans, the offspring are generally heterozygous at the MHC locus, with different alleles contributed by each of the parents. Mice in a traditional inbred mouse strain are said to be syngeneic, or identical at all genetic loci. Two strains are congenic if they are bred to be genetically identical everywhere except at a single genetic region.

What occurs once the peptide in to the lumen of the RER?

In the RER, chaperone proteins and proteases assist with the loading and processing of peptide fragments as they associate with MHC class I molecules, stabilizing this protein complex and allowing peptide-loaded MHC class I molecules to move out of the RER and toward the cell surface. In particular: - Calnexin, ERp57, calreticulin, and tapasin help fold MHC class I and put it in close proximity to TAP - ER aminopeptidase ERAP1 trims long peptides to a suitable size for MHC class I grooves at 56 of feb 27 he says what you need to know

focusing on MHC class I molecules; what are the two distinguishing features of their bound peptides? What are anchor residues?

Let's focus on MHC class I - peptide interactions. MHC class I molecules bind peptides from intracellular sources and present these to CD8+ T cells. The bound peptides isolated from various class I molecules have two distinguishing features: they are 8 to 10 amino acids in length (most are 9, and are called nonamers), and they contain specific amino acid residues at key locations in the sequence called anchor residues. The side chains of the anchor residues in the peptide are complementary with surface features of the binding groove of the MHC class I molecule. The amino acid residues lining the binding sites vary among different class I allelic variants, and this is what determines the chemical identity of the anchor residues that can interact with a given class I molecule. While some amino acids anchor the peptide into the groove, others are available to interact with a TCR. Evidence suggests that even a single MHC-peptide complex may be sufficient to target a cell for recognition and lysis by a cytotoxic T lymphocyte with a receptor specific for that target structure!!! Each human or mouse cell can express several unique MHC class I molecules, each with slightly different rules for peptide binding at these anchor residues. Because a single nucleated cell expresses about 105 copies of each of these unique class I molecules each with its own peptide promiscuity rules, a wide range of different peptides can be expressed simultaneously on the surface of a nucleated cell. This means that although many of the peptide fragments of a given foreign antigen will be presented to CD8+ T cells, the particular set of MHC class I alleles inherited by each individual will determine which specific set of peptide fragments from a larger protein will be presented. In general, peptides binding to class I molecules contain a hydrophobic carboxyl-terminal anchor. In addition, another anchor is often found at the second, or second and third, positions at the amino-terminal end of the peptide. In general, any peptide of the correct length that contains the same or chemically similar anchor residues will bind to the same MHC class I molecule. The anchor residues at both ends of the peptide are buried within the binding groove, thereby holding the peptide firmly in place. Between the anchors, the peptide can arch away from the floor of the groove in the middle, allowing peptides that are slightly longer or shorter to be accommodated. Amino acids in the center of the peptide that arch away from the MHC molecule are more exposed and presumably can interact more directly with the T-cell receptor.

Are MHC molecules membrane bound or soluble?

MHC class I molecules and MHC class II molecules are membrane-bound glycoproteins that are closely related in both structure and function despite being encoded differently.

what is the structure of a MHC class I molecule?

MHC class I molecules consist of one large transmembrane glycoprotein α chain with an inherent binding pocket that accommodates peptides of approximately 8 to 10 amino acids, plus a much smaller, noncovalently associated β chain, called β2-macroglobulin: - 45 kDa glycoprotein α chain that includes an Ig domain - 12 kDa β2-microglobulin protein - α chain passes through plasma membrane - α1 and α2 domain α-helix and β-pleated sheet form walls and floor of peptide binding site, respectively SO the MHC class I molecule is composed of both α and β chains BUT ONLY THE α CHAIN GOES THROUGH THE MEMBRANE. also, the binding groove is only composed of α chains in MHC class I molecules.

MHC class I & II expression can change with changing conditions. What are some of these conditions?

MHC class I proteins are expressed on all nucleated cells, but the level of expression differs among different cell types, with the highest levels of class I molecules found on the surface of lymphocytes. On these cells, class I molecules may constitute approximately 1% of the total plasma membrane proteins, or some 5 × 105 MHC class I molecules per cell. In contrast, cells such as fibroblasts, muscle cells, liver hepatocytes, and some neural cells express very low to undetectable levels of MHC class I molecules. MHC class I & II expression can change with changing conditions: •Genetic regulatory components (promoters that drive up transcription during times of infection, NLRs are core component transcriptional activators) •Viral interference (viruses like to shut down MHC Class I expression because it targets the cells they're in for destruction). For example, in the case of cytomegalovirus infection, a viral protein binds to β2-microglobulin, preventing assembly of MHC class I molecules and their transport to the plasma membrane. •Cytokine-mediated signaling (some cytokines like IFN-α and TNF-α expressed first during infection/disease can drive up MHC expression, whereas corticosteroids and prostaglandins downregulate MHC expression)

what is the structure of a MHC class II molecule?

MHC class II molecules are composed of two noncovalently associated transmembrane glycoproteins (an α chain and a β chain) with similar structures, where their extracellular domains together form a binding pocket accommodating peptides of approximately 13 to 18 residues in length: - Possesses Ig domains - Heterodimeric: 33 kDa α chain + 28 kDa β chain - Both chains pass through the plasma membrane - A peptide-binding cleft is formed by the pairing of the α1 and β1 domains - Accommodates peptides of 13-18 amino acids in length SO MHC class II molecules are also composed of α and β chains and BOTH have transmembrane regions. Furthermore, the peptide-binding groove is composed of both the α and β chains.

can only peptides bind to the MHC binding grooves?

NO non-antigenic fragments can also bind Some nonprotein antigens can be recognized by T cells (for example mycolic acid derived from pathogens such as Mycobacterium tuberculosis). These antigens are presented via a small group of nonclassical class I molecules classic MHC molecules including the CD1 family of proteins and the MHC class I-related protein (MR1). Unlike classical MHC molecules, CD1 and MR1 display very limited polymorphism. We now understand that natural killer (NK) T cells, many skin and mucosal γδ T cells, and T cells responsible for recognizing Mycobacterium tuberculosis recognize CD1 molecules presenting lipid antigens.

How are peptides created in the endogenous pathway?

Peptides generated by the (immune)proteasome are transported from the cytosol to the rough endoplasmic reticulum (RER), where the transmembrane MHC class I molecules are synthesized. The transporter protein, designated TAP (transporter associated with antigen processing), is an ER-membrane-spanning heterodimer consisting of two proteins: TAP1 and TAP2. - active transport Peptides generated in the cytosol by the proteasome are translocated by TAP into the RER by a process that requires the hydrolysis of ATP. TAP has affinity for peptides containing 8 to 16 amino acids (recall that the optimal peptide length for final association with MHC class I is nine amino acids). In addition, TAP appears to favor peptides with hydrophobic or basic carboxyl-terminal amino acids, the preferred anchor residues for MHC class I molecules. Thus, TAP is pre-optimized to transport peptides that are likely to interact with MHC class I molecules. SOO in the membrane of the RER, you have a protein called TAP which is a transporter protein that requires ATP hydrolysis in order to transport a peptide from the cytosome - which is degraded by immunoproteasomes - into the lumen of the RER

What occurs in the exogenous pathway?

Phagocytosis of extracellular antigens by pAPCs results in transport of these antigens through a series of protease-containing intracellular vesicles, each with increasingly lower pH, where proteins are partially degraded into peptide fragments and eventually meet up with MHC class II molecules in vesicles coming from the RER. Particulate material by simple phagocytosis, where material is engulfed by pseudopods of the cell membrane; or by receptor-mediated endocytosis, where the material first binds to specific surface receptors, followed by clathrin-mediated internalization. The process is fast, it takes 1-3 hours for an internalized antigen to travel through the endocytic pathway and ultimately appear at the cell surface as a MHC class II-peptide complex. Peptides (13-18 amino acids) are generated from internalized antigens in endocytic vesicles. Simultaneously, MHC class II molecules are produced, associated with Invariant chain (Ii, CD74), and exported in vesicles from ER to the Golgi. In essence, Ii blocks any endogenously derived peptides from binding while the class II molecule is still in the RER (and so prevent the class II molecules to be loaded from peptides destined for class I molecules). Thus, the invariant chain (Ii) serves as a chaperone, assisting in the assembly and transport of peptide-empty MHC class II molecules from the RER to late endosomes, where they encounter exogenous peptide fragments derived from phagocytosed antigens. A nonclassical MHC class II molecule called HLA-DM is required to catalyze the exchange of CLIP with antigenic peptides. The DMα and DMβ genes are located near the TAP and LMP genes in the MHC complex of humans, with similar genes in mice. Like other MHC class II molecules, HLA-DM is a heterodimer of α and β chains. However, unlike other class II molecules it is relatively nonpolymorphic and is not normally expressed at the cell membrane but is found predominantly within the endosomal compartment. As with MHC class I molecules, peptide binding is required to maintain the structure and stability of class II molecules. Once a peptide has bound, the MHC class II-peptide complex is transported to the plasma membrane, where the neutral pH appears to enable the complex to assume a compact, stable form. Peptide is bound so strongly in this compact form that it is difficult to replace a class II-bound peptide on the membrane with another peptide under physiologic conditions. HLA-DO, another nonclassical class II molecule in mostly DCs may regulate the activity of HLA-DM and encourage class II presentation of self-peptides in a manner that encourages self-tolerance

How many class I and class II MHC molecules can one individual express?

Several hundred different allelic variants of MHC class I and II molecules have been identified in the human population. However, anyone individual expresses only a small subset of these molecules: up to 6 class I and about 12 class II molecules. Even though any individual only expresses limited number of MHC proteins, they present a vast array of antigen peptide fragments. Indeed, a given MHC molecule can bind numerous different peptides, and some peptides can bind to several different MHC molecules. Because of this broad specificity, the binding between a peptide and an MHC molecule is often referred to as "promiscuous." Consistent with the similarities in the structures of the peptide-binding grooves in MHC class I and II molecules, these proteins exhibit some common peptide-binding features. In class I and class II, peptide ligands are held in a large extended conformation that runs the length of the groove. 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, hence the longer peptides bound by class II molecules. SO basically we have 18 MHC molecules that have to bind billions of combinations of T cell receptors. But the identity of the peptides that are presented inside the grooves is also extremely diverse. One peptide can bind to several MHC and one MHC can bind to 1000s of peptides. Furthermore, the different ways peptides can be presented inside the MHC molecule creates further diversity

What about class II molecules?

Similar principles apply, but the open ends and less conserved nature of the class II binding groove, compared with class I, allow for greater variability in the sequence and length of class II-bound peptides. One common feature that the class II peptides have is that they maintain a roughly constant elevation on the floor of the binding groove. The peptides that bind to a particular class II molecule often have internal conserved sequence motifs, but unlike class I-binding peptides they appear to lack conserved anchor residues. Instead, 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, as is seen in class I-bound peptides. Peptides that bind to MHC class II molecules contain an internal sequence of 7 to 10 amino acids that provide the major contact points. MHC class II molecules do not have an affinity for anchor residues so rather the peptides are bound in the groove via hydrogen bonding. The binding grooves for MHC class II molecules is created by α and β chains which also have different alleles increasing the diversity. MHC class II molecules are more diverse.

Which MHC molecule has a greater change to generate diversity?

Since the MHC alleles are also codominantly expressed, heterozygous individuals will express the gene products encoded by both alleles at each MHC gene locus. In a fully heterozygous individual this amounts to six unique classical class I molecules on each nucleated cell. An F1 mouse, for example, expresses the H2-K, -D, and -L class I molecules from each parent on the surface of each of its nucleated cells. The expression of so many individual MHC class I molecules, each with its own promiscuity of binding, allows a cell to display or present a large number of different peptides. MHC class II molecules have even greater potential for diversity. Each of the classical MHC class II molecules is composed of two different polypeptide chains encoded by different loci, which come together to form one class II binding pocket. Therefore, a heterozygous individual can express α-β combinations that originate from the same chromosome (maternal only or paternal only) as well as class II molecules arising from unique chain pairing derived from separate chromosomes (new maternal-paternal α-β combinations). To date, there are ~15,000 identified alleles in humans. the theoretical number of potential class I haplotypes in the human population is over 40 billion. If the most polymorphic class II loci are considered, the numbers are even more staggering, with over 1013 different possible class II haplotypes. Because each HLA haplotype contains both class I and class II genes, theoretically, there could be as many as 10^23 possible ways to combine HLA class I and II alleles within the human population (there are less than 10 billion human beings). Although the sequence divergence among alleles of the MHC within a species is very high, this variation is not randomly distributed along the entire polypeptide chain. Instead, polymorphism in the MHC is clustered in short stretches, largely within the membrane-distal α1 and α2 domains of class I molecules. Similar patterns of diversity are observed in the α1 and β1 domains of class II molecules. Polymorphic residues in MHC alleles cluster in the peptide-binding pocket, influencing the fragments of antigen that are presented to the immune system, and thereby influencing susceptibility to a number of diseases.

T or F: Despite differences in the architectures of MHC class I & II molecules, the peptide-binding grooves are closely related structurally

T

Do B or T cells interact with MHC molecules?

T cell receptors In contrast to antibodies or B-cell receptors, T-cell receptors only recognize pieces of antigen that are first positioned on the surface of other cells. These antigen pieces, or antigenic peptides, are held within the binding groove of a cell-surface protein called the major histocompatibility complex (MHC) molecule. The peptide fragments that bind to MHC molecules are generated inside the cell following antigen digestion, and the complex of the antigenic peptide plus MHC molecule is transported to the cell surface. MHC molecules thus act as cell-surface vessels for holding and displaying fragments of antigen so that approaching T cells can engage with these molecular complexes via their T-cell receptors.

what are the two likely explanations behind why one person might get a virus while another individual might not?

The MHC haplotype will influence both the specific peptides that can be presented as well as the T-cell repertoire in an individual, shaping and sometimes limiting the ways in which foreign antigen can be recognized by that host. As such, MHC alleles play a critical role in immune responsiveness. In other words, different capability to present antigens may dictate overall strength of immune response from individual to individual. There are two likely explanations: 1. Determinant selection model: MHC class II molecules differ in ability to bind particular processed antigen peptides 2. Holes-in-the-repertoire model: T cells with TCRs that recognize certain foreign antigens closely resembling self-antigens may be eliminated during thymic development

What is cross presentation?

The answer to this dilemma is a process called cross-presentation, blending the exogenous and endogenous pathways in a process that is still being fully resolved. The phenomenon of cross-presentation requires that antigens acquired from extracellular sources, normally handled by the exogenous pathway leading to MHC class II presentation, are redirected to a class I peptide loading pathway. When this form of antigen presentation leads to the activation of a naïve CD8+ T cell it is referred to as cross-priming; when it leads to the induction of tolerance in a CD8+ T cell, such as when the APCs are not activated, it is called cross-tolerance. Dendritic cells in particular can cross-present exogenous antigen via MHC class I molecules. The mechanism that underlies this redirection remains unclear. The advantage of cross-presentation is not: it allows these DCs to capture antigen, such as viral proteins, from the extracellular environment or from dying cells, process these antigens, and activate CTLs that can then seek out and attack virus-infected cells, inhibiting further spread of the infection. SO in cross presentation you can have a class II antigen from the exogenous pathway being diverted towards the endogenous pathway Ability of certain APC to present Antigen peptides on both MHC class 1 and 2

The genes within the MHC locus exhibit a ____________ form of expression. what does this mean?

The genes within the MHC locus exhibit a codominant form of expression. This means that both maternal and paternal gene products (both haplotypes) are expressed at the same time and in the same cells. Therefore, if two mice from inbred strains possessing different MHC haplotypes are mated, the F1 generation inherits both parental haplotypes and will express all these MHC alleles; twice as many as either parent. For example, if an H2b strain is crossed with an H2k strain, then the F1 generation inherits both parental sets of alleles and is said to be H2b/k. Because such an F1generation expresses the MHC proteins of both parental strains on its cells, it is said to be histocompatible, or MHC matched, with both parental strains.

how do these peptides make in onto the cell surface? is the process different for MHC class I vs. MHC class II?

There is experimental evidence of at least two distinct routes of antigen processing and presentation that differ in their source of antigen, intracellular trafficking, and MHC association. In general, antigens from intracellular sources are presented in MHC class I molecules (endogenous pathway) to CD8+ T cells while antigens from the extracellular spaces are presented in MHC class II molecules (exogenous pathway) to CD4+ T cells. Thus: •Class I presentation requires cytosolic or endogenous processing •Class II presentation requires exogenous processing SO class I requires endogenous processing (so something inside the cytoplasm is being degraded) while class II requires exogenous processing (so bringing something from outside the cell in to degrade it

How is cross-presentation of DCs regulated?

These cells need to be licensed before they can cross-present. Here is a potential mechanism. First, the classical exogenous pathway of antigen processing in DCs leads to presentation of antigen to CD4+ T cells via class II, leading to activation of these cells. These activated helper cells might then return the favor by inducing costimulatory molecule expression in the DC and by secreting stimulatory cytokines (e.g., IL-2). In principle, this would supply a "second opinion" that, respectively, licenses the DC to cross pathways and present internalized antigens via MHC class I, activating the more recalcitrant naïve CD8+ T cells SO if you have an exogenous antigen is will bind to a dendritic cell and process that antigen to present to MHC class II molecules. Once presented Helper T cells are activated. THIS IS AWESOME BUT wouldn't you also way to activate cytotoxic T cells so that they can also recognize that antigen and destroy it? WELL THIS IS WHY WE HAVE CROSS PRESENTATION an exogenous antigen is presented by a MHC class II to a T helper cell. This helper cell in return, b c of the activation signaling pathways that it activates, releases IL-2. IL-2 once released binds to neieve t cytotoxic t cells and activates them. These activated cytotoxic t cells then bind to a peptide from the same antigen now presented by a class I molecules. HOW the peptide is diverted towards the endogenous pathway is unknown.

what are immunoproteasomes?

We are first going to look at the endogenous pathway While all cells have constitutive proteasomes involved in the processing and presentation of cytosolic proteins in MHC class I molecules, infected cells or activated APCs can temporarily express immunoproteasomes, which generate peptide fragments that are optimized for MHC class I binding. The principles of protein degradation you have already learned still apply to these immunoproteasomes: proteins tagged with ubiquitin will be destined for processing. The immunoproteasome has the same basic structure as the traditional proteasome with some unique subunit substitutions. In most cells, these new subunits are not constitutively expressed like the other components of the proteasome but are induced by exposure to certain cytokines, such as IFN-γ or TNF. LMP2 and LMP7, genes that are located within the class II region and are responsive to these cytokines, encode replacement catalytic protein subunits that convert standard proteasomes into immunoproteasomes, increasing the efficiency with which cytosolic proteins are cleaved into peptide fragments that specifically bind to MHC class I molecules. The proteasome degrades proteins into peptides which can then be recycled to make new proteins, etc. BUT in some instances, mainly in immune cells, we have a more advanced proteasome called a immunoproteasome. - It is essentially the same thing but instead of β1,β5, and β2 it has β1i, β5i, and β2i which are protease that can generate peptides more SPECIFIC for MHC class I molecules. - for ex. they can generate peptides that contain an anchor residue at position 9 and a hydrophobic region at the C terminus. - BUT keep in mind that both the proteasome can generate peptides for MHC molecules, but the immunoproteasome just generates MORE SPECIFIC peptides.

T cells are restricted to recognizing peptides presented in the context of self-MHC alleles:

both CD4+ and CD8+ T cells can recognize antigen only when it is presented in the groove of an MHC molecule the MHC haplotype of the APC and the T cell must match

So far, the rules appear simple: endogenous peptides are presented by MHC class I proteins while exogenous peptides are presented by MHC class II proteins. Also, MHC class I proteins activate cytotoxic T cells MHC class II proteins activate helper T cells. However, there are exceptions.

pAPCs internalize extracellular antigen they can process and present these antigens via the conventional exogenous pathway, leading to MHC class II association. Because pAPCs also express costimulatory molecules, engagement of CD4+ T cells with these MHC class II-peptide complexes can lead to activation of T helper responses. On the other hand, infected cells will generally process and present cytosolic peptides via the endogenous pathway, leading to MHC class I-peptide complexes on their surface. However, unless these infected cells express the costimulatory molecules, they cannot activate naïve CD8+ T cells. This leaves us with a dilemma: how does the immune system activate CD8+ T cells to eliminate intracellular microbes unless a professional antigen-presenting cell happens to become infected? Similarly, a pAPC that phagocytoses a virus from extracellular sources should send these viral proteins through endocytic vesicles to associate with MHC class II molecules, activating CD4+ T cells rather than the CD8+ cytotoxic T lymphocytes (CTLs) that are required to combat this type of infection. SOOO so far we have said that class I molecules --> all nucleated cells and class II molecules --> pACPs. Class II activate helper T cells and class I activate cytotoxic T cells. Helper cells help and cytotoxic t cells kill also remember that if you have a cel that is nucleated expressing MHC class I is activates cytotoxic t cells but in order to these cells to kill they require a costimoatory signals. BUT HERE IS THE PROBLEM: not also nucleated cells have costimoatory signals!!