Antigen Processing And Presentation
In discussing the MHC and the T-cell receptor (see Figs 11 and 12), frequent allusion has been made to the foreign peptides that bind to the former and are recognized by the latter. These peptides become associated with MHC molecules through two quite separate pathways (see figure), usually known for convenience as the class I pathway (left) and the class II pathway (right).
The first evidence that the MHC was involved in presenting antigens to T cells was the demonstration of ‘MHC restriction’ – the fact that T cells are specific for both antigen and MHC molecule. Then it was dis- covered that cytotoxic T cells could respond to viral nuclear antigens, which are not displayed on the surface of the virus! How could a T cell ‘see’such a well-concealed antigen? The answer is shown in the left-hand figure above: virus-derived peptides become bound to class I MHC molecules inside the cell and are then transported to the surface, where T cells can recognize the peptide–MHC combination and, under appropriate circumstances, kill the virus-infected cell (for more details see Fig. 21).
At the same time, it was shown that a rather similar process occurs in the ‘antigen-presenting’ cells, mainly macrophages and dendritic cells, which activate helper T cells, with the difference that here it is the class II MHC molecules that transport the peptides to the surface (right-hand figure). This process is kept separate from the class I pathway by occurring in the endosomal/lysosomal vacuoles in which foreign material is normally digested (see Fig. 9). B lymphocytes can also process and present antigen, but only when they are able to bind it via their surface immunoglobulin (top right). Presentation by B cells to T cells is an essential step in T-cell help (see Fig. 19).
One can now appreciate that the real role of the MHC system is to transport samples of intracellular proteins to the cell surface for T cells to inspect them and react if necessary – by proliferating into clones and then helping macrophages or B cells or killing virus-infected cells, as described in the following pages.
Virus Because they are synthesized in the cell, viral proteins are avail- able in the cytoplasm, alongside self-proteins.
RER Rough endoplasmic reticulum, where proteins, including those of the MHC, are synthesized.
MHC I The single three-domain α chain associates with β2- microglobulin to make a class I MHC molecule, whose structure is not fully stable until a peptide has been bound (see below). The effi- cient folding of MHC molecules around an antigen peptide requires a set of other ‘chaperone’ molecules found within the RER.
Proteasome A cylindrical complex of proteolytic enzymes with the property of digesting proteins into short peptides. This organelle has an essential role in regulating protein turnover in all cells. Its function has been hijacked by the immune system to provide peptides for class I MHC presentation. Two components of the proteasome that can alter its properties so as to produce peptides with better binding properties for MHC are encoded by the LMP genes that are found within the MHC region of the chromosome.
TAP TAP (transporter of antigen peptide) genes are found within the MHC region of the chromosome, and encode transporter proteins that carry the proteolytic fragments of antigen generated by the proteasome from the cytosol into the lumen of the endoplasmic reticulum where they bind to the peptide-binding groove of the class I MHC. Some viruses (e.g. human papillomavirus [HPV], Epstein – Barr virus [EBV], cytomegalovirus [CMV]; see Fig. 27) diminish immune recognition by encoding proteins that block TAP function or peptide binding to MHC.
Peptides of 8–10 amino acids are able to bind into the groove between the outer two α helices of the MHC molecule. If the peptides produced by the proteasome are too long special ‘trimming’ enzymes in the RER cut them to the right length. This binding is of high affinity but not as specific as that of antibody or the TCR. Thus, the six different types of class I MHC molecules on each cell (see Fig. 11) can between them bind a wide range of peptides, including many derived from ‘self’ proteins. Even after viral infection only a few percent of the available MHC molecules become loaded with viral peptides, and the rest will be derived from ‘self’ proteins from within the cell.
Golgi The Golgi complex, responsible for conveying proteins from the RER to other sites, including the cell surface.
TCR The T-cell receptor. Because of selection in the thymus (see Fig. 16), only a T cell whose receptor recognizes both the MHC molecule and the peptide bound in it will respond. This is a highly specific interaction, ensuring that cells displaying only ‘self’ peptides are not killed.
CD8 This molecule, expressed on cytotoxic T cells, recognizes the class I MHC molecule, a further requirement before killing of the virus-infected cell by the cytotoxic T cell can take place.
Cross-presentation Some antigens ‘break the rules’ and enter the class I processing pathway from the outside of the cell. Dendritic cells appear to be particularly efficient at cross-presentation, which may be of importance in trying to stimulate an immunological response against tumours (see Fig. 42). against tumours (see Fig. 42).
The class II pathway
Antigen Any foreign material taken in by phagocytosis or endocytosis will find itself in vesicles of the endocytic pathway, collectively known as endosomes, but including the acidic lysosomes, so that various digestive enzymes can act at the appropriate pH. In the case of microbial infection, the whole microbe is taken into the phagolysosome. Macrophages and dendritic cells carry many receptors on their surface (see Figs 3 and 5), which can bind sugars or other common constituents of pathogen surfaces and greatly increase the efficiency of uptake, by receptor-mediated uptake.
Sig Surface immunoglobulin allows the B lymphocyte to bind and subsequently endocytose antigen. Once within the cell, the antigen is processed in the usual way and peptides are presented on class II MHC. Because uptake is via a specific receptor, B cells selectively process only those antigens against which they carry specific antibody.
MHC II The two-chain MHC class II molecule forms a peptide- binding groove between the α1 and β1 domains, the β chain contributing most of the specificity. When first synthesized, this binding is prevented by a protein called the invariant chain, which is progressively cleaved off and replaced by newly produced peptides in the endosomes.
Inv (invariant chain) So called because, in contrast to the class II MHC molecules, it is not polymorphic. It acts as a ‘chaperone’ in helping MHC molecules to fold correctly as they are synthesized, and then binds to them, preventing peptides from associating with the peptide-binding site while still within the endoplasmic reticulum. It then directs the transport of the associated class II MHC molecules to specialized processing endosomes where, finally, it is proteolytically cleaved. This allows antigen peptides to bind the MHC, and allows the MHC carrying the peptides to exit the endosome and go to the cell membrane.
Peptides MHC class II molecules can bind peptides up to 20 amino acids long, which can extend out of each end. The peptides include some derived from microbes in the endosomes (e.g. persistent bacteria such as the tubercle bacillus), but also includes many self-peptides, some of which are derived from MHC molecules themselves. Peptides carrying post-translational modifications such as sugars or phosphate groups are also presented.
LC (class II loading compartment) Specialized acidic endosomes within which peptides are loaded on to the peptide-binding cleft of MHC class II molecules. The binding of peptides to MHC within this compartment is facilitated by two other class II-like molecules, HLA-DM and HLA-DO, which ensure that only those peptides with the best MHC fit are presented at the cell surface.
CD4 This molecule, expressed on helper T cells, interacts with MHC class II molecules, ensuring that the T-cell response (i.e. cytokine secretion; see Figs 21 and 23) is focused on an appropriate cell, i.e. either a B lymphocyte or a macrophage harbouring an intracellular infection. Thus, the type of T-cell response that occurs is determined by a sequence of factors: (i) the type of T cell (CD8 cytotoxic or CD4 helper); (ii) the class of MHC (I or II); (iii) the source of the peptide bound by the MHC (cytoplasmic or endocytosed); and, ultimately, (iv) the type of infection (viral or microbial). However, there are exceptions to this tidy scheme as described in Figs 26–32.