MHC and Antigen Presentation

In order to be capable of engaging the key elements of adaptive immunity (specificity, memory, diversity, self/nonself discrimination), antigens have to be processed and presented to immune cells. Antigen presentation is mediated by MHC class I molecules, and the class II molecules found on the surface of antigen-presenting cells (APCs) and certain other cells.

MHC class I and class II molecules are similar in function: they deliver short peptides to the cell surface allowing these peptides to be recognised by CD8+ (cytotoxic) and CD4+ (helper) T cells, respectively. The difference is that the peptides originate from different sources – endogenous, or intracellular, for MHC class I; and exogenous, or extracellular for MHC class II. There is also so called cross-presentation in which exogenous antigens can be presented by MHC class I molecules. Endogenous antigens can also be presented by MHC class II when they are degraded through autophagy.

MHC class I presentation

MHC class I molecules are expressed by all nucleated cells. MHC class I molecules are assembled in the endoplasmic reticulum (ER) and consist of two types of chain – a polymorphic heavy chain and a chain called β2-microglobulin. The heavy chain is stabilised by the chaperone calnexin, prior to association with the β2-microglobulin. Without peptides, these molecules are stabilised by chaperone proteins: calreticulin, Erp57, protein disulfide isomerase (PDI) and tapasin. The complex of TAP, tapasin, MHC class I, ERp57 and calreticulin is called the peptide-loading complex (PLC). Tapasin interacts with the transport protein TAP (transporter associated with antigen presentation) which translocates peptides from the cytoplasm into the ER. Prior to entering the ER, peptides are derived from the degradation of proteins, which can be of viral- or self origin. Degradation of proteins is mediated by cytosolic- and nuclear proteasomes, and the resulting peptides are translocated into the ER by means of TAP. TAP translocates peptides of 8 –16 amino acids and they may require additional trimming in the ER before binding to MHC class I molecules. This is possibly due to the presence of ER aminopeptidase (ERAAP) associated with antigen processing.

It should be noted that 30–70% of proteins are immediately degraded after synthesis (they are called DRiPs – defective ribosomal products, and they are the result of defective transcription or translation). This process allows viral peptides to be presented very quickly – for example, influenza virus can be recognised by T cells approximately 1.5 hours post-infection. When peptides bind to MHC class I molecules, the chaperones are released and peptide–MHC class I complexes leave the ER for presentation at the cell surface. In some cases, peptides fail to associate with MHC class I and they have to be returned to the cytosol for degradation. Some MHC class I molecules never bind peptides and they are also degraded by the ER-associated protein degradation (ERAD) system.

There are different proteasomes that generate peptides for MHC class-I presentation: 26S proteasome, which is expressed by most cells; the immunoproteasome, which is expressed by many immune cells; and the thymic-specific proteasome expressed by thymic epithelial cells.

Antigen presentation

On the surface of a single cell, MHC class I molecules provide a readout of the expression level of up to 10,000 proteins. This array is interpreted by cytotoxic T lymphocytes and Natural Killer cells, allowing them to monitor the events inside the cell and detect infection and tumorigenesis.

MHC class I complexes at the cell surface may dissociate as time passes and the heavy chain can be internalised. When MHC class I molecules are internalised into the endosome, they enter the MHC class-II presentation pathway. Some of the MHC class I molecules can be recycled and present endosomal peptides as a part of a process which is called cross-presentation.

The usual process of antigen presentation through the MHC I molecule is based on an interaction between the T-cell receptor and a peptide bound to the MHC class I molecule. There is also an interaction between the CD8+ molecule on the surface of the T cell and non-peptide binding regions on the MHC class I molecule. Thus, peptide presented in complex with MHC class I can only be recognised by CD8+ T cells. This interaction is a part of so-called ‘three-signal activation model’, and actually represents the first signal. The next signal is the interaction between CD80/86 on the APC and CD28 on the surface of the T cell, followed by a third signal – the production of cytokines by the APC which fully activates the T cell to provide a specific response.

MHC class I polymorphism

Human MHC class I molecules are encoded by a series of genes – HLA-A, HLA-B and HLA-C (HLA stands for ‘Human Leukocyte Antigen’, which is the human equivalent of MHC molecules found in most vertebrates). These genes are highly polymorphic, which means that each individual has his/her own HLA allele set. The consequences of these polymorphisms are differential susceptibilities to infection and autoimmune diseases that may result from the high diversity of peptides that can bind to MHC class I in different individuals. Also, MHC class I polymorphisms make it virtually impossible to have a perfect tissue match between donor and recipient, and thus are responsible for graft rejection.

MHC class II presentation

MHC class II molecules are expressed by APCs, such as dendritic cells (DC), macrophages and B cells (and, under IFNγ stimuli, by mesenchymal stromal cells, fibroblasts and endothelial cells, as well as by epithelial cells and enteric glial cells). MHC class II molecules bind to peptides that are derived from proteins degraded in the endocytic pathway. MHC class II complexes consists of α- and β-chains that are assembled in the ER and are stabilised by invariant chain (Ii). The complex of MHC class II and Ii is transported through the Golgi into a compartment which is termed the MHC class II compartment (MIIC). Due to acidic pH, proteases cathepsin S and cathepsin L are activated and digest Ii, leaving a residual class II-associated Ii peptide (CLIP) in the peptide-binding groove of the MHC class II. Later, the CLIP is exchanged for an antigenic peptide derived from a protein degraded in the endosomal pathway. This process requires the chaperone HLA-DM, and, in the case of B cells, the HLA-DO molecule. MHC class II molecules loaded with foreign peptide are then transported to the cell membrane to present their cargo to CD4+ T cells. Thereafter, the process of antigen presentation by means of MHC class II molecules basically follows the same pattern as for MHC class I presentation.

As opposed to MHC class I, MHC class II molecules do not dissociate at the plasma membrane. The mechanisms that control MHC class II degradation have not been established yet, but MHC class II molecules can be ubiquitinised and then internalised in an endocytic pathway.

MHC class II polymorphism

Like the MHC class I heavy chain, human MHC class II molecules are encoded by three polymorphic genes: HLA-DR, HLA-DQ and HLA-DP. Different MHC class II alleles can be used as genetic markers for several autoimmune diseases, possibly owing to the peptides that they present.

Figure 3. Genetic map of the MHC regions. This map has been simplified to demonstrate organizational themes within the MHC. There are more than 200 genes within these regions. [Bellanti, JA (Ed). Immunology IV: Clinical Applications in Health and Disease. I Care Press, Bethesda, MD, 2012]

• The principal function of the MHC is to present antigen to T cells to discriminate between self (our cells and tissues) and nonself (the invaders or modified self).

• Two main characteristics of the MHC make it difficult for pathogens to evade immune responses:

  • First, the MHC is polygenic. It contains several different MHC-I and MHC-II genes so that every individual possesses a set of MHC molecules with different ranges of peptide-binding specificities.

  • Second, the MHC is extremely polymorphic. The MHC genes display the greatest degree of polymorphism in the human genome. There are multiple variants of each gene within the population as a whole. The different variants that are inherited by an individual from a parent are known as alleles. 

• Polymorphic sites are found predominantly in specific regions of the MHC-I and MHC-II molecules called domains.

• Although each HLA molecule shows slight differences in its amino acid sequence from one another, causing a slightly altered three-dimensional structure in the peptide-binding cleft, the basic structures of MHC-I and MHC-II molecules are very similar

• The charge characteristics of the groove determine which peptides can be presented. Since different antigenic peptides have different shapes and charge characteristics, it is important that the human population overall has a large array of different HLA molecules, each with different shaped peptide-binding areas (clefts) to cope with the multitude of self and nonself peptides presented.

MHC Structure and Function

• The MHC has three regions: MHC-I, MHC-II, and MHC-III (Figure 3).

• The classical HLA antigens encoded in each region include HLA-A, -B, and -C in the MHC-I region, and HLA-DR, -DQ, and -DP in the MHC-II region.

• The MHC-III region includes several genes involved in the complement cascade (C4A, C4B, C2, and FB) (see section 6, Complement), the TNF-a and TNF-b (LTa) genes, the CYP21 gene that encodes an enzyme in steroid metabolism, the HSP70 gene that encodes a chaperone, and many other genes of unknown immunological function.

• In general, when we refer to MHC, we are referring to either MHC-I or MHC-II molecules.

• Shown in Figure 4 is a schematic representation of the chromosomal locations and genetic loci responsible for MHC-I and MHC-II synthesis.

• MHC-I molecules consist of two polypeptide chains, a larger a chain encoded on chromosome 6 in the MHC region and a smaller b2 microglobulin encoded on chromosome 15 (Figures 3 and 4).

• The class I a chains consist of a single polypeptide composed of three extracellular domains named a1, a2, and a3, a transmembrane region that anchors it in the plasma membrane, and a short intracytoplasmic tail (Figure 3).

• The b2 microglobulin consists of a single non-polymorphic molecule noncovalently bound to the alpha chain and is encoded on chromosome 15 (Figure 3 and Figure 4). The a1 and a2 domains fold together into a single structure consisting of two segmented a helices lying on a sheet of eight antiparallel b strands.

• The folding of the a1 and a2 domains creates a long cleft or groove that is the site at which peptide antigens bind to the MHC-I molecule and are presented to the CD8 lymphocyte.

• MHC-II molecules consist of two polypeptide chains, a and b, both encoded in the MHC-II region on chromosome 6 and noncovalently linked to one another (Figure 3 and Figure 4).

• The a and b chains each consist of two extracellular domains referred to as a1 and a2 and b1 and b2, respectively, and, similar to the MHC-I a chain, the a and b chains of the MHC-II molecule also consist of a transmembrane segment and a cytoplas-mic tail (Figure 3).

• The extracellular membrane-proximal a2 and b2 domains are homologous to immunoglobulin-constant domains.

• The crystallographic structure of the MHC-II molecule shows that it is folded very much like the MHC-I molecule (Figure 5).

• The major differences between the two MHC class molecules lie at the ends of their peptide-binding clefts, which are more open in MHC-II molecules compared with MHC-I molecules. The MHC-II molecule cleft is made up of a noncovalent association between the a1 and b1 domains and that binds the peptide through multiple van der Waals forces and hydrogen bonds (Figure 6).

• The main consequence of this difference is that the ends of a peptide bound to an MHC-I molecule are buried within the molecule whereas the ends of peptides bound to MHC-II molecules are not.

• This difference allows more flexibility in the length and types of peptides that MHC-II molecules can bind. Peptides that bind a specific class II molecule will share the same middle anchor residues but may vary in length and sequence of other residues.

Expression of MHC Molecules MHC-I

• MHC- I proteins are expressed on all nucleated cells, in contrast to MHC-II molecules, which are restricted to antigen-presenting cells (APCs)

• Lymphocytes, macrophages, dendritic cells, Langherans cells, and some endothelial cells are the predominant cells that express MHC-II.

• Nonnucleated cells such as mammalian red blood cells express little or no MHC-I and thus, pathogens within red blood cells can go undetected by cytotoxic T cells, e.g., malaria.

• The expression of both MHC-I and MHC-II molecules is regulated by cytokines.

• Interferon-g (INF-y) increases the expression of MHC-I or MHC-II molecules and can induce the expression of MHC-II molecules on certain cell types that do not normally express them. This may be very important both in normal immunologic function and in autoimmunity.

• The level of MHC molecule expression plays an important role in T cell activation and therefore differences in levels of expression are significant.

• Shown in Table 1 is a comparison of the principal differences between MHC-I and MHC-II molecules.

Table 1. Features of MHC-I and MHC-II molecules

FeatureMHC-IMHC-II

Polypeptide chains

A single a chain (44–47 kD) noncova-lently linked to the b2-microglobulin chain (12 kD)

A single a chain (32–34 kD) non-covalently linked to a single b chain (29–32 kD)

Distribution

All nucleated cells

Antigen-presenting cells

Composition of antigen-binding clefts

a1 and a2 domains

a1 and b1 domains

Binding site for T cell co-receptor

CD8 binds to the a3 region

CD4 binds to the b2 region

Size of peptide-binding cleft

Accommodates peptides of 8–11 residues

Accommodates peptides of 10–30 residues or more

Nomenclature in the human

HLA-A, HLA-B, HLA-C

HLA-DR, HLA-DQ, HLA-DP

Antigen Presentation

• T cells recognize foreign antigens in the form of short peptides that have been processed and dis-played on the cell surface bound to MHC-I or MHC-II molecules (Figure 6).

• Antigens are often categorized according to whether they are derived from (1) viruses, intracellular bacteria, or protozoan parasites (endogenous pathogens); or (2) exogenous pathogens that replicate outside of the cell.

• Intracellular antigens are presented to T cells by any nucleated cell because MHC-I expression is ubiquitous.

• In contrast, exogenous antigens are taken up by professional APCs, which process the antigens and present them in the context of MHC-II. An important function of a professional APC, e.g., dendritic cell (DC), is to deliver a second signal (costimulation) to the T cell to alert it to the presence of infection.

• Endogenous antigens, including misfolded proteins and pathogen-derived peptides, are processed by the proteasome (Figure 7A).

• This complex of proteases typically generates peptides of four to twenty amino acids with a hydrophobic carboxy terminus. After trimming of the peptide by cytosolic proteases, the antigenic peptides are translocated to the endoplasmic reticulum by the transporters associated with antigen processing (TAP1 and TAP2 molecule).

• Meanwhile, a new MHC-I molecule is being synthesized in the endoplasmic reticulum.

• As it folds, it is bound by calnexin, which is then replaced by calreticulin and b2

• The new MHC-I molecule associates with the MHC-I peptide loading complex. Tapasin physically links the MHC-I molecules and the TAP transporters. As the peptide enters from the cytosol, the cleft of the class I molecule receives it and the peptide-bound MHC-I molecule dissociates from the peptide-loading complex and is recruited to the cell surface.

• This complex machinery has several quality-control steps, such that MHC-I molecules that fail to assemble properly are degraded. Ultimately, the peptide presented on MHC-I molecule will stimulate a CD8 T cell response (Figure 8)

• Exogenous antigens are processed quite differently (Figure 7B).

• Bacterial proteins are cleaved by proteases, cathepsins, and metalloproteases in the acid environment of the endocytic pathway.

• Meanwhile, MHC-II molecules assemble in the endoplasmic reticulum with another molecule called the invariant chain (li). The newly synthesized molecules transit the endoplasmic reticulum and the Golgi apparatus.

• After passage of the li-loaded MHC-II-DM complex through the Golgi into the late endosomes, the invariant chain is cleaved by acid proteases, leaving a residual peptide referred to as the CLass II-associated Invariant chain Peptide (CLIP) in the MHC-II cleft.

• CLIP occludes the MHC-II cleft and prevents peptides from loading until the molecule is in the lysosomal or late endosomal compartment containing the peptides.

• At that point, HLA-DM molecules remove CLIP from the cleft and stabilize the molecule while the peptide is loaded into the cleft.

• HLA-DO molecules can also facilitate this process in some settings.

• The fully assembled and loaded MHC-II molecule is recruited to the surface and serves to stimulate predominantly CD4 positive T cells.

 Nomenclature of HLA

• The HLA nomenclature has developed historically from the original serological designations. Polymorphisms in proteins were originally defined by antibody reaction patterns. Modern definitions utilize DNA sequences to define alleles. The current nomenclature was recommended during the Tenth International Histocompatibility Workshop in 1987, with minor modifications added in 1990.

• Each chromosome is found twice (diploid) in each individual, and therefore a normal tissue type of an individual will involve twelve HLA antigens (three HLA class I loci [A, B, and C] from each parent and three class II loci [DR, DQ, and DP] from each parent).

• HLA-DM and HLA-DO are not highly polymorphic and are not typed. These twelve antigens are inherited co-dominantly.

• The MHC phenotype of a person describes which alleles the person carries without reference to inheritance. For example, someone might be typed as HLA-A1, -A3; B7, B8; Cw2, Cw4; DR15, DR4, DQ3, DQ6, DP4, DP4.

• A haplotype is the set of HLA antigens inherited from one parent. For example, the mother of the person whose HLA type is given above might have HLA-A3, -A69; B7, B45; Cw4, Cw9; DR15, DR17, DQ6, DQ2, DP2, DP4. Therefore, the A3, B7, Cw4, DR15, DQ6, and DP4 were all passed on from the mother to the child above. This group of antigens is a haplotype.

• Despite the enormous number of alleles at each expressed locus, the number of haplotypes observed in the population is much smaller than theoretical expectations. This is because certain alleles tend to occur together on the same haplotype rather than segregating randomly. This is called linkage disequilibrium.

Linkage Disequilibrium

• Linkage disequilibrium is a genetic phenomenon in which two alleles are found together with a higher frequency than normally expected.

• It is the non-random association between alleles at different loci. For example, if 16 percent of the population has a particular HLA-A antigen (A1) and 10 percent of the population has a particular HLA-B antigen (B8), the chance of finding A1 genetically linked to B8 on the same chromosome is given by the product of their gene frequencies (16 percent x 10 percent = 6 percent).

• In practice, this does not always occur. Certain combinations of A and B specificities occur more frequently than would be expected if their association were random. The combination of A1 and B8 is found at a frequency of 8.8 percent in human populations compared to an expected frequency of 1.6 percent. Such paired specificities are said to be in linkage disequilibrium.

• In Caucasians, the HLA-A1, B8, DR3 (DRB1*0301), DQ2 (DQB1*0201) haplotype is highly conserved in the population.

• At HLA class II, this phenomenon is so pronounced that the presence of specific HLA-DR alleles can be used to predict the HLA-DQ allele with a high degree of accuracy before testing. The HLA alleles are ordered on chromosome 6 as DP-DQ-DR-B-Cw-A.

• Those alleles that are physically closest to each other usually have the highest linkage disequilibrium. It is possible that certain haplotypes may be advantageous in some immunological sense, so that they have a positive selective advantage.

Rules that dictate the nomenclature of HLA:

• The prefix HLA precedes all antigens or alleles.

• A capital letter indicates a specific locus (A, B, C, or D). All genes in the region D are prefixed by the letter D followed by a second letter indicating the subregion of D (DR, DQ, DP, DM, or DO).

• Loci coding for the specific class II peptide chains are next identified (A1, A2, B1, and B2). Greek letters are used for protein designations, whereas Latin capital letters are used for gene/allele designations, i.e., DRp1 versus DRB1.

• Specific alleles are designated by an ‘‘*’’ followed by a two-digit number indicating the most closely associated serologic specificity, followed by a two-digit number that defines the unique allele. For example, the serologically defined HLA-A2 specificity actually comprises seventy-seven distinct variant alleles. These alleles are now referred to as HLA-A*02:01 through *02:99.

• Some alleles have a third two-digit number (HLA-B*35:01:01 and B*35:01:02) which indicates that the two variants differ by a silent nucleotide substitution, but not in amino acid sequence 6.