Antigen Presentation

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Chapter 8 Antigen Presentation

Summary

T cells survey proteins derived from intracellular or extracellular pathogens by recognizing peptide fragments that have been processed and become bound to major histocompatibility complex (MHC) class I or II molecules, respectively. These MHC–antigen complexes are presented at the cell surface.

MHC class I molecules associate with endogenously synthesized peptides, produced by degradation of the cells’ internal molecules. This type of antigen processing is carried out by proteasomes, which cleave the proteins and transporters, which take the fragments to the endoplasmic reticulum (ER).

MHC class II molecules bind to peptides produced following the breakdown of proteins that the cell has endocytosed. The peptides produced by degradation of these external antigens are loaded onto MHC class II molecules in a specialized endosomal compartment called MIIC.

The highly ordered area of contact between the T cell and APC is an immunological synapse. TCRs and costimulatory receptors occupy the center of the synapse. Adhesion molecules are found in the periphery.

Costimulatory molecules are essential for T cell activation. Molecules such as B7 (CD80/86) on the APC bind to CD28 on the T cell to cause activation. Antigens presented without costimulation usually induce T cell anergy. Intercellular adhesion molecules also contribute to the interaction between a T cell and an antigen-presenting cell (APC). Interactions between intercellular cell adhesion molecule-1 (ICAM-1) and leukocyte functional antigen-1 (LFA-1) and between CD2 and its ligands extend the interaction between T cells and APCs.

CD4 binds to MHC class II and CD8 to MHC class I molecules. These interactions increase the affinity of T cell binding to the appropriate MHC–antigen complex and bring kinases to the TCR complex.

Binding of CTLA-4 or PD-1 on the T cell limits activation. Both of these ligands inhibit the costimulatory signal that the T cell receives from CD28.

T cell activation induces enzyme cascades, leading to the production of interleukin-2 (IL-2) and the high-affinity IL-2 receptor on the T cell. IL-2 is required to drive T cell division.

Antigen presentation affects the subsequent course of an immune response. The immune system responds to clues that an infection has taken place before responding strongly to antigens.

Antigen presenting cells

T cells only recognize antigen peptides bound to MHC-encoded molecules. Endogenous peptides, derived from intracellular sources such as replicating viruses, are presented on MHC class-I molecules to CD8+ T cells, while exogenous peptides, derived from extracellular sources such as microbes, are presented on MHC class-II molecules to CD4+ T cells. Before peptides can associate with the MHC molecules they are generated by partial proteolysis from the original protein antigen. Antigen processing refers to the degradation of antigen into peptide fragments, which may become bound to MHC class I or class II molecules (see Chapter 5). Whether a peptide binds to an MHC molecule depends on the amino-acid sequence of the peptide and on whether a suitable binding MHC molecule is available, which depends on the set of MHC molecules present in the individual. Broadly speaking, a single T cell recognizes a specific peptide(s) bound in the peptide-binding groove of a specific MHC molecule. However there are instances where T cells can respond to a different MHC/peptide combination, and this is equivalent to the cross-reactivity that may occur when antibodies bind to cross-reactive antigens.

Antigen presentation plays a central role in initiating and maintaining an appropriate immune response to antigen. The process is tightly controlled at several levels as follows:

The four stages of antigen presentation are outlined in Figure 8.1. In lymphoid organs, all four stages of the process can occur, resulting in T cell proliferation. However, antigen presentation can also occur to a more limited degree in tissues, resulting in cytokine production, but with little T cell division.

Interactions with antigen-presenting cells direct T cell activation

The way in which a T cell first encounters antigen largely dictates how it will react subsequently. A wide spectrum of cells can present antigen, depending on how and where the antigen is first encountered by cells of the immune system. In a lymphoid organ, the three main types of APC are:

Activation of naive T cells on first encounter with antigen on the surface of an APC is called priming, to distinguish it from the responses of effector T cells to antigen on the surface of their target cells and the responses of primed memory T cells.

Dendritic cells are crucial for priming T cells

Dendritic cells which are found in abundance in the T cell areas of lymph nodes and spleen, are the most effective cells for the initial activation of naive T cells. They pick up antigens in peripheral tissues, then migrate to lymph nodes, where they express high levels of adhesion and costimulatory molecules, as well as MHC class II molecules, which allow them to interact with CD4+ TH cells.

Once they have migrated, DCs stop synthesizing MHC class II molecules, but maintain high levels of MHC class II molecules containing peptides from antigens derived from the tissue where they originated. Interdigitating DCs are believed to be the major APCs involved in primary immune responses because they induce T cell proliferation more effectively than any other APC.

The majority of dendritic cells enter lymph nodes via afferent lymphatics. Originally it was thought that these cells were mostly derived from Langerhans’ cells in the skin, but it now appears that a substantial proportion of the early migrating DCs in afferent lymph are dermal dendritic cells (they do not express langerin (CD207) a marker of Langerhans’ cells). Moreover DCs derived from Langerhans’ cells tend to localize in the paracortex of the lymph node, whereas dermal DCs remain near lymphoid follicles. Dendritic cells arriving from the periphery of the body transport antigen to the lymph node and process it for presentation to T cells. A minor proportion of the DCs in lymph nodes, arrive from the blood across the HEV, using the same route as T cells and B cells (see Fig. 6.15), however these cells have not acquired antigen in the periphery and they can only acquire it from lymph or transfer from other cells. As they mature, dendritic cells express CCR7 which allows them to localize to the lymphoid tissues. There is also some evidence that DCs from skin and the gut have distinctive chemokine receptors, which allow them to selectively recirculate to their own lymphoid organs. As they mature, DCs also increase expression of key costimulatory molecules, including CD40, CD80 and CD86 (B7-1 and B7-2).

Macrophages and B cells present antigen to primed T cells

Macrophages and B cells are less effective than DCs at antigen presentation to naive T cells, partly because they only express appropriate costimulatory molecules upon infection or contact with microbial products. Although they migrate to lymph nodes, the numbers of macrophages in afferent lymph is relatively few by comparison with DCs and this too limits their effectiveness in activating naive T cells. Macrophages:

B cells can:

If antigen concentrations are very low, B cells with high-affinity antigen receptors (IgM or IgD) are the most effective APC because other APCs simply cannot capture enough antigen. Therefore, for secondary responses, when the number of antigen-specific B cells is high, B cells may be a major APC.

The properties and functions of some APCs are summarized in Figures 8.3 and 8.4.

Antigen processing

Antigen processing involves degrading the antigen into peptide fragments. The vast majority of epitopes recognized by T cells are fragments from a peptide chain. Only a minority of peptide fragments from a protein antigen are able to bind to a particular MHC molecule. Furthermore, different MHC molecules bind different sets of peptides (see Chapter 5). For example, the great majority of the immune response in humans against the HIV matrix protein is directed against a single immunodominant region, i.e. one which is recognized by a large number of T cells. However, exactly which part of this region is recognized, depends on the MHC haplotypes of the individual (Fig. 8.5).

MHC class I pathway

MHC class I-restricted T cells (CTLs) recognize endogenous antigens synthesized within the target cell, whereas class II-restricted T cells (TH) recognize exogenous antigen.

Manipulation of the location of a protein can determine whether it elicits an MHC class I- or class II-restricted response. For example:

Proteasomes are cytoplasmic organelles that degrade cytoplasmic proteins

Although the assembly of MHC class I molecules occurs in the ER of the cell, peptides destined to be presented by MHC class I molecules are generated from cytosolic proteins. The initial step in this process involves an organelle called the proteasome – a multi-protein complex which forms a barrel-like structure (Fig. 8.6).

Proteasomes provide the major proteolytic activity of the cytosol. They have a range of different endopeptidase activities and they degrade denatured or ubiquitinated proteins to peptides of about 5–15 amino acids (ubiquitin is a protein that tags other proteins for degradation).

Two genes, PSMB8 and PSMB9 located in the class II region of the MHC (Fig. 8.7), encode proteasome components that subtly modify the range of peptides produced by proteasomes. The expression of these genes is induced by interferon-γ (IFNγ). The proteins displace constitutive subunits of the proteasome and along with a third inducible proteasome component (PSMB10 encoded on a different chromosome) influence processing of peptides by creating a wider range of peptide fragments suitable for binding MHC class I molecules. Additional subunits associate with the ends of core (20 S) proteasomes and may influence antigen processing. These include interferon-inducible PA28 (proteasome-activator-28) molecules as well as a complex of proteins that result in a larger 26 S particle.

Proteasomes may not be the only proteases involved in producing peptides for presentation by MHC class I molecules. There is evidence for the involvement of enzymes, such as the giant tripeptidyl aminopeptidase II (TPPII) complex.

Transporters move peptides to the ER

The products of two genes, TAP1 and TAP2, that map in the MHC (see Fig. 8.7), function as a heterodimeric transporter that translocates peptides into the lumen of the ER. TAP is a member of the large ATP-binding cassette (ABC) family of transporters localized in the ER membrane. Microsomes from cells lacking TAP1 or TAP2 could not take up peptide in experiments in vitro. Using a similar system it was shown that the most efficient transport occurred with peptide substrates of 8–15 amino acids. Although this size is close to the length preference of MHC class I molecule binding sites, it suggests that some additional trimming may be required by enzymes in the lumen of the ER, particularly ERAAP (ER-associated aminopeptidase).

Antigen processing affects which peptides are presented

Originally it was thought that the MHC haplotype of an individual largely controlled which sets of antigenic peptides would be presented to T cells. We now know that antigen processing is at least as important: The availability of peptides to load onto MHC class-I molecules in the ER is dependent on:

Each one of these factors also depend on the amino-acid sequence of the original protein (Fig. 8.9), and to some extent on genetic variations in molecules involved in antigen processing (Fig. 8.10). All of these considerations are important in developing vaccines, where the aim is to identify an immunodominant region of a pathogen to stimulate T cells; but it is not enough for a peptide to bind to MHC molecules, it must also be processed properly if it is to be immunogenic.

Some class I-like molecules can present limited sets of antigens

In addition to the standard MHC class I molecules (class Ia), a number of class I-like molecules (class Ib), encoded in the MHC or elsewhere on the genome, can present very limited sets of antigens.

MHC class II pathway

Class II molecules are loaded with exogenous peptides

MHC class II molecules are produced in the ER, complexed to a polypeptide called the invariant chain (Ii) (encoded outside the MHC), which stabilizes the complex and prevents the inappropriate binding of antigen. The αβ–Ii complex is transported from the Golgi to an antigen processing compartment which appears as a multivesicular body (also called the MIIC compartment), specialized for the transport and loading of MHC class II molecules. The compartment has characteristics of both endosomes and lysosomes with an onion-skin appearance under the electron microscope, comprising multiple membrane structures (Fig. 8.11). The αβ complex spends 1–3 hours in this compartment before reaching the cell surface (Fig. 8.12).

Exogenous antigens reach the MIIC compartment from acidic endosomes, where they have been partly degraded by the actions of proteases and chaperone proteins. The Ii chain is cleaved by cathepsins into small fragments, one of which, termed CLIP (class II-associated invariant peptide), is located in the groove of the class II molecule until replaced by peptides destined for presentation. The exchange of CLIP for other peptides is orchestrated by HLA-DM, an MHC class-II-like chaperone protein, consisting of α and β chains both encoded within the MHC class II region, but which does not itself have a peptide binding site (Fig. 8.13). HLA-DM binds to the αβ-CLIP complex to stabilize it until it has bound a suitable antigenic peptide. In cell lines lacking HLA-DM, the class II molecules are unstable and the cells no longer process and present proteins. Their class II molecules end up at the cell surface occupied by CLIP fragments of the invariant chain.

A further MHC-encoded molecule, HLA-DO (see Fig. 8.7), which associates with DM, regulates peptide loading. Like conventional MHC class II molecules, HLA-DO is a heterodimer, consisting of the DOA and DOB chains.

Peptide loading is also affected by the amount of antigenic peptide supplied to the MIIC compartment which varies depending on the cell-type. Macrophages are more efficient at degrading antigen than dendritic cells, and are therefore less efficient at antigen presentation.

T cell interaction with APCS

The interactions between a T cell and an antigen presenting cell develops over time, in three phases.

The initial encounter of T cells with APCs is by non-specific binding through adhesion molecules, particularly ICAM-1 (CD54) on the APC and the integrin LFA-1 (CD11/18), present on all immune cells. Transient binding permits the T cell to interact with many APCs; T cells in vivo are highly active and a single T cell may contact up to 5000 dendritic cells in one hour. Adhesion between the cells is enhanced by the interaction of CD2 (LFA-2) on the T cell with CD58 (LFA-3) on the APC (in rodents, CD48 performs a similar function to CD58). CD2 contributes towards the initial activation signal for the T cell, but more importantly, it allows the TCR time to recognize specific MHC/peptide on the APC. The initial phase of antigen presentation may last for several hours, but in the absence of a specific interaction, the APC and T cell dissociate.

When the T cell encounters the appropriate MHC/peptide, a conformational change in LFA-1 on the T cell, signaled via the TCR, results in tighter binding to ICAM-1 and prolonged cell–cell contact. (Fig. 8.14) The joined cells can exist as a pair for up to 12 hours, and this marks the second phase of interaction. At this stage an ‘immunological synapse’ forms and the T cell may be activated (Fig. 8.15).

In the third phase, the APC and T cell dissociate and the activated T cell undergoes several rounds of division and differentiation.

Costimulation by B7 binding to CD28 is essential for T cell activation

Productive T cell proliferation appears to depend on the formation of a stable central cluster of TCRs interacting with MHC molecules. The affinity of the binding of a single TCR molecule to its specific MHC/peptide is not high, and the formation of the immunological synapse requires the concerted interactions of a number of additional molecules, including CD4 which enhances binding of TH cells to MHC class-II molecules and CD8 to MHC class-I molecules. These molecules increase the sensitivity of a T cell for its target antigen by ~100fold. Although signaling efficiency for CD8+ T cells and thymocytes relates closely to the affinity of their TCR for the MHC/peptide, this is only partly true for the CD4+ T cells.

The specific MHC/peptide/TCR interaction, though necessary, is not sufficient to fully activate the T cell. A second signal, referred to as costimulation, is of crucial importance for T cell activation. The most potent costimulatory molecules are B7s, which are homodimeric members of the immunoglobulin superfamily molecules; they include B7–1 (CD80) and B7–2 (CD86). They are constitutively expressed on DCs, but can be upregulated on monocytes, B cells, and other APCs, particularly when stimulated by inflammatory cytokines and by interaction of microbial products with Toll-like receptors on the APC.

The B7 co-receptors bind to CD28 and its homolog CTLA-4 (CD152), which is expressed after T cell activation. CD28 is the main costimulatory ligand expressed on naive T cells. CD28 stimulation:

Many cells in the tissues can be induced to express MHC class-II molecules and present antigenic peptides to CD4+ T cells, however, they are mostly ineffective in inducing T cell activation and proliferation, because they lack the necessary costimulatory molecules (Fig. 8.16).

Ligation of CTLA-4 inhibits T cell activation

CTLA-4 (CD152) is an alternative ligand for B7, with higher affinity than CD28. It is an inhibitory receptor limiting T cell activation, resulting in less IL-2 production. CTLA-4 appears to act by reducing the time for interaction between the APC and the T cell, so a stronger activation signal is needed otherwise incomplete signaling will occur. As a T cell matures, it expresses higher levels of CTLA-4 and hence requires stronger activation stimuli to continue division (Fig. 8.17).

Intracellular signaling pathways activate transcription factors

An appropriate stimulatory signal initiates a cascade of intracellular signals, leading to the activation of transcription factors and expression of genes required for cell division. Two widely-used immunosuppressive drugs, cyclosporin and tacrolimus, interfere with the activation pathways.image

TCR-binding activates tyrosine kinases

Receptors on the surface of T cells signal to the interior of the cell using signal transduction pathways that are common to many other cell types, including B cells. A key principle is the clustering of receptors upon ligand binding which leads to activation of associated tyrosine kinases, that phosphorylate tyrosine residues in the cytoplasmic tails of the clustered receptors, followed by recruitment of additional kinases and signaling molecules, in cascades.

TCR α and β chains are associated with the CD3γ, δ, and ε molecules, the ζ and η chains and the enzyme Lck (p56lck), which is attached to the intracellular portions of CD4 or CD8 (Fig. 8.w1). (The label p56lck signifies a lymphocyte-specific tyrosine kinase of 56 kDa.) The first steps involve tyrosine kinases of the Src family, particularly Lck and Fyn, which phosphorylate target sequences found in the TCR ζ chain termed immunoreceptor tyrosine-based activation motifs (ITAMs).

image

Fig. 8.w1 Intracellular signaling in T cell activation

T cell activation involves the transduction of signals from both the TCR and CD28. Clustering of surface receptors such as TCR, CD4, CD28, and CD45 results in activation of tyrosine kinases Fyn and Lck. CD4, which is associated with the TCR complex, binds to the kinase, Lck. Such kinases become activated by dephosphorylation, possibly by phosphatase domains on CD45 (leukocyte common antigen). Lck can now phosphorylate the ITAM domains on the γ chains of CD3 (see Figs 5.3 and 5.15), which allows them to associate with other kinases including Fyn and ZAP-70. Fyn activates phospholipase C (PLCγ), which leads to two pathways by the cleavage of phosphatidylinositol bisphosphate (PIP2) into diacylglycerol (DAG) and inositol trisphosphate (IP3). IP3 releases Ca2+ from intracellular (ER) stores to activate calcium-dependent enzymes such as calcineurin. Calcineurin removes phosphate from the transcription factor NF-AT (nuclear factor of activation of T cells), which causes its translocation to the nucleus. DAG activates protein kinase C (PKC), which then activates the transcription factor NF-κB. Meanwhile, ZAP-70, Fyn, and PI-3 kinase (PI-3 K) (associated with CD28) integrate signals via kinase cascades in the cytoplasm that activate specific transcription factors. Adapter proteins are used to link the various receptors to the common intracellular signaling components. GTP-binding proteins (G proteins) are involved in activating a set of protein kinases in the MAP kinase cascade. The transcription factors translocate to the nucleus to activate genes, including ‘immediate early genes’ Fos and Jun for cell division and the promoter AP-1, which acts with NF-AT on the IL-2 gene.

Phosphorylation of the ITAMs initiates a series of steps (see Fig. 8.w1), that lead to the activation of transcription factors including NFAT, and NFκB, and their translocation to the nucleus. The IL-2 enhancer contains a binding site for a nuclear factor, NF-AT (nuclear factor of activation of T cells), which also interacts with Fos and Jun, to induce IL-2 gene expression of the IL-2 receptor (IL-2R) gene.

In summary, TCR stimulation results in activation of a variety of tyrosine kinases and downstream effectors that regulate cellular responses, resulting in the regulation of IL-2 gene expression, which is largely responsible for activating the T cell and inducing division. An understanding of the requirements for T cell division has allowed researchers to generate long-lived T cell lines, which are used in many areas of immunological research (Method box 8.1).

Interleukin-2 drives T cell division

T cell activation leads to the production of IL-2 and IL-2 receptors, so a T cell can act on itself and surrounding cells. In most CD4+ cells and some CD8+ T cells, there is a transient production of IL-2 for 1–2 days. During this time the interaction of IL-2 with the high-affinity IL-2R results in T cell division.

On resting T cells, the IL-2R is predominantly present as a low-affinity form consisting of two polypeptide chains, a β chain (p75) that binds IL-2 and a common γc chain that signals to the cell. When the T cell is activated, it produces an α chain (CD25), which contributes to IL-2 binding and, together with the β and γc chains, forms the high-affinity receptor (Fig. 8.18). IL-2 is internalized within 10–20 minutes and the β and γc chains are degraded in lysosomes while the α chain is recycled to the cell surface. Sustained signaling by IL-2 over several hours is needed to drive T-cell division.

The transient expression of the high-affinity IL-2R for about 1 week after stimulation of the T cell, together with the induction of CTLA-4, helps limit T cell division. In the absence of positive signals, the T cells will start to die by apoptosis.

In view of the importance of IL-2 in T cell division, it was surprising that the rare patients who lack CD25 (and IL-2 receptor knockout mice) develop an immunoproliferative condition. These observations lead to an awareness that IL-2 also has a regulatory function in T cell development – regulatory T cells (Tregs) are characterized by high CD25 expression, and IL-2 is required for their generation in the thymus and maintenance in the periphery (see Chapter 11).

Types of immune response

APCs may be activated rapidly in an immune response, for example by the immunogenic entity itself, in the case of bacteria and some viruses. Antigen presentation is not a unidirectional process. T cells, as they become activated:

When APCs are activated, they express more MHC class I and II molecules, Fc receptors, and costimulatory adhesion molecules, including B7–1 and B7–2, CD11a/b/c, ICAM-1, and ICAM-3. They also produce numerous cytokines (e.g. IL-1, IL-6, TNFα), enzymes, and other mediators.

Activation of lymphocytes leads to two partially competing processes:

The fate of lymphocytes responding to antigen is varied; some can persist for a long time as memory cells – the life span of memory cells can be more than 40 years in humans. Other lymphocytes have a short life span, which explains why moderate antigenic stimulation does not lead to lymphoid enlargement – this is nevertheless sufficient for generating effective cell-mediated and antibody responses. Apoptosis is critically important for disposing of unwanted cells after an immune response.

Danger signals enhance antigen presentation

For appropriate immune responses to be generated, APCs must respond to infection, but not to high levels of harmless substances that may fluctuate in the environment. Mucosal tissue in the gut are in contact with high concentrations of harmless food antigens, while respiratory mucosa contacts many airborne antigens such as pollen, but strong immune responses against these antigens are undesirable.

APC activation is generally a response to infection, or at least the presence of substances, such as constituents of bacterial cell walls, characteristic of infection. This requirement explains the action of adjuvants derived from bacterial components, which are used to enhance immune responses in vaccines.

The concept of immune activation only in response to infection (or adjuvant as a surrogate for infection), and not to other antigens, has been promoted as the ‘danger’ hypothesis. This idea proposes that the immune system does not merely distinguish self from non-self, but responds to clues that an infection has taken place before responding strongly to antigens.

In other words, foreign substances may be innocuous or invisible to the immune system unless accompanied by danger signals, such as infection. These danger signals are provided by receptors for microbial products on APCs, such as the Toll-like receptors (TLRs, see Fig. 6.21).

Further reading

Ackerman A.L., Cresswell P. Cellular mechanisms governing cross-presentation of exogenous antigens. Nat Immunol. 2004;5:678–684.

Bell D., Young J.W., Banchereau J. Dendritic cells. Annu Rev Immunol. 1999;17:255–305.

Berger A.C., Roche P.A. MHC class II transport at a glance. J Cell Sci. 2009;122:1–4.

Boes M., Ploegh H.L. Translating cell biology in vitro to immunity in vivo. Nature. 2004;430:264–271.

Brocke P., Garbi N., Momburg F., Hammerling G.J. HLA-DM, HLA-DO and tapasin: functional similarities and differences. Curr Opin Immunol. 2002;14:22–29.

Cresswell P, Ackerman AL, Giodin A, et al. Mechanisms of MHC class-I restricted antigen processing and cross presentation. Imm Revs 205;207:145–157

Fooksman D.R., Vardhana S., Vasiliver-Shamis G., et al. Functional anatomy of T cell activation and synapse formation. Ann Revs Immunol. 2010;28:79–106.

Kloetzel P.M. Generation of MHC class I antigens: functional interplay between proteasomes and TPPII. Nat Immunol. 2004;5:661–669.

Okazaki T., Honjo T. PD-1 and PD-1 ligands: from discovery to clinical application. Int Immunol. 2007;19:813–824.

Randolph G., Orchando J., Partida-Sanchez S. Migration of dendritic cell subsets and their precursors. Ann Revs Immunol. 2008;26:293–316.

Tenzer S., Wee E., Burgevin A., et al. Antigen processing influences HIV-specific cytotoxic lymphocyte immunodominance. Nat Immunol. 2009;10:636–646.

Watts C., Powis S. Pathways of antigen processing and presentation. Rev Immunogenet. 1999;1:60–74.