Immunology_Janeway

Immunology_Janeway. membrane-associated Ii, leaving the CLIP fragment bound to the MHC molecule. This cleavage is carried out by cathepsin S in most MHC class II-positive cells but by cathepsin L in thymic epithelial cells. Being associated with CLIP, the MHC class II molecules cannot yet bind other peptides. However, since CLIP does not carry the Ii-encoded signals that retain the complex in the endocytic compartment, the MHC–CLIP complex is now free to escape to the cell surface.


Immunology_Janeway

Immunology_Janeway. To allow another peptide to bind to the MHC class II molecule, CLIP must either dissociate or be displaced. Newly synthesized MHC class II molecules are brought toward the cell surface in vesicles, most of which at some point fuse with incoming endosomes. However, some MHC class II:Ii complexes may first be transported to the cell surface and reinternalized into endosomes. In either case, MHC class II:Ii complexes enter the endosomal pathway, where they encounter and bind peptides derived from either internalized pathogen proteins or self proteins. Initially, specialized endosomal compartments were thought to exist for antigen-presenting cells. One was an early endosomal compartment in dendritic cells that was called the CIIV (MHC class II vesicle). Another, a late endosomal compartment containing Ii and MHC class II molecules, was the MHC class II compartment, or MIIC (Fig. 6.12). The current view is that MHC class II molecules use many common endocytic compartments, including


Immunology_Janeway

Immunology_Janeway. containing Ii and MHC class II molecules, was the MHC class II compartment, or MIIC (Fig. 6.12). The current view is that MHC class II molecules use many common endocytic compartments, including lysosomes, to allow for the exchange of CLIP for as many peptides as possible. MHC class II molecules that do not bind peptide after dissociation from CLIP are unstable in the acidic pH after fusion with lysosomes, and they are rapidly degraded.


Immunology_Janeway

Immunology_Janeway. 6-8 The MHC class II-like molecules HLA-DM and HLA-DO regulate exchange of CLIP for other peptides.


Immunology_Janeway

Immunology_Janeway. Because an MHC class II:CLIP complex cannot be released to the cell surface unless another peptide replaces it, antigen-presenting cells possess a mechanism that facilitates the efficient exchange of CLIP for other peptides. This process was uncovered by analysis of mutant human B-cell lines with a defect in antigen presentation. MHC class II molecules in these mutant cells assemble correctly with Ii and seem to follow the normal vesicular route, but fail to bind peptides derived from internalized proteins and often arrive at the cell surface with the CLIP peptide still bound. The defect in these cells lies in an MHC class II-like molecule called HLA-DM in humans (H-2DM in mice). The HLA-DM genes (see Section 6-10) are found near the TAP and PSMB8/9 genes in the MHC class II region (see Fig. 6.16); they encode an α chain and a β chain that closely resemble those of other MHC class II molecules. The HLA-DM molecule is not present at the cell surface, however, but is found predominantly


Immunology_Janeway

Immunology_Janeway. 6.16); they encode an α chain and a β chain that closely resemble those of other MHC class II molecules. The HLA-DM molecule is not present at the cell surface, however, but is found predominantly in the endosomal compartment that contains Ii and MHC class II molecules. HLA-DM binds to and stabilizes empty MHC class II molecules and catalyzes the release of CLIP, thus allowing the binding of other peptides to the empty MHC class II molecule (Fig. 6.13). The HLA-DM molecule does not contain the open groove found in other MHC class II molecules, and it does not bind peptides. Instead, HLA-DM binds to the α chain of the MHC class II molecule near the region of the floor of the peptide-binding site (Fig. 6.14). This binding induces changes in the structure of the MHC class II molecule, and holds this part of the peptide binding groove in a partially ‘open’ configuration (see Fig. 6.14, right panel). In this way, HLA-DM catalyzes the release of CLIP and of other unstably bound peptides


Immunology_Janeway

Immunology_Janeway. holds this part of the peptide binding groove in a partially ‘open’ configuration (see Fig. 6.14, right panel). In this way, HLA-DM catalyzes the release of CLIP and of other unstably bound peptides from MHC class II molecules.


Immunology_Janeway

Immunology_Janeway. In the presence of a mixture of peptides capable of binding to MHC class II molecules, HLA-DM continuously binds and rebinds to newly formed peptide:MHC class II complexes, allowing for the dissociation of weakly bound peptides and for other peptides to replace them. Antigens presented by MHC class II molecules may have to persist on the surface of antigen-presenting cells for some days before encountering T cells able to recognize them. The ability of HLA-DM to remove unstably bound peptides, sometimes called peptide editing (see Section 6-4), ensures that the peptide:MHC class II complexes displayed on the surface of the antigen-presenting cell survive long enough to stimulate the appropriate CD4 T cells. During this process, it is likely that some peptides are captured first as longer polypeptides that undergo amino-terminal trimming by exopeptidases, further increasing the number of possible peptides that can be bound.


Immunology_Janeway

Immunology_Janeway. A second atypical MHC class II molecule, called HLA-DO in humans (H-2O in mice), is produced in thymic epithelial cells, B cells, and dendritic cells. MOVIE 6.2 Invariant chain (Ii) forms a complex with MHC class II molecule, blocking the binding of peptides and misfolded proteins Ii is cleaved in an acidifed endosome, leaving a short peptide fragment, CLIP, still bound to the MHC class II molecule Endocytosed antigens are degraded to peptides in endosomes, but the CLIP peptide blocks the binding of peptides to MHC class II molecules HLA-DM binds to the MHC class II molecule, releasing CLIP and allowing other peptides to bind. The MHC class II molecule then travels to the cell surface HLA-DM endoplasmic reticulum cytosol Ii LIP10 CLIP


Immunology_Janeway

Immunology_Janeway. Fig. 6.13 HLA-DM facilitates the loading of antigenic peptides leaving CLIP bound to the MHC class II molecules. Third panel: onto MHC class II molecules. First panel: the invariant chain pathogens and their proteins are broken down into peptides within (Ii) binds to newly synthesized MHC class II molecules and blocks acidified endosomes, but these peptides cannot bind to MHC peptides from binding class II molecules in the endoplasmic class II molecules that are occupied by CLIP. Fourth panel: the class reticulum and during their transport to acidified endosomes. Second II-like molecule HLA-DM binds to MHC class II:CLIP complexes, panel: in late endosomes, proteases cleave the invariant chain, catalyzing the release of CLIP and the binding of antigenic peptides.


Immunology_Janeway

Immunology_Janeway. Fig. 6.14 HLA-DM and HLA-DO regulate loading of peptides into MHC class II molecules. First panel: the HLA-DM dimer, composed of α (green) and β (turquoise) chains, binds to the HLA-DR MHC class II molecule (side view). HLA-DM contacts the MHC molecule near the peptide-binding groove where the peptide amino terminus would reside. Second panel: HLA-DO binds to HLA-DM in a similar configuration as HLA-DR, thus blocking DM’s peptide-editing activity. Third panel: top view of HLA-DR with bound peptide in the absence of HLA-DM. Fourth panel: top view of HLA-DR with HLA-DM bound. The amino-terminal end of the MHC peptide-binding groove is open and devoid of bound peptide, enabling peptide exchange.


Immunology_Janeway

Immunology_Janeway. This molecule is a heterodimer of the HLA-DOα chain and the HLA-DOβ chain. HLA-DO is not present at the cell surface, being found only in intracellular vesicles, and it does not seem to bind peptides. HLA-DO acts as a negative regulator of HLA-DM. HLA-DO binds to HLA-DM in the same manner as MHC class II molecules (see Fig. 6.14), and it must be bound to HLA-DM in order to leave the endoplasmic reticulum. When the DM–DO dimer reaches an acidified endocytic compartment, HLA-DO appears to dissociate slowly from HLA-DM, which is then free to catalyze peptide editing for MHC class II molecules. Moreover, IFN-γ increases the expression of HLA-DM, but not of the HLA-DOβ chain. Thus, during inflammatory responses, IFN-γ produced by T cells and NK cells can increase the expression of HLA-DM, and so overcome the inhibitory effects of HLA-DO. Why HLA-DO is expressed in this way remains obscure. The loss of HLA-DO in mice does not dramatically alter adaptive immunity, but does cause a


Immunology_Janeway

Immunology_Janeway. and so overcome the inhibitory effects of HLA-DO. Why HLA-DO is expressed in this way remains obscure. The loss of HLA-DO in mice does not dramatically alter adaptive immunity, but does cause a spontaneous production of autoantibodies with age. As thymic epithelial cells function in the selection of developing CD4 T cells, perhaps HLA-DO influences the repertoire of self peptides that these T cells encounter at different stages, as discussed further in Chapter 8.


Immunology_Janeway

Immunology_Janeway. The role of HLA-DM in peptide editing for MHC class II molecules parallels the role of tapasin in facilitating peptide binding to MHC class I molecules. HLA-DM carries out this function by mediating peptide exchange and driving the association of high-affinity peptides. Thus, it seems likely that specialized mechanisms of delivering peptides have coevolved with the MHC molecules themselves. It is also likely that pathogens have evolved strategies to inhibit the loading of peptides onto MHC class II molecules, much as viruses have found ways of subverting antigen processing and presentation through the MHC class I molecules. We will return to these topics in Chapter 13 when we discuss pathogen immunoevasion mechanisms.


Immunology_Janeway

Immunology_Janeway. The peptide editing conferred by DM and removing unstable MHC molecules provide important safeguards. To reveal the presence of an intracellular pathogen, the peptide:MHC complex must be stable at the cell surface. If peptides were to dissociate too readily, an infected cell could escape detection, and if peptides could too easily be acquired from other cells, then healthy cells might be mistakenly targeted for destruction. Tight binding of peptides to MHC molecules reduces the chance of these unwanted outcomes. MHC class I molecules display peptides derived largely from cytosolic proteins, so it is important that dissociation of a peptide from a cell-surface MHC molecule does not allow extracellular peptides to bind in the empty peptide-binding site. Fortunately, when an MHC class I molecule at the surface of a living cell loses its peptide, its conformation changes, the β2-microglobulin dissociates, and the α chain is internalized and rapidly degraded. Thus, most empty MHC class I


Immunology_Janeway

Immunology_Janeway. at the surface of a living cell loses its peptide, its conformation changes, the β2-microglobulin dissociates, and the α chain is internalized and rapidly degraded. Thus, most empty MHC class I molecules are quickly lost from the cell surface, largely preventing them from acquiring peptides directly from the surrounding extracellular fluid. This helps ensure that primed T cells target infected cells while sparing surrounding healthy cells.


Immunology_Janeway

Immunology_Janeway. Empty MHC class II molecules are also removed from the cell surface. Although at neutral pH, empty MHC class II molecules are more stable than empty MHC class I molecules, they aggregate readily, and internalization of such aggregates may account for their removal. Moreover, peptide loss from MHC class II molecules is most likely when the molecules are transiting through acidified endosomes as part of the normal process of cell-membrane recycling. At acidic pH, MHC class II molecules are able to bind peptides that are present in the vesicles, but those that fail to do so are rapidly degraded.


Immunology_Janeway

Immunology_Janeway. Some binding of extracellular peptides to MHC molecules at the cell surface can occur, however, as the addition of peptides to living or even chemically fixed cells in vitro can generate peptide:MHC complexes that are recognized by T cells specific for those peptides. This has been readily demonstrated for many peptides that bind MHC class II and class I molecules. Whether this phenomenon is due to the presence of empty MHC proteins on the cells or to peptide exchange is not clear. Nevertheless it can happen and is a widely used technique to load synthetic peptides for analyzing the specificity of T cells. 6-9 Cessation of antigen processing occurs in dendritic cells after their activation through reduced expression of the MARCH-1 E3 ligase.


Immunology_Janeway

Immunology_Janeway. Dendritic cells that have not yet been activated by infection carry out active surveillance of the antigens in their location, for example, through macropinocytosis of soluble proteins. Peptides derived from proteins are continuously processed and loaded onto MHC class II molecules for expression on the cell surface. In addition, peptide:MHC complexes are also continuously being recycled from the surface and degraded in cells by ubiquitination and proteasomal degradation. MHC class II molecules contain a conserved lysine residue in the cytoplasmic tails of the β chain; this lysine residue is a target of an E3 ligase (see Section 3-7) called membrane associated ring finger (C3HC4) 1, or MARCH-1, expressed in B cells, dendritic cells, and macrophages. MARCH-1 is expressed constitutively in B cells and induced by the cytokine IL-10 in other cells. It resides in the membrane of a recycling endosomal compartment, where it ubiquitinates the cytoplasmic tail of MHC class II molecules,


Immunology_Janeway

Immunology_Janeway. in B cells and induced by the cytokine IL-10 in other cells. It resides in the membrane of a recycling endosomal compartment, where it ubiquitinates the cytoplasmic tail of MHC class II molecules, leading to their eventual degradation in lysosomes, thereby regulating their steady-state level of expression (Fig. 6.15).


Immunology_Janeway

Immunology_Janeway. The MARCH-1 pathway is shut down during infection to increase the stability of peptide:MHC complexes. Dendritic cells that capture antigens at sites of infection must first migrate to local lymph nodes in order to activate naive T cells; this may take many hours. Since continuous recycling limits the lifetime of peptide:MHC complexes on the cell surface, pathogen-derived peptide:MHC complexes could be lost during this migration, preventing T-cell activation. To prevent this situation, when dendritic cells are activated by pathogens, expression of MARCH-1 is shut off. This may be mediated directly by innate pathogen sensors, since TLR signaling in dendritic cells rapidly reduces the level of mRNA for MARCH-1. The MARCH-1 protein half-life is only around 30 minutes, so that activated dendritic cells soon accumulate peptide:MHC complexes on their cell surface produced at the time of encounter with pathogen.


Immunology_Janeway

Immunology_Janeway. In addition to regulating MHC class II expression in dendritic cells, MARCH-1 similarly regulates expression in dendritic cells of the co-stimulatory molecule (see Section 1-15) CD86 (or B7-2), which like MHC class II molecules, is also MHC molecules accumulate on the cell surface, presenting peptides they acquired at the time of dendritic cell activation


Immunology_Janeway

Immunology_Janeway. Fig. 6.15 Activation of dendritic cells reduces MARCH-1 expression, thus increasing the lifetime of MHC molecules. Before activation by innate recognition of pathogens, dendritic cells express the membrane-associated E3 ligase MARCH-1, which resides in the recycling endosomes compartment, where it attaches K-48-linked ubiquitin chains to the β chain of MHC class II molecules. This causes MHC molecules to move from the recycling endosomes and eventually to be degraded, leading to a reduced overall half-life and level of MHC expression on the cell surface. Signals emanating from innate sensors, such as TLR-4, reduce the level of MARCH-1 mRNA, and with the half-life of MARCH-1 now being short, MHC molecules are free to accumulate on the cell surface. Because innate signaling also triggers acidification of endocytic compartments and activates caspases associated with antigen processing, the MHC molecules that accumulate on the cell surface will bear peptides from the pathogens captured


Immunology_Janeway

Immunology_Janeway. acidification of endocytic compartments and activates caspases associated with antigen processing, the MHC molecules that accumulate on the cell surface will bear peptides from the pathogens captured around the time of innate activation of the dendritic cells.


Immunology_Janeway

Immunology_Janeway. regulated by ubiquitination. This means that by the time dendritic cells arrive at lymph nodes, they express peptides derived from the pathogens that activated them and have higher CD86 levels that provide signals for greater CD4 T-cell activation. However, we will see in Chapter 13 that viral pathogens have taken advantage of this pathway by producing MARCH-1-like proteins to downregulate MHC class II molecules as a means of evading adaptive immunity. Summary.


Immunology_Janeway

Immunology_Janeway. The ligand recognized by the T-cell receptor is a peptide bound to an MHC molecule. MHC class I and MHC class II molecules acquire peptides at different intracellular sites and activate either CD8 or CD4 T cells, respectively. Infected cells presenting peptides derived from virus replication in the cytosol are thus recognized by CD8 cytotoxic T cells, which are specialized to kill any cells displaying foreign antigens. MHC class I molecules are synthesized in the endoplasmic reticulum and typically acquire their peptides at this location. The peptides loaded onto MHC class I molecules are derived from proteins degraded in the cytosol by the proteasome, transported into the endoplasmic reticulum by the heterodimeric ATP-binding protein TAP, and further processed by the aminopeptidase ERAAP before being loaded onto the MHC molecules. Peptide binding to MHC class I molecules is required for them to be released from chaperones in the endoplasmic reticulum and to travel to the cell


Immunology_Janeway

Immunology_Janeway. ERAAP before being loaded onto the MHC molecules. Peptide binding to MHC class I molecules is required for them to be released from chaperones in the endoplasmic reticulum and to travel to the cell surface. Certain subsets of dendritic cells are able to produce peptides from exogenous proteins and load them onto MHC class I molecules. Such cross-presentation of antigens ensures that CD8 T cells can be activated by pathogens that may not directly infect antigen-presenting cells.


Immunology_Janeway

Immunology_Janeway. MHC class II molecules do not acquire their peptide ligands in the endoplasmic reticulum, because the invariant chain (Ii) first inserts CLIP into their peptide-binding groove. Association with Ii targets these MHC molecules to an acidic endosomal compartment where active proteases cleave Ii, and HLA-DM helps to catalyze dissociation of CLIP. The MHC molecules can then associate with peptides derived from proteins that have entered the vesicular compartments of macrophages, dendritic cells, or B cells. The process of autophagy can deliver cytosolic proteins to the vesicular system for presentation by MHC class II molecules. The CD4 T cells that recognize peptide:MHC class II complexes have a variety of specialized effector activities. Subsets of CD4 T cells activate macrophages to kill the intravesicular pathogens they harbor, help B cells to secrete immunoglobulins against foreign molecules, and regulate immune responses. The major histocompatibility complex and its function.


Immunology_Janeway

Immunology_Janeway. The major histocompatibility complex and its function. The function of MHC molecules is to bind peptide fragments derived from pathogens and display them on the cell surface for recognition by the appropriate T cells. The consequences are almost always deleterious to the pathogen—virus-infected cells are killed, macrophages are activated to kill bacteria living in their intracellular vesicles, and B cells are activated to produce antibodies that eliminate or neutralize extracellular pathogens. Thus, there is strong selective pressure in favor of any pathogen that has mutated in such a way that it escapes presentation by an MHC molecule.


Immunology_Janeway

Immunology_Janeway. Two separate properties of the major histocompatibility complex (MHC) make it difficult for pathogens to evade immune responses in this way. First, the MHC is polygenic: it contains several different MHC class I and MHC class II genes, so that every individual possesses a set of MHC molecules with different ranges of peptide-binding specificities. Second, the MHC is highly polymorphic; that is, there are multiple variants, or alleles, of each gene within the population as a whole. The MHC genes are, in fact, the most polymorphic genes known. In this section we describe the organization of the genes in the MHC and discuss how the variation in MHC molecules arises. We also consider how the effect of polygeny and polymorphism on the range of peptides that can be bound contributes to the ability of the immune system to respond to the multitude of different and rapidly evolving pathogens.


Immunology_Janeway

Immunology_Janeway. 6-10 Many proteins involved in antigen processing and presentation are encoded by genes within the MHC.


Immunology_Janeway

Immunology_Janeway. The MHC is located on chromosome 6 in humans and chromosome 17 in the mouse and extends over at least 4 million base pairs. In humans it contains more than 200 genes. As work continues to define the genes within and around the MHC, it becomes difficult to establish precise boundaries for this genetic region, which is now thought to span as many as 7 million base pairs. The genes encoding the α chains of MHC class I molecules and the αand βchains of MHC class II molecules are linked within the complex; the genes for β2-microglobulin and the invariant chain are on different chromosomes (chromosomes 15 and 5, respectively, in humans, and chromosomes 2 and 18 in the mouse). Figure 6.16 shows the general organization of the MHC class I and II genes in human and mouse. In humans these genes are called human leukocyte antigen or HLA genes, because they were first discovered through antigenic differences between white blood cells from different individuals; in the mouse they are known as the


Immunology_Janeway

Immunology_Janeway. called human leukocyte antigen or HLA genes, because they were first discovered through antigenic differences between white blood cells from different individuals; in the mouse they are known as the H-2 genes. The mouse MHC class II genes were in fact first identified as genes that controlled whether an immune response was made to a given antigen and were originally called Ir (immune response) genes. Because of this, the mouse MHC class II A and E genes were in the past referred to as I-A and I-E, but this terminology could be confused with MHC class I genes and it is no longer used.


Immunology_Janeway

Immunology_Janeway. Fig. 6.16 The genetic organization of the major histocompatibility complex (MHC) in humans and mice. The organization of the MHC genes is shown. In humans, the cluster is called HLA (short for human leukocyte antigen) and is on chromosome 6, and in mice, it is called H-2 (for histocompatibility) and is on chromosome 17. The organization is similar in both species, with separate clusters of MHC class I genes (red) and MHC class II genes (yellow). In mice, the MHC class I gene H-2K has been translocated relative to the human MHC, splitting the class I region in two. Both species have three main class I genes, which are called HLA-A, HLA-B, and HLA-C in humans, and H2-K, H2-D, and H2-L in the mouse. These encode the α chain of the respective MHC class I proteins, HLA-A, HLA-B, and so on. The other subunit of an MHC class I molecule, β2-microglobulin, is encoded by a gene located on a different chromosome—chromosome 15 in humans and chromosome 2 in the mouse. The class II region includes


Immunology_Janeway

Immunology_Janeway. other subunit of an MHC class I molecule, β2-microglobulin, is encoded by a gene located on a different chromosome—chromosome 15 in humans and chromosome 2 in the mouse. The class II region includes the genes for the α and β chains (designated A and B) of the MHC class II molecules HLA-DR, -DP, and -DQ (H-2A and -E in the mouse). Also in the MHC class II region are the genes for the TAP1:TAP2 peptide transporter, the PSMB (or LMP) genes that encode proteasome subunits, the genes encoding the DMα and DMβ chains (DMA and DMB), the genes encoding the α and β chains of the DO molecule (DOA and DOB, respectively), and the gene encoding tapasin (TAPBP). The so-called class III genes encode various other proteins with functions in immunity (see Fig. 6.17).


Immunology_Janeway

Immunology_Janeway. There are three class I α-chain genes in humans, called HLA-A, -B, and -C. There are also three pairs of MHC class II α-and β-chain genes, called HLA-DR, -DP, and -DQ. In many people, however, the HLA-DR cluster contains an extra β-chain gene whose product can pair with the DRα chain. This means that the three sets of genes can give rise to four types of MHC class II molecules. All the MHC class I and class II molecules can present peptides to T cells, but each protein binds a different range of peptides (see Sections 4-14 and 4-15). Thus, the presence of several different genes for each MHC class means that any one individual is equipped to present a much broader range of peptides than if only one MHC molecule of each class were expressed at the cell surface.


Immunology_Janeway

Immunology_Janeway. Figure 6.17 shows a more detailed map of the human MHC region. Many genes within this locus participate in antigen processing or antigen presentation, or have other functions related to the innate or adaptive immune response. The two TAP genes lie in the MHC class II region near the PSMB8 and PSMB9 genes, whereas the gene encoding tapasin (TAPBP) lies at the edge of the MHC nearest the centromere. The genetic linkage of the MHC class I genes (whose products deliver cytosolic peptides to the cell surface) with the TAP, tapasin, and proteasome (PSMB or LMP) genes (whose products deliver cytosolic peptides into the endoplasmic reticulum) suggests that the entire MHC has been selected during evolution for antigen processing and presentation.


Immunology_Janeway

Immunology_Janeway. When cells are treated with the interferons IFN-α, -β, or -γ, there is a marked increase in the transcription of MHC class I α-chain and β2-microglobulin genes and of the proteasome, tapasin, and TAP genes. Interferons are produced early in viral infections as part of the innate immune response, as described in Chapter 3. The increase in MHC expression they produce helps all cells to process viral proteins and present the resulting virus-derived peptides on their surface (except for red blood cells). On dendritic cells, this helps to activate the appropriate T cells and initiate the adaptive immune response to the virus. The coordinated regulation of the genes encoding these components may be facilitated by the linkage of many of them in the MHC.


Immunology_Janeway

Immunology_Janeway. The DMA and DMB genes encoding the subunits of the HLA-DM molecule that catalyzes peptide binding to MHC class II molecules are clearly related to the MHC class II genes, as are the DOA and DOB genes that encode the subunits of the regulatory HLA-DO molecule. Gene expression of the classical MHC class II proteins, along with the invariant-chain, DMα, DMβ, and DOα, but not DOβ, is coordinately increased by IFN-γ, which is produced by activated TH1 cells, CD8 T cells, and NK cells. This form of regulation allows dendritic cells and macrophages to upregulate molecules involved in processing of intravesicular antigens when presenting antigens to T cells and NK cells. Expression of all these molecules is induced by IFN-γ (but not by IFN-αor -β), via the production of a protein known as MHC class II transactivator (CIITA), which acts as a positive transcriptional co-activator of MHC class II genes. An absence of CIITA causes severe immunodeficiency due to the nonproduction of MHC class II


Immunology_Janeway

Immunology_Janeway. II transactivator (CIITA), which acts as a positive transcriptional co-activator of MHC class II genes. An absence of CIITA causes severe immunodeficiency due to the nonproduction of MHC class II molecules—MHC class II deficiency. Finally, the MHC contains many ‘non-classical’ MHC genes, so-called because while they resemble MHC genes in structure, their products do not function in presenting peptides to conventional α:β T cells. Many of these genes are now referred to as MHC class Ib genes, and their protein products have a variety of different functions, which we will describe in Section 6-16 , following our discussion of the conventional MHC genes.


Immunology_Janeway

Immunology_Janeway. Fig. 6.17 Detailed map of the human MHC. The organization of the class I, class II, and class III regions of the human MHC is shown, with approximate genetic distances given in thousands of base pairs. Most of the genes in the class I and class II regions are mentioned in the text. The additional genes indicated in the class I region (for example, E, F, and G) are class I-like genes encoding class Ib molecules; the additional class II genes are pseudogenes. The genes shown in the class III region encode the complement proteins C4 (two genes, shown as C4A and C4B), C2, and factor B (shown as Bf), as well as genes that encode the cytokines tumor necrosis factor-α (TNF) and lymphotoxin (LTA, LTB). Closely linked to the C4 genes is the gene encoding 21-hydroxylase (shown as CYP 21B), an enzyme involved in steroid biosynthesis. Immunologically important functional protein-coding genes mentioned in the text are color coded, with the MHC class I genes being shown in red, except for the MIC


Immunology_Janeway

Immunology_Janeway. involved in steroid biosynthesis. Immunologically important functional protein-coding genes mentioned in the text are color coded, with the MHC class I genes being shown in red, except for the MIC genes, which are shown in blue; these are distinct from the other class I-like genes and are under different transcriptional control. The immunologically important MHC class II genes are shown in yellow. Genes in the MHC region that have immune functions but are not related to the MHC class I and class II genes are shown in purple. Genes in dark gray are pseudogenes related to immune-function genes. Unnamed genes unrelated to immune function are shown in light gray.


Immunology_Janeway

Immunology_Janeway. Fig. 6.18 Human MHC genes are highly polymorphic. With the notable exception of the DRα locus, which is functionally monomorphic, each gene locus has many alleles. The number of functional proteins encoded is less than the total number of alleles. Shown in this figure as the heights of the bars are the number of different HLA proteins assigned by the WHO Nomenclature Committee for Factors of the HLA System as of January 2010. 6-11 The protein products of MHC class I and class II genes are highly polymorphic. Because of the polygeny of the MHC, every person expresses at least three different MHC class I molecules and three (or sometimes four) MHC class II molecules on his or her cells. In fact, the number of different MHC molecules expressed by most people is greater because of the extreme polymorphism of the MHC (Fig. 6.18).


Immunology_Janeway

Immunology_Janeway. The term polymorphism comes from the Greek poly, meaning many, and morphe, meaning shape or structure. As used here, it means within-species variation at a gene locus, and thus in the gene’s protein product; the variant genes that can occupy the locus are termed alleles. For several MHC class I and class II genes, there are more than 1000 alleles in the human population, far more than the number of alleles for other genes found within the MHC region. Each MHC class I and class II allele is relatively frequent in the population, so there is only a small chance that the corresponding gene loci on both homologous chromosomes of an individual will have the same allele; most individuals will be heterozygous for the genes encoding MHC class I and class II molecules. The particular combination of MHC alleles found on a single chromosome is known as an MHC haplotype. Expression of MHC alleles is codominant, meaning that the protein products of both of the alleles at a locus are expressed


Immunology_Janeway

Immunology_Janeway. of MHC alleles found on a single chromosome is known as an MHC haplotype. Expression of MHC alleles is codominant, meaning that the protein products of both of the alleles at a locus are expressed equally in the cell, and both gene products can present antigens to T cells. The number of MHC alleles discovered that do not code for a functional protein is remarkably small. The extensive polymorphism at each locus thus has the potential to double the number of different MHC molecules expressed in an individual and thereby increase the diversity already available through polygeny (Fig. 6.19).


Immunology_Janeway

Immunology_Janeway. Because most individuals are heterozygous, most matings will produce offspring that receive one of four possible combinations of the parental MHC haplotypes. Thus siblings are also likely to differ in the MHC alleles they express, there being one chance in four that an individual will share both haplotypes with a sibling. One consequence of this is the difficulty of finding suitable donors for tissue transplantation, even among siblings. All MHC class I and II proteins are polymorphic to a greater or lesser extent, with the exception of the DRα chain and its mouse homolog Eα. These chains do not vary in sequence between different individuals and are said to be monomorphic. This might indicate a functional constraint that prevents variation in the DRαand Eα proteins, but no such special function has been found. Fig. 6.19 Polymorphism and polygeny both contribute to the diversity of MHC molecules expressed by an individual.


Immunology_Janeway

Immunology_Janeway. Fig. 6.19 Polymorphism and polygeny both contribute to the diversity of MHC molecules expressed by an individual. Many mice, both domestic and wild, have a mutation in the Eα gene that prevents synthesis of the Eα protein. They thus lack cell-surface H-2E molecules, so if H2-E does have a special function it is unlikely to be essential.


Immunology_Janeway

Immunology_Janeway. MHC polymorphisms at individual MHC genes seem to have been strongly selected by evolutionary pressures. Several genetic mechanisms contribute to the generation of new alleles. Some new alleles arise by point mutations and others by gene conversion, a process in which a sequence in one gene is replaced, in part, by sequences from a different gene (Fig. 6.20). The effects of selective pressure in favor of polymorphism can be seen clearly in the pattern of point mutations in the MHC genes. Point mutations can be classified as replacement substitutions, which change an amino acid, or silent substitutions, which simply change the codon but leave the amino acid the same. Replacement substitutions occur within the MHC at a higher frequency relative to silent substitutions than would be expected, providing evidence that polymorphism has been actively selected for in the evolution of the MHC. influencing both peptide binding and the contacts between T-cell receptor and MHC molecule.


Immunology_Janeway

Immunology_Janeway. influencing both peptide binding and the contacts between T-cell receptor and MHC molecule. The next few sections describe how MHC polymorphisms benefit the immune response and how pathogen-driven selection can account for the large number of MHC alleles. The products of individual MHC alleles, often known as protein isoforms, can differ from one another by up to 20 amino acids, making each variant protein quite distinct. Most of the differences are localized to exposed surfaces of the extracellular domain furthest from the membrane, and to the peptide-binding groove in particular (Fig. 6.21). We have seen that peptides bind to MHC class I and class II molecules through the interaction of specific anchor residues with peptide-binding pockets in the peptide-binding groove (see Sections 4-15 and 4-16). Many of the polymorphisms in MHC molecules alter the amino acids that line these pockets and thus change


Immunology_Janeway

Immunology_Janeway. Fig. 6.20 Gene conversion can create new alleles by copying sequences from one MHC gene to another. Multiple MHC genes of generally similar structure were derived over evolutionary time by duplication of an unknown ancestral MHC gene (gray) followed by genetic divergence. Further interchange between these genes can occur by a process known as gene conversion, in which sequences can be transferred from part of one gene to a similar gene. For this to happen, the two genes must become apposed during meiosis. This can occur as a consequence of the misalignment of the two paired homologous chromosomes when there are many copies of similar genes arrayed in tandem—somewhat like buttoning in the wrong buttonhole. During the process of crossing-over and DNA recombination, a DNA sequence from one chromosome is sometimes copied to the other, replacing the original sequence. In this way, several nucleotide changes can be inserted all at once into a gene and can cause several simultaneous amino


Immunology_Janeway

Immunology_Janeway. chromosome is sometimes copied to the other, replacing the original sequence. In this way, several nucleotide changes can be inserted all at once into a gene and can cause several simultaneous amino acid changes in the gene product. Because of the similarity of the MHC genes to each other and their close linkage, gene conversion has occurred many times in the evolution of MHC alleles.


Immunology_Janeway

Immunology_Janeway. The high polymorphism of the classical MHC genes ensures diversity in MHC gene expression in the population as a whole. However, no matter how polymorphic a gene is, no individual can express more than two alleles at a single gene locus. Polygeny, the presence of several different related genes with similar functions, ensures that each individual produces a number of different MHC molecules. The combination of polymorphism and polygeny produces the diversity of MHC molecules seen both within an individual and in the population at large.


Immunology_Janeway

Immunology_Janeway. Fig. 6.21 Allelic variation in MHC molecules occurs Moreover, allelic variability is clustered in specific sites within the predominantly within the peptide-binding region. Variability amino-terminal domains, lying in positions that line the peptide-plots of the amino acid sequences of MHC molecules show that binding groove, either on the floor of the groove or inward from the the variation arising from genetic polymorphism is restricted to walls. For the MHC class II molecule, the variability of the HLA-DR the amino-terminal domains (α1 and α2 domains of MHC class I alleles is shown. For HLA-DR, and its homologs in other species, the molecules, and α1 and β1 domains of MHC class II molecules). α chain is essentially invariant and only the β chain shows significant These are the domains that form the peptide-binding groove. polymorphism.


Immunology_Janeway

Immunology_Janeway. the pockets’ binding specificities. This in turn changes the anchor residues of peptides that can bind to each MHC isoform. The set of anchor residues that allows binding to a given isoform of an MHC class I or class II molecule is called a sequence motif, and this can be used to predict peptides within a protein that might bind that variant (Fig. 6.22). Such predictions may be very important in designing peptide vaccines, as we will see in Chapter 16, where we discuss recent progress in cancer immunotherapy.


Immunology_Janeway

Immunology_Janeway. In rare cases, processing of a protein does not generate any peptides with a suitable sequence motif for binding to any of the MHC molecules expressed by an individual. This individual fails to respond to the antigen. Such failures in responsiveness to simple antigens were first reported in inbred animals and were called immune response (Ir) gene defects. These defects were mapped to genes within the MHC long before the structure or function of MHC molecules was understood, and they were the first clue to the antigen-presenting function of MHC molecules. We now understand that Ir gene defects are common in inbred strains of mice because the mice are homozygous at all their MHC gene loci, which limits the range of peptides they can present to T cells. Ordinarily, MHC polymorphism guarantees a sufficient number of different MHC molecules in a single individual to make this type of nonresponsiveness unlikely, even to relatively simple antigens such as small toxins.


Immunology_Janeway

Immunology_Janeway. Initially, the only evidence linking Ir gene defects to the MHC was genetic— mice of one MHC genotype could make antibody in response to a particular antigen, whereas mice of a different MHC genotype, but otherwise genetically identical, could not. The MHC genotype was somehow controlling the ability


Immunology_Janeway

Immunology_Janeway. Fig. 6.22 Different allelic variants of an MHC class I molecule bind different peptides. Shown are cutaway views of (a) ovalbumin peptide bound to the mouse H2-Kb MHC class I molecule and (b) influenza nucleoprotein (NP) peptide bound to the H2-Kd MHC class I molecule. The solvent-accessible surface of the MHC molecules is shown as a blue dotted surface. Class I MHC molecules typically have six pockets in the peptide-binding groove, which are conventionally called A–F. The bound peptides, shown as space-filling models, fit into the peptide-binding groove, with side chains from the anchor residues extending to fill the pockets. H2-Kb is binding SIINFEKL (single-letter amino acid code), a peptide of eight residues (P1–8) from ovalbumin, and H2-Kd is binding TYQRTRALV, a peptide of nine residues (P1–9) from the influenza nucleoprotein (NP). Anchor residues (shown in yellow) may be primary or secondary in their influence on peptide binding. For H2-Kb, the sequence motif is determined by


Immunology_Janeway

Immunology_Janeway. (P1–9) from the influenza nucleoprotein (NP). Anchor residues (shown in yellow) may be primary or secondary in their influence on peptide binding. For H2-Kb, the sequence motif is determined by two primary anchors, P5 and P8; the C pocket binds the P5 side chain of the peptide [a tyrosine (Y) or a phenylalanine (F)], and the F pocket binds the P8 residue [a non-aromatic hydrophobic side chain from leucine (L), isoleucine (I), methionine (M), or valine (V)]. The B pocket binds P2, a secondary anchor residue in H-2Kb. For H2-Kd, the sequence motif is primarily determined by the two primary anchors, P2 and P9. The B pocket accommodates a tyrosine side chain. The F pocket binds leucine, isoleucine, or valine. Beneath the structures are shown sequence motifs from peptides that are known to bind to the MHC molecule. CSP, circumsporozoite antigen; ERK4, extracellular signal-related kinase 4; HBV, hepatitis B virus; JAK1, Janus-associated kinase 1; LCMV, lymphocytic choriomeningitis virus;


Immunology_Janeway

Immunology_Janeway. to the MHC molecule. CSP, circumsporozoite antigen; ERK4, extracellular signal-related kinase 4; HBV, hepatitis B virus; JAK1, Janus-associated kinase 1; LCMV, lymphocytic choriomeningitis virus; NS2, NS2 protein; P198, modified tumor-cell antigen; P. berghei, Plasmodium berghei; P. yoelii, Plasmodium yoelii; VSV, vesicular stomatitis virus. An extensive collection of motifs can be found at http://www. syfpeithi.de. Structures courtesy of V.E. Mitaksov and D. Fremont.


Immunology_Janeway

Immunology_Janeway. of the immune system to detect or respond to specific antigens, but it was not clear at the time that direct recognition of MHC molecules was involved. Later experiments showed that the antigen specificity of T-cell recognition was controlled by MHC molecules. The immune responses affected by the Ir genes were known to depend on T cells, and this led to a series of experiments in mice to ascertain how MHC polymorphism might control T-cell responses. The earliest of these experiments showed that T cells could be activated only by macrophages or B cells that shared MHC alleles with the mouse in which the T cells originated. This was the first evidence that antigen recognition by T cells depends on the presence of specific MHC molecules in the antigen-presenting cell—the phenomenon we now know as MHC restriction.


Immunology_Janeway

Immunology_Janeway. Fig. 6.23 T-cell recognition of antigens is MHC-restricted. The antigen-specific T-cell receptor (TCR) recognizes a complex consisting of an antigenic peptide and a self MHC molecule. One consequence of this is that a T cell specific for peptide x and an MHC molecule that is the product of a particular MHC allele, MHCa (left panel), will usually not recognize the complex of peptide x bound to a different MHC allele product, MHCb (center panel), or the complex of a different peptide, peptide y, bound to MHCa (right panel). The co-recognition of a foreign peptide and an MHC molecule is known as MHC restriction because the particular MHC allele product is said to restrict the ability of the T cell to recognize antigen. This restriction may either result from direct contact between the MHC molecule and T-cell receptor or be an indirect effect of MHC polymorphism on the peptides that bind or on their bound conformation.


Immunology_Janeway

Immunology_Janeway. We first mentioned MHC restriction in Section 4-17 in the context of the crystal structure of the T-cell receptor bound to peptide:MHC complexes. But the phenomenon of MHC restriction was discovered much earlier and is illustrated by the studies of virus-specific cytotoxic T cells carried out by Peter Doherty and Rolf Zinkernagel, for which they received the Nobel Prize in 1996. When mice are infected with a virus, they generate cytotoxic T cells that kill the virus-infected cells while sparing both uninfected cells and cells infected with unrelated viruses. The cytotoxic T cells are thus virus-specific. The additional and striking outcome of these experiments was the demonstration that the ability of cytotoxic T cells to kill virus-infected cells was also affected by the polymorphism of MHC molecules. Cytotoxic T cells induced by viral infection in mice of MHC genotype a (MHCa) would kill any MHCa cell infected with that virus. But these same T cells would not kill cells of MHC


Immunology_Janeway

Immunology_Janeway. of MHC molecules. Cytotoxic T cells induced by viral infection in mice of MHC genotype a (MHCa) would kill any MHCa cell infected with that virus. But these same T cells would not kill cells of MHC genotype b, or c, and so on, even if they were infected with the same virus. In other words, cytotoxic T cells kill cells infected by virus only if those cells express the same MHC by which the T cells were primed. Because the MHC genotype ‘restricts’ the antigen specificity of the T cells, this effect was called MHC restriction. Together with the earlier studies on both B cells and macrophages, this work showed that MHC restriction is a critical feature of antigen recognition by all functional classes of T cells.


Immunology_Janeway

Immunology_Janeway. We now know that MHC restriction is due to the fact that the binding specificity of an individual T-cell receptor is not for its peptide antigen alone but for the complex of peptide and MHC molecule, as discussed in Section 4-17. MHC restriction is explained in part by the fact that different MHC molecules bind different peptides. In addition, some of the polymorphic amino acids in MHC molecules are located in the α helices that flank the peptide-binding groove but have side chains oriented toward the exposed surface of the peptide:MHC complex that can directly contact the T-cell receptor (see Figs. 6.21 and 4.24). In retrospect, it is therefore not surprising that T cells can distinguish between a peptide bound to MHCa and the same peptide bound to MHCb. This restricted recognition may sometimes be caused both by differences in the conformation of the bound peptide imposed by the different MHC molecules and by direct recognition of polymorphic amino acids in the MHC molecule itself.


Immunology_Janeway

Immunology_Janeway. be caused both by differences in the conformation of the bound peptide imposed by the different MHC molecules and by direct recognition of polymorphic amino acids in the MHC molecule itself. Thus, the specificity of a T-cell receptor is defined both by the peptide it recognizes and by the MHC molecule bound to it (Fig. 6.23).


Immunology_Janeway

Immunology_Janeway. 6-13 Alloreactive T cells recognizing nonself MHC molecules are very abundant.


Immunology_Janeway

Immunology_Janeway. The discovery of MHC restriction also helped to explain the otherwise puzzling phenomenon of recognition of nonself MHC in the rejection of organs and tissues transplanted between members of the same species. Transplanted organs from donors bearing MHC molecules that differ from those of the recipient—even by as little as one amino acid—are rapidly rejected owing to the presence in any individual of large numbers of T cells that react to nonself, or allogeneic, MHC molecules. Early studies on T-cell responses to allogeneic MHC molecules used the mixed lymphocyte reaction, in which T cells from one individual are mixed with lymphocytes from a second individual. If the T cells of this individual recognize the other individual’s MHC molecules as ‘foreign,’ the T cells will divide and proliferate. The lymphocytes from the second individual are usually prevented from dividing by irradiation or treatment with the cytostatic drug mitomycin C. Such studies have shown that roughly 1–10% of all


Immunology_Janeway

Immunology_Janeway. The lymphocytes from the second individual are usually prevented from dividing by irradiation or treatment with the cytostatic drug mitomycin C. Such studies have shown that roughly 1–10% of all T cells in an individual will respond to stimulation by cells from another, unrelated, member of the same species. This type of T-cell response is called an alloreaction or alloreactivity, because it represents the recognition of allelic polymorphisms in MHC molecules.


Immunology_Janeway

Immunology_Janeway. Before the role of the MHC molecules in antigen presentation was understood, it was a mystery why so many T cells should recognize nonself MHC molecules, as there is no reason that the immune system should have evolved a defense against tissue transplants. Once it was realized that T-cell receptors have evolved to recognize foreign peptides in combination with polymorphic MHC molecules, alloreactivity became easier to explain. We now know of at least two processes that can contribute to the high frequency of alloreactive T cells. The first is the process of positive selection. When developing in the thymus, T cells whose T-cell receptors interact weakly with the self MHC molecules receive survival signals, and so are favored for representation in the peripheral repertoire. It is thought that T-cell receptors that interact with one type of MHC molecule are more likely to cross-react with other (nonself ) MHC variants. We discuss positive selection in greater detail in Chapter 8.


Immunology_Janeway

Immunology_Janeway. But positive selection is not the only basis for alloreactivity. This conclusion was implied by observations that T cells artificially driven to mature in animals lacking MHC class I and class II, in which positive selection in the thymus cannot occur, still display frequent alloreactivity. It appears that T-cell receptor genes encode the inherent ability to recognize MHC molecules. X-ray crystallographic studies of T-cell receptors bound to MHC molecules provide a structural basis for an inherent binding interaction (Fig. 6.24). Specific amino acid residues within the germline-encoded region of certain TCRβ genes interact with conserved features of the MHC molecule, implying a type of germlineencoded affinity. Given the large number of variable-region sequences in T-cell receptors, each T-cell receptor may bind MHC molecules in its own idiosyncratic way using both germline-encoded regions and variable regions.


Immunology_Janeway

Immunology_Janeway. In principle, alloreactive T cells might depend on recognizing either a foreign peptide antigen or the nonself MHC molecule to which it is bound for their reactivity against nonself MHC; these options have been called peptide-dependent and peptide-independent allorecognition. But as the number of individual alloreactive T-cell clones studied has increased, it seems that most alloreactive T cells actually recognize both; that is, most individual alloreactive T-cell clones respond to a foreign MHC molecule only when a particular peptide is bound to it. In this sense, the structural basis of allorecognition may be quite similar to normal MHC-restricted peptide recognition and be dependent on contacts with both peptide and MHC molecule (see Fig. 6.23, left panel), but in this case a foreign MHC molecule. In practice, alloreactive responses against a transplanted organ are likely to represent the combined


Immunology_Janeway

Immunology_Janeway. Fig. 6.24 Germline-encoded residues in CDR1 and CDR2 of V-region genes confer on T-cell receptors an inherent affinity for MHC molecules. Shown is the structure for several T-cell receptors bound to a class II MHC molecule. Conserved residues (Lys39, Gln57, and Gln61) within the α1 helix of the MHC (green) make an extended hydrogen-bonded network with germline-encoded and nonpolymorphic residues located in the CDR1 (Asn31) and CDR2 (Glu56, Tyr50) regions of the Vβ 8.2 gene, respectively. The configuration of these contacts is very similar between different structures, implying that the germline sequence of the CDR1 and CDR2 confers an inherent bias for T-cell receptor affinity for MHC. Courtesy of K.C. Garcia. activity of many alloreactive T cells, and it is not possible to determine what peptides from the donor might be involved in recognition by the alloreactive T cells. We will return to alloreactivity when we discuss organ transplantation in more detail in Chapter 15.


Immunology_Janeway

Immunology_Janeway. 6-14 Many T cells respond to superantigens. Superantigens are a distinct class of antigens that stimulate a primary T-cell response similar in magnitude to a response to allogeneic MHC molecules. Such responses were first observed in mixed lymphocyte reactions using lymphocytes from strains of mice that were MHC-identical but otherwise genetically distinct. The antigens provoking this reaction were originally designated as minor lymphocyte stimulating (Mls) antigens, and it seemed reasonable to suppose that they might be functionally similar to the MHC molecules themselves. We now know that this is not true. The Mls antigens in these mouse strains are encoded by retroviruses, such as the mouse mammary tumor virus, that have become stably integrated at various sites in the mouse chromosomes. Superantigens are produced by many different pathogens, including bacteria, mycoplasmas, and viruses, and the responses they provoke are helpful to the pathogen rather than the host.


Immunology_Janeway

Immunology_Janeway. Mls proteins act as superantigens because they have a distinctive mode of binding to both MHC and T-cell receptor molecules that enables them to stimulate very large numbers of T cells. Superantigens are unlike other protein antigens, in that they are recognized by T cells without being processed into peptides that are captured by MHC molecules. Indeed, fragmentation of a superantigen destroys its biological activity, which depends on binding as an intact protein to the outside surface of an MHC class II molecule that has already bound peptide. In addition to binding MHC class II molecules, superantigens are able to bind the Vβ region of many T-cell receptors (Fig. 6.25). Bacterial superantigens bind mainly to the Vβ CDR2 loop, and, to a smaller extent, to the Vβ CDR1 loop and an additional loop called the hypervariable 4 or HV4 loop. The HV4 loop is the predominant binding site for viral superantigens, at least for the Mls antigens encoded by the endogenous mouse mammary tumor


Immunology_Janeway

Immunology_Janeway. loop called the hypervariable 4 or HV4 loop. The HV4 loop is the predominant binding site for viral superantigens, at least for the Mls antigens encoded by the endogenous mouse mammary tumor viruses.


Immunology_Janeway

Immunology_Janeway. Fig. 6.25 Superantigens bind directly to T-cell receptors and to MHC molecules. Superantigens can bind independently to MHC class II molecules and to T-cell receptors. As shown in the top panels, the superantigens (red bars) can bind to the Vβ domain of the T-cell receptor (TCR), away from the complementarity-determining regions, and to the outer faces of the MHC class II molecule, outside the peptide-binding site. In the bottom panel, a reconstruction of the interaction between a T-cell receptor, an MHC class II molecule, and a staphylococcal enterotoxin (SE) superantigen is shown by superimposing separate structures of an enterotoxin:MHC class II complex onto an enterotoxin:T-cell receptor complex. The two enterotoxin molecules (actually SEC3 and SEB) are shown in turquoise and blue, binding to the α chain of the MHC class II molecule (yellow) and to the β chain of the T-cell receptor (colored gray for the Vβ domain and pink for the Cβ domain). Molecular model courtesy of


Immunology_Janeway

Immunology_Janeway. H.M. Li, B.A. Fields, and R.A. Mariuzza. Thus, the α-chain V region and the CDR3 of the β chain of the T-cell receptor have little effect on superantigen recognition, which is determined largely by the germline-encoded V gene segments that encode the expressed Vβ chain. Each superantigen is specific for one or a few of the different Vβ gene products, of which there are 20–50 in mice and humans; a superantigen can thus stimulate 2–20% of all T cells.


Immunology_Janeway

Immunology_Janeway. This mode of stimulation does not prime an adaptive immune response specific for the pathogen. Instead, it causes a massive production of cytokines by CD4 T cells, the predominant responding population of T cells. These cytokines have two effects on the host: systemic toxicity and suppression of the adaptive immune response. Both these effects contribute to microbial pathogenicity. Among the bacterial superantigens are the staphylococcal enterotoxins (SEs), which cause food poisoning, and the toxic shock syndrome toxin-1 (TSST-1) of Staphylococcus aureus, the etiologic principle in toxic shock syndrome, which can be caused by a localized infection with toxin-producing strains of the bacterium. The role of viral superantigens in human disease is less clear. 6-15 MHC polymorphism extends the range of antigens to which the immune system can respond.


Immunology_Janeway

Immunology_Janeway. Most polymorphic genes encode proteins that vary by only one or a few amino acids, whereas the allelic variants of MHC proteins differ from each other by up to 20 amino acids. The extensive polymorphism of the MHC proteins has almost certainly evolved to outflank the evasive strategies of pathogens. The requirement that pathogen antigens must be presented by an MHC molecule provides two possible ways in which pathogens could evolve to evade detection. One is through mutations that eliminate from the pathogen’s proteins all peptides able to bind MHC molecules. The Epstein–Barr virus provides an example. There are small isolated populations in southeast China and Papua New Guinea in which about 60% of the people carry the HLA-A11 allele. Many isolates of the Epstein–Barr virus obtained from these populations have mutations in a dominant peptide epitope normally presented by HLA-A11; the mutant peptides no longer bind to HLA-A11 and cannot be recognized by HLA-A11-restricted T cells.


Immunology_Janeway

Immunology_Janeway. these populations have mutations in a dominant peptide epitope normally presented by HLA-A11; the mutant peptides no longer bind to HLA-A11 and cannot be recognized by HLA-A11-restricted T cells. This strategy is clearly much less successful if there are many different MHC molecules, and the polygeny of the MHC may have evolved in response.


Immunology_Janeway

Immunology_Janeway. In addition, in large outbred populations, polymorphism at each locus can potentially double the number of different MHC molecules expressed by an individual, as most individuals will be heterozygotes. Polymorphism has the additional advantage that individuals in a population will differ in the combinations of MHC molecules that they express and will therefore present different sets of peptides from each pathogen. This makes it unlikely that all individuals in a population will be equally susceptible to a given pathogen, and its spread will therefore be limited. The fact that exposure to pathogens over an evolutionary timescale can select for particular MHC alleles is indicated by the strong association of the HLA-B53 allele with recovery from a potentially lethal form of malaria. This allele is very common in people from West Africa, where malaria is endemic, and rare elsewhere, where lethal malaria is uncommon.


Immunology_Janeway

Immunology_Janeway. Similar arguments apply to a second strategy by which pathogens could evade recognition. Pathogens that can block the presentation of their peptides by MHC molecules can avoid the adaptive immune response. Adenoviruses encode a protein that binds to MHC class I molecules in the endoplasmic reticulum and prevents their transport to the cell surface, thus preventing the recognition of viral peptides by CD8 cytotoxic T cells. This viral MHC-binding protein interacts with a polymorphic region of the MHC class I molecule, as some allelic variants are retained in the endoplasmic reticulum by the adenoviral protein, whereas others are not. Increasing the variety of MHC molecules expressed reduces the likelihood that a pathogen will be able to block presentation by all of them and completely evade an immune response.


Immunology_Janeway

Immunology_Janeway. These arguments raise a question: if having three MHC class I loci is better than having one, why are there not far more? The probable explanation is that each time a distinct MHC molecule is added to the repertoire, all T cells that can respond to self peptides bound to that MHC molecule must be removed to maintain self tolerance. It seems that the number of MHC genes present in humans and mice is about optimal to balance the advantages of presenting an increased range of foreign peptides with the disadvantages of losing T cells from the repertoire. Summary.


Immunology_Janeway

Immunology_Janeway. The major histocompatibility complex (MHC) of genes consists of a linked set of genetic loci encoding many of the proteins involved in antigen presentation to T cells, most notably the MHC class I and class II glycoproteins (the MHC molecules) that present peptides to the T-cell receptor. The outstanding feature of the MHC molecules is their extensive polymorphism. This polymorphism is of critical importance in antigen recognition by T cells. A T cell recognizes antigen as a peptide bound by a particular allelic variant of an MHC molecule, and will not recognize the same peptide bound to other MHC molecules. This behavior of T cells is called MHC restriction. Most MHC alleles differ from one another by multiple amino acid substitutions, and these differences are focused on the peptide-binding site and the surface-exposed regions that make direct contact with the T-cell receptor. At least three properties of MHC molecules are affected by MHC polymorphism: the range of peptides bound;


Immunology_Janeway

Immunology_Janeway. site and the surface-exposed regions that make direct contact with the T-cell receptor. At least three properties of MHC molecules are affected by MHC polymorphism: the range of peptides bound; the conformation of the bound peptide; and the direct interaction of the MHC molecule with the T-cell receptor. Thus, the highly polymorphic nature of the MHC has functional consequences, and the evolutionary selection for this polymorphism suggests that it is critical to the role of the MHC molecules in the immune response. Powerful genetic mechanisms generate the variation that is seen among MHC alleles, and a compelling argument can be made that selective pressure to maintain a wide variety of MHC molecules in the population comes from infectious agents. As a consequence, the immune system is highly individualized—each individual responds differently to a given antigen.


Immunology_Janeway

Immunology_Janeway. Generation of ligands for unconventional T-cell subsets.


Immunology_Janeway

Immunology_Janeway. So far we have focused on how peptide:MHC complexes—the ligands for α:β T cells—are generated. We now turn to the question of how other types of T cells recognize their ligands and how these ligands are generated. Our current knowledge in this area is still incomplete, and is perhaps most apparent in the area of γ:δ T cells, where a growing list of ligands for individual γ:δT cells suggests an innate-like pattern of recognition. The recent discovery that the mucosal associated invariant T (MAIT) cells (see Section 4-18) recognize a microbial metabolite when it is presented by a nonpolymorphic MHC class I-like molecule solved a long-standing mystery regarding the function of this particular T-cell subset. Another invariant subset, the invariant NKT cells, provides a system for detecting and responding to lipid rather than peptide antigens. These findings suggest that these invariant and unconventional T cells operate somewhere between innate and adaptive immunity. In this part of the


Immunology_Janeway

Immunology_Janeway. responding to lipid rather than peptide antigens. These findings suggest that these invariant and unconventional T cells operate somewhere between innate and adaptive immunity. In this part of the chapter, we will discuss the ligands they recognize and what is known about how they are generated or expressed.


Immunology_Janeway

Immunology_Janeway. 6-16 A variety of genes with specialized functions in immunity are also encoded in the MHC. In addition to the highly polymorphic ‘classical’ MHC class I and class II genes, there are many ‘nonclassical’ MHC genes, many encoded in the MHC but others encoded outside this region. The MHC class I-type molecules show comparatively little polymorphism; many of these have yet to be assigned a function. They are linked to the class I region of the MHC, and their exact number varies greatly among species and even among members of the same species. These genes have been termed MHC class Ib genes; like MHC class I genes, many, but not all, associate with β2-microglobulin when expressed on the cell surface. Their expression on cells is variable, both in the amount present at the cell surface and in tissue distribution. The characteristics of several MHC class Ib gene products are shown in Fig. 6.26.


Immunology_Janeway

Immunology_Janeway. One mouse MHC class Ib molecule, H2-M3, can present peptides with N-formylated amino termini, which is of interest because all bacteria initiate protein synthesis with N-formylmethionine. Cells infected with cytosolic bacteria can be killed by CD8 T cells that recognize N-formylated bacterial peptides bound to H2-M3. Whether an equivalent MHC class Ib molecule exists in humans is not known. Two other closely related mouse MHC class Ib genes, T22 and T10, are expressed by activated lymphocytes and are recognized by a subset of γ:δT cells. Although the precise purpose remains unclear, it has been proposed that this interaction allows γ:δ T cells to regulate these activated lymphocytes expressing T22 and T10 proteins.


Immunology_Janeway

Immunology_Janeway. The other genes that map within the MHC include some that encode complement components (for example, C2, C4, and factor B) and some that encode cytokines—for example, tumor necrosis factor-α (TNF-α) and lymphotoxin— all of which have important functions in immunity. These genes lie in the so-called ‘MHC class III’ region (see Fig. 6.17), a somewhat misleading name, since genes in this region are not MHC molecules at all.


Immunology_Janeway

Immunology_Janeway. Many studies have established associations between susceptibility to certain diseases and particular alleles of MHC genes (see Chapter 15), and we now have considerable insight into how polymorphism in the classical MHC class I and class II genes can affect disease resistance or susceptibility. Most MHC-influenced traits or diseases are known or suspected to have an immunological cause, but this is not so for all of them: some genes residing within the MHC have no known or suspected immunological function. For example, the class Ib gene M10 encodes a protein that functions in the vomeronasal organ as a chaperone to escort certain types of pheromone receptors to the cell surface. M10 could potentially influence mating preference, a trait that has been linked to the MHC region in rodents.


Immunology_Janeway

Immunology_Janeway. The HFE gene, encoding the hemochromatosis protein, lies some 4 million base pairs from HLA-A. Its protein product is expressed in cells of the intestinal cells (see the text and Section 3-24). HLA-C, which is a classical MHC molecule (class Ia), is included here because, in addition to presenting peptides to T-cell receptors, all HLA-C isoforms interact with the KIR class of NK-cell receptors to regulate NK-cell function in the innate immune response. CTL, cytotoxic T lymphocyte.


Immunology_Janeway

Immunology_Janeway. tract and acts in iron metabolism by regulating the uptake of dietary iron into the body. It seems to interact with the transferrin receptor and decrease the receptor’s affinity for iron-loaded transferrin. Individuals defective for this gene have an iron-storage disease, hereditary hemochromatosis, in which an abnormally high level of iron is retained in the liver and other organs. Mice lacking β2-microglobulin have defective expression of all class I molecules and thus also show a similar iron overload. Another MHC gene with a nonimmune function encodes the enzyme 21-hydroxylase, which, when deficient, causes congenital adrenal hyperplasia and, in severe cases, salt-wasting syndrome. Even where a disease-related gene is clearly homologous to immune-system genes, as is the case with HFE, the disease mechanism may not be immune-related. Disease associations mapping to the MHC must therefore be interpreted with caution, in the light of a detailed understanding of its genetic structure


Immunology_Janeway

Immunology_Janeway. the disease mechanism may not be immune-related. Disease associations mapping to the MHC must therefore be interpreted with caution, in the light of a detailed understanding of its genetic structure and the functions of its individual genes. Much remains to be learned about the significance of all the genetic variation localized within the MHC. For instance, the human complement component C4 comes in two versions, C4A and C4B, not to be confused with the C4 convertase cleavage products C4a and C4b, and different individuals have variable numbers of the gene for each type in their genomes, but the adaptive significance of this genetic variability is not well understood.


Immunology_Janeway

Immunology_Janeway. 6-17 Specialized MHC class I molecules act as ligands for the activation and inhibition of NK cells and unconventional T-cell subsets.


Immunology_Janeway

Immunology_Janeway. In Sections 3-24 to 3-27, we introduced NK cells and briefly discussed their activation by members of the MIC gene family. These are MHC class Ib genes that are under a different regulatory control than the classical MHC class I genes and are induced in response to cellular stress (such as heat shock). There are seven MIC genes, but only two—MICA and MICB—are expressed and produce protein products (see Fig. 6.26). They are expressed in fibroblasts and epithelial cells, particularly in intestinal epithelial cells, and have a role in innate immunity or in the induction of immune responses in circumstances in which interferons are not produced. The MICA and MICB proteins are recognized by the NKG2D receptor expressed by NK cells. But in addition, NKG2D is also expressed by γ:δ T cells and some CD8 T cells, and it can activate these cells to kill MIC-expressing targets. NKG2D is an ‘activating’ member of the NKG2 family of NK-cell receptors (see Fig. 3.42); its cytoplasmic domain lacks


Immunology_Janeway

Immunology_Janeway. some CD8 T cells, and it can activate these cells to kill MIC-expressing targets. NKG2D is an ‘activating’ member of the NKG2 family of NK-cell receptors (see Fig. 3.42); its cytoplasmic domain lacks the inhibitory sequence motif found in other members of this family, which act as inhibitory receptors (see Section 3-26). NKG2D is coupled to the adaptor protein DAP10, which transmits the signal into the interior of the cell by interacting with and activating intracellular phosphatidylinositol 3-kinase.


Immunology_Janeway

Immunology_Janeway. Even more distantly related to MHC class I genes is a small family of proteins known in humans as the UL16-binding proteins (ULBPs) or the RAET1 proteins (see Fig. 6.26); the homologous proteins in mice are known as Rae1 (retinoic acid early inducible 1) and H60. These proteins also bind NKG2D (see Section 3-27). They seem to be expressed under conditions of cellular stress, such as when cells are infected with pathogens (UL16 is a human cytomegalovirus protein) or have undergone transformation to tumor cells. By expressing ULBPs, stressed or infected cells can bind and activate NKG2D molecules expressed on NK cells, γ:δ T cells, and CD8 cytotoxic α:β T cells, and so be recognized and eliminated.


Immunology_Janeway

Immunology_Janeway. The human MHC class Ib molecule HLA-E and its mouse counterpart Qa-1 (see Fig. 6.26) have an unusual and somewhat puzzling role in cell recognition by NK cells and CD8 T cells. HLA-E and Qa-1 bind a very restricted subset of nonpolymorphic peptides, called Qa-1 determinant modifiers (Qdm), that are derived from the leader peptides of other HLA class I molecules. These peptide:HLA-E complexes can bind to the inhibitory receptor NKG2A:CD94 expressed on NK cells, and so should inhibit the cytotoxic activity of NK cells. This function might seem redundant, since expression of other MHC class I molecules by cells should prevent NK-cell activation (see Section 3-25). Nonetheless, it has been shown that Qa-1 expression by activated CD4 T cells protects them from lysis by NK cells and so Qa-1 expression by other host cells may provide them with additional protection from being killed by NK cells. HLA-E and Qa-1 can also bind leader peptides from the heat shock protein Hsp60sp, and CD8 T cells


Immunology_Janeway

Immunology_Janeway. by other host cells may provide them with additional protection from being killed by NK cells. HLA-E and Qa-1 can also bind leader peptides from the heat shock protein Hsp60sp, and CD8 T cells that are specific for these complexes have been identified in mice and humans. Some recent evidence suggests that CD8 T cells restricted by HLA-E/Qa-1 may help maintain self-tolerance by killing or suppressing potentially autoreactive T cells.


Immunology_Janeway

Immunology_Janeway. In Section 3-26, we introduced the killer cell immunoglobulin-like receptors (KIRs) expressed by NK cells. Members of the KIRs recognize the classical class Ia MHC molecules HLA-A, -B, and -C, which present a diverse repertoire of peptides to CD8 T cells. Although KIRs interact with the same face of the MHC class I molecule as do T-cell receptors, the KIRs bind only at one end, and not over the whole area recognized by the T-cell receptor. Like MHC molecules, KIRs themselves are highly polymorphic, and they have undergone rapid evolution in humans. Only a few HLA-A and HLA-B alleles code for proteins that bind KIRs, but all HLA-C alleles express proteins that bind KIRs, indicating a specialization of HLA-C for regulating NK cells in humans.


Immunology_Janeway

Immunology_Janeway. Two other MHC class Ib molecules, HLA-F and HLA-G (see Fig. 6.26), can also inhibit cell killing by NK cells. HLA-G is expressed on fetus-derived placental cells that migrate into the uterine wall. These cells express no classical MHC class I molecules and cannot be recognized by CD8 T cells but, unlike other cells lacking such proteins, they are not killed by NK cells. This seems to be because HLA-G is recognized by another inhibitory receptor on NK cells, the leukocyte immunoglobulin-like receptor subfamily B member 1 (LILRB1), also called ILT-2 or LIR-1, which prevents the NK cell from killing the placental cells. HLA-F is expressed in a variety of tissues, although it is usually not detected at the cell surface except, for example, on some monocyte cell lines or on virus-transformed lymphoid cells. HLA-F is also thought to interact with LILRB1. 6-18 Members of the CD1 family of MHC class I-like molecules present microbial lipids to invariant NKT cells.


Immunology_Janeway

Immunology_Janeway. Some MHC class I-like genes map outside the MHC region. One small family of such genes is called CD1 and is expressed on dendritic cells, monocytes, and some thymocytes. Humans have five CD1 genes, CD1a through e, whereas mice express only two highly homologous versions of CD1d, namely, CD1d1 and CD1d2. CD1 proteins can present antigens to T cells, but they have two features that distinguish them from classical MHC class I molecules. The first is that CD1, although similar to an MHC class I molecule in its subunit organization and association with β2-microglobulin, behaves like an MHC class II molecule. It is not retained within the endoplasmic reticulum by association with the TAP complex but is targeted to vesicles, where it binds its ligand. The second unusual feature is that, unlike MHC class I, CD1 molecules have a hydrophobic channel that is specialized for binding hydrocarbon alkyl chains. This confers on CD1 molecules an ability to bind and present a variety of glycolipids.


Immunology_Janeway

Immunology_Janeway. CD1 molecules are classified into group 1, comprising CD1a, CD1b, and CD1c, and group 2, containing only CD1d; CD1e is considered intermediate. Group 1 molecules bind various microbial glycolipids, phospholipids, and lipopeptide antigens, such as the mycobacterial membrane components mycolic acid, glucose monomycolate, phosphoinositol mannosides, and lipoarabinomannan (Fig. 6.27). Group 2 CD1 molecules are thought to bind mainly self


Immunology_Janeway

Immunology_Janeway. Fig. 6.27 CD1c binds microbial lipids for presentation to iNKT cells. Top panel: the structure of mannosyl-β1-phosphomycoketides (MPMs) from the cell walls of Mycobacterium tuberculosis (Mtb) (R = C7H15) and M. avium (R = C5H11). Middle panel: MPM (stick figure) bound to CD1c (purple) as viewed from the top, facing the surface of the cell bearing CD1c. Bottom panel: side view of MPM bound to CD1c. The general resemblance with peptide:MHC complexes is apparent. Note: the long acyl chain of MPM extends deep into the binding groove of CD1c, to beneath the α1 helical domain. Courtesy of E. Adams.


Immunology_Janeway

Immunology_Janeway. lipid antigens such as sphingolipids and diacylglycerols. Structural studies show that the CD1 molecule has a deep binding groove into which the glycolipid antigens bind (Fig. 6.28). Unlike the binding of peptide to MHC, in which the peptide takes on a linear, extended conformation, CD1 molecules bind their antigens by anchoring the alkyl chains in the hydrophobic groove, which orients the variable carbohydrate headgroups (or other hydrophilic parts of these molecules) so that they protrude from the end of the binding groove, allowing recognition by the T-cell receptors on CD1-restricted T cells.


Immunology_Janeway

Immunology_Janeway. The T cells that recognize lipids presented by CD1 molecules are largely negative for CD4 and CD8 expression, although some express CD4. Most of the T cells recognizing lipids presented by group 1 CD1 molecules have a diverse repertoire of α:β receptors, and respond to these lipids presented by CD1a, CD1b, and CD1c. In contrast, CD1d-restricted T cells are less diverse, many using the same TCRα chain (Vα24–Jα18 in humans), but they also express NK-cell receptors. These CD1-restricted T cells are called invariant NKT (iNKT) cells.


Immunology_Janeway

Immunology_Janeway. One recognized ligand for CD1d molecules is α-galactoceramide (α-GalCer), which was isolated from an extract of marine sponge. Related glycosphingolipids are produced by various bacteria, including Bacteroides fragilis, which is present in the normal human microbiota. When α-galactoceramide is bound to CD1d, it forms a structure that is recognized by many iNKT cells. The ability of iNKT cells to recognize different glycolipid constituents from microorganisms presented by CD1d molecules places them in an ‘innate’ category, while their possession of a fully rearranged T-cell receptor, despite its relatively limited repertoire, makes them ‘adaptive.’


Immunology_Janeway

Immunology_Janeway. CD1 proteins have evolved as a separate lineage of antigen-presenting molecules able to present microbial lipids and glycolipids to T cells. Just as peptides are loaded onto classical MHC proteins at various cellular locations, the various CD1 proteins are transported differently through the endoplasmic reticulum and endocytic compartments; this provides access to different lipid antigens. Transport is regulated by an amino acid sequence motif at the terminus of the cytoplasmic domain of the CD1 protein through interaction with adaptor-protein (AP) complexes. CD1a lacks this binding motif and moves to the cell surface, where it is transported only through the early endocytic compartment. CD1c and CD1d have motifs that interact with the adaptor AP-2 and are transported through early and late endosomes; CD1d is also targeted to lysosomes. CD1b and mouse CD1d bind AP-2 and AP-3 and can be transported through late endosomes, lysosomes, and the MIIC. CD1 proteins can thus bind lipids


Immunology_Janeway

Immunology_Janeway. late endosomes; CD1d is also targeted to lysosomes. CD1b and mouse CD1d bind AP-2 and AP-3 and can be transported through late endosomes, lysosomes, and the MIIC. CD1 proteins can thus bind lipids delivered into and processed within the endocytic pathway, such as by the internalization of mycobacteria or the ingestion of mycobacterial lipoarabinomannans mediated by mannose receptors.


Immunology_Janeway

Immunology_Janeway. From an evolutionary perspective it is interesting that some class Ib genes seem to have evolved early, before the divergence of the cartilaginous fishes from the vertebrate line, and are likely to have homologs in all vertebrates. Other class I genes have independently evolved into classical and nonclassical loci within the vertebrate lineages that have been studied (for example, cartilaginous fishes, lobe-finned fishes, ray-finned fishes, amphibians, and mammals). Sequence data have also revealed homologs of the mammalian MHC-I and MHC-II gene families in virtually all jawed vertebrates including sharks, bony fishes, reptiles, and birds. In contrast, CD1 genes may not be as old as Chapter 6: Antigen Presentation to T Lymphocytes


Immunology_Janeway

Immunology_Janeway. Fig. 6.28 Structure of CD1 binding to a lipid antigen. Shown are top and side views of the structure of mouse CD1d bound to C8PhF, a synthetic lipid that is an analog of α-GalCer. The helical side chains of CD1d (blue) form a binding pocket that is generally similar in shape to the binding pockets of MHC class I and II molecules. However, the C8PhF (red) ligand binds to CD1 molecules in a distinctly different conformation from that of peptides. The two long alkyl side chains extend deep inside the binding groove (see side view), where they make contacts with hydrophobic residues. This orientation of the alkyl side chains places the carbohydrate component of α-GalCer to the outer surface of CD1, where it can be recognized by the T-cell receptor. In addition, the CD1 molecule contains an endogenous lipid molecule (yellow) derived from cellular sources that binds to a distinct region within the groove and prevents a large pocket adjacent to the α-GalCer-binding region from collapsing.


Immunology_Janeway

Immunology_Janeway. endogenous lipid molecule (yellow) derived from cellular sources that binds to a distinct region within the groove and prevents a large pocket adjacent to the α-GalCer-binding region from collapsing. The ability to incorporate additional ligands into the binding groove may provide flexibility to CD1d in accommodating a variety of exogenous glycosphingolipids from microorganisms. Courtesy of I.A. Wilson.


Immunology_Janeway

Immunology_Janeway. other MHC class Ib genes. They have been found only in a subset of these animal groups and appear to be missing in fish. This pattern of CD1 occurrence in the genomes of living species suggests the emergence of CD1 in an early terrestrial vertebrate. 6-19 The nonclassical MHC class I molecule MR1 presents microbial folate metabolites to MAIT cells.


Immunology_Janeway

Immunology_Janeway. Another nonclassical MHC class Ib molecule is MR1 (MHC-related protein 1). MR1 associates with β2-microglobulin and is encoded outside the MHC, but its function was originally known only in relation to a conserved population of α:β T cells known as mucosal associated invariant T cells (MAIT cells). In Section 4-18, we introduced MAIT cells as one population of T cells expressing the CD8α homodimer, but they are uniquely characterized by expressing an invariant α chain of the T-cell receptor, specifically human Vα7.2J2–Jα33 (or in mouse, Vα19) . This α chain pairs with a limited number of Vβ chains, typically Vβ2 or Vβ13. MAIT cells are very abundant in humans and can comprise up to 10% of the lymphocytes in the peripheral blood and tissues such as the liver. They are also present in mesenteric lymph nodes and the mucosa of the intestine. Studies of MAIT cells revealed that their development requires the expression of MR1, and further, that a wide spectrum of microbes, including


Immunology_Janeway

Immunology_Janeway. mesenteric lymph nodes and the mucosa of the intestine. Studies of MAIT cells revealed that their development requires the expression of MR1, and further, that a wide spectrum of microbes, including diverse bacteria and yeast, can activate MAIT cells. However, when they were originally identified around a decade ago, it was unclear what, if any, ligand is being recognized by these cells.


Immunology_Janeway

Immunology_Janeway. Structural studies of MR1 uncovered an important clue. The MR1 protein was unstable when produced in vitro by cell lines grown in typical tissue culture conditions. It was discovered that the protein was stabilized when it was refolded in media containing B vitamins or folic acid (vitamin B9). Chemical analysis revealed that a small molecule—identified as a folate derivative, 6-formyl pterin (6-FP)—was bound to the stabilized MR1. X-ray crystallographic studies showed that 6-FP was bound in the central groove of the MR1 molecule; this helped explain how folate derivatives might stabilize MR1. However, MAIT cells were not activated by cells expressing the 6-FP:MR1 complex, suggesting other molecules might be the physiological ligands to activate MAIT cells. Analysis of MR1 proteins that were refolded in the presence of supernatants from cultures of Salmonella typhimurium eventually led to the identification of several riboflavin metabolites that are formed by biosynthetic pathways in


Immunology_Janeway

Immunology_Janeway. refolded in the presence of supernatants from cultures of Salmonella typhimurium eventually led to the identification of several riboflavin metabolites that are formed by biosynthetic pathways in most bacteria and yeast. These metabolites not only bind to MR1, but also activate MAIT cells. Thus, MAIT cells are activated in response to infection by these organisms by detecting products specific to their folate metabolism. As such, MAIT cells appear to hold an intermediate place in the spectrum of innate and adaptive immunity, similar to iNKT cells, in that they use an antigen receptor assembled by somatic gene rearrangement, but recognize a molecular structure that falls within the definition of a PAMP.


Immunology_Janeway

Immunology_Janeway. 6-20 γ:δ T cells can recognize a variety of diverse ligands. γ:δ T cells and α:β T cells have been known to be distinct developmental lineages almost since the T-cell receptor genes were identified. But unlike α:βT cells, the function of γ:δ T cells has remained somewhat obscure, due primarily to difficulty in identifying the ligands they recognize. Yet the abundance of γ:δ T cells across vertebrate species, their rapid expansion to form more than 50% of the blood lymphocytes during infections, and their abundant cytokine production all argue for an important role in immunity. Over time, many different ligands recognized by γ:δ T-cell clones have been identified (Fig. 6.29), and their diversity suggests that, like iNKT and MAIT cells, they hold an intermediate, or transitional, position in the spectrum of innate versus adaptive immunity.


Immunology_Janeway

Immunology_Janeway. In Section 4-20, we discussed how one γ:δ T-cell receptor binds to the non-classical MHC class I molecule T22. Instead of binding centrally over the MHC binding groove, similar to an α:β T-cell receptor, the γ:δ T-cell receptor interacts obliquely from one side of the T22 molecule. However, fewer than 1% of γ:δ T cells recognize this ligand. Other antigens recognized by murine γ:δT cells are the protein phycoerythrin (PE) from algae, the inner mitochondrial membrane lipid cardiolipin, glycoprotein I of herpes simplex virus, and a peptide derived from the hormone insulin. Among antigens that can activate human γ:δ T cells are the nonclassical MHC class I proteins MICA and ULBP4 and the endothelial protein C receptor (EPCR), which is expressed by endothelial cells. Like MICA and ULBPs, EPCR appears to be induced upon stress, such as during infection of cells by cytomegalovirus, suggesting that reactive γ:δ T cells could serve in an innate capacity similar to that of NK cells activated


Immunology_Janeway

Immunology_Janeway. appears to be induced upon stress, such as during infection of cells by cytomegalovirus, suggesting that reactive γ:δ T cells could serve in an innate capacity similar to that of NK cells activated by stress-induced nonclassical MHC class Ib molecules. Several other antigens can activate human γ:δ T cells (see Fig. 6.29), although there is still limited structural information about their interaction with the T-cell receptor, and even reservations about whether such an interaction is always


Immunology_Janeway

Immunology_Janeway. Chapter 6: Antigen Presentation to T Lymphocytes the basis for activation. Among these activating antigens is Skint-1 (selection and upkeep of intraepithelial T cells 1), an immunoglobulin superfamily member that is expressed by thymic epithelial cells and by keratinocytes. Skint-1 seems to be required for the generation of a subset of Vγ5:Vδ1 T cells that develop in the thymus and home to the skin to become ‘dendritic epidermal T cells’ (DETCs). Some evidence suggests a direct interaction between Skint-1 and the γ:δ T-cell receptor, although structural studies are not yet available. Conceivably, DETCs localize to the skin due to recognition by their T-cell receptor of Skint-1 expressed by keratinocytes. There, they might provide a ‘transitional’ mode of immune defense, becoming activated through innate receptors that are triggered locally during infections. Summary.


Immunology_Janeway

Immunology_Janeway. Antigen presentation to various nonconventional T-cell subsets and γ:δT cells generally does not involve the generation of peptide:MHC complexes. Instead, these cells recognize surface proteins, such as ULBPs and RAET-1 proteins, that may indicate cellular stress, transformation, or intracellular infection, or nonpeptide antigens, such as microbial glycolipids or folate metabolites presented by CD1 molecules. The MHC region contains many genes whose structure is closely related to the MHC class I molecules—the so-called non-classical, or class Ib, MHC. Some of these genes serve purposes that are unrelated to the immune system, but many are involved in recognition by activating and inhibitory receptors expressed by NK cells, γ:δ T cells, and α:β T cells. MHC class Ib proteins called CD1 molecules are encoded outside the MHC region. CD1c and CD1d can bind lipids and glycolipid antigens for presentation to iNKT cells expressing invariant T-cell receptors. The T-cell population called


Immunology_Janeway

Immunology_Janeway. molecules are encoded outside the MHC region. CD1c and CD1d can bind lipids and glycolipid antigens for presentation to iNKT cells expressing invariant T-cell receptors. The T-cell population called MAIT cells, which are abundant in humans, recognize vitamin B9 metabolites presented by the MR1 MHC class Ib molecule, suggesting that the MAIT cells have a ‘transitional’ role between innate and adaptive immunity. Likewise, many antigens that activate γ:δ T cells may be indicators of stress or infection, and these cells are able to generate cytokines that amplify immune defense pathways.


Immunology_Janeway

Immunology_Janeway. Summary to Chapter 6. T-cell receptors on conventional α:β T cells recognize peptides bound to MHC molecules. In the absence of infection, MHC molecules are occupied by self peptides, which do not normally provoke a T-cell response, because of various tolerance mechanisms. But during infections, pathogen-derived peptides become bound to MHC molecules and are displayed on the cell surface, where they can be recognized by T cells that have been previously activated and armed for the specific peptide:MHC complex. Naive T cells become activated when they encounter their specific antigen presented on activated dendritic cells. MHC class I molecules in most cells bind to peptides derived from proteins that have been synthesized and then degraded in the cytosol. Some dendritic cells can obtain and process exogenous antigens and present them on MHC class I molecules. This process of cross-presentation is important for priming CD8 T cells to many viral infections.


Immunology_Janeway

Immunology_Janeway. Through assembly with the invariant chain (Ii), MHC class II molecules bind peptides derived from proteins degraded in endocytic vesicles, but they can also acquire self antigens through autophagy. Stable peptides are bound after a process of peptide editing in the endocytic compartment involving HLA-DM and HLA-DO. CD8 T cells recognize peptide:MHC class I complexes and are activated to kill cells displaying foreign peptides derived from cytosolic pathogens, such as viruses. CD4 T cells recognize peptide:MHC class II complexes and are specialized to activate other immune effector cells, for example, B cells or macrophages, to act against the foreign antigens or pathogens that they have taken up.


Immunology_Janeway

Immunology_Janeway. For each class of MHC molecule, there are several genes arranged in clusters within a larger region known as the major histocompatibility complex (MHC). Within the MHC, the genes for the MHC molecules are closely linked to genes involved in the degradation of proteins into peptides, the formation of the complex of peptide and MHC molecule, and the transport of these complexes to the cell surface. Because the several different genes for the MHC class I and class II molecules are highly polymorphic and are expressed in a codominant fashion, each individual expresses a number of different MHC class I and class II molecules. Each different MHC molecule can bind stably to a range of different peptides, and thus the MHC repertoire of each individual can recognize and bind many different peptide antigens. Because the T-cell receptor binds a combined peptide:MHC ligand, T cells show MHC-restricted antigen recognition, such that a given T cell is specific for a particular peptide bound to a


Immunology_Janeway

Immunology_Janeway. antigens. Because the T-cell receptor binds a combined peptide:MHC ligand, T cells show MHC-restricted antigen recognition, such that a given T cell is specific for a particular peptide bound to a particular MHC molecule.


Immunology_Janeway

Immunology_Janeway. Unconventional T-cell subsets include iNKT cells, MAIT cells, and γ:δ T cells, which recognize nonpeptide ligands of various types. Some CD1 molecules bind self lipids and pathogen-derived lipid molecules and present them to iNKT cells. MAIT cells recognize vitamin metabolites that are specific to bacteria and yeast and that are presented by MR1. γ:δ T cells are activated by a diverse array of ligands, including MHC class Ib molecules and EPCR, that are induced by infection or cellular stress. These T-cell subsets function in the transitional area between innate and adaptive immunity, relying on a repertoire of receptors produced by somatic gene rearrangement but recognizing ligands in a manner somewhat similar to the way PAMPs are recognized by TLRs and other fully innate receptors. Questions.