7 - The MCH and Ag Presentation

Question 1

MCH class I structure

Answer 1

one large glycoprotein heavy chain + a small protein light chain.

2 polypeptide chains: α and β (β is called β2-microglobulin). The α is organized in 3 external domains (α1, α2, α3) of approx 90 AA each; a transmembrane domains (25 hybdrophobic AA) followed by a short stretch of chargen hydroohilic AA, in addition to a cytoplasmic anchor segment of abour 30 AA. β2-microglobulin is not transmembrane, but noncovalently bound to the α chain.

between the α1 and α2 domains there is a groove (peptide-binding groove), large enough to bind a peptide of 8-10 AA.

α3 and β2-microglobulin are similar in structure, and similar to the Ig domains.

Question 2

MCH class II structure
αβγδ

Answer 2

composed of two noncovalently associated transmembrane glycoproteins (one α and one β chain) with similar structures. The extracellular domains together form a binding pocket accomodating peptides of approc 13-18 AA in length.

MCH class I and II are structurally and functionally similar, despide being encoded differently.

Question 3

Class I and II exhibit polymorphism in the region that binds to peptides

Answer 3

one individual can express 6 different alleles of class I and 12 of class II

Any given MCH molecule can bind numerous different peptides, and some peptides can bind to several different MCH molecules.

Class I and II share some common peptide-binding features. In both types; peptide ligands are held in largely extended conformation that runs the length of the groove. The peptide-binding groove in class I is blocked at both ends, and they are open in class II. Result = class I can bind shorter than II

Question 4

MCH class I-peptide interaction

Answer 4

bind from intracellular sources, present to CD8+ T cells. The bound peptides have some similarities: all 8-10 AA (most 9, aka nonamers), and they contains specific AA residues at key locations in the sequence. The MHC molecule’s ability to bind these peptides is due to the presence of same or similar AAs in these positions. They are called “anchor residues” for obvious reasons. The side chains of the anchor residues in the peptide are complementary with surface features of the binding groove of the MHC class I molecule. The AA residues lining the binding sites vary among alleles of the MCH class I molecule, and this is what determines the chemical identity of the ancor residues that can interact with a given class I molecule.

several unique MCH class I molecules can be expressed in the same individual. This means that although many of the peptide fragments of a given foreign agent will be presented to CD8+, the particular set of MCH class I alleles inherited by each individual will determine which specific set of peptide fragments from a larger protein will be presented.

Key positions for anchor residues = 2 and/or 3 + 9. they tend to be hydrophobic. The anchor residues are buried deep within the binding groove, thus holding the peptide firmly in place. Between the anchord, the peptide can “arch” outwards, leaving this region more exposed and presumably can interact more directly with the TCR.

Question 5

MHC class II-peptide interactions

Answer 5

also binds a variety of peptides

present to CD4+ cells

the open ends allow longer peptides to extend past them, like a hot dog

open ends + less conserved nature = greater variability in the seq and length of the class II-bound peptides. It seems a central core of 13 AA on the peptide determines the ability to bind to MCH II.

the peptides that bind to class II often have internal conserved seq motifs, but unlike class I-binding peptides they appear to lack conserved anchor peptides. Instead, H-bonds between the backbone of the peptide and the MCH II are distributed throughout the whole binding site. 7-10 internal AA of the peptide provide the major contact points.

Question 6

The organization and ingeritance of MCH genes

Answer 6

BCR and TCRs use recombination to make sure a wide variety of Ags can be bound tightly.

MCH relies more on the promiscuity of the peptide binding + several different MCH molecule variants on every cell.

MCH genes are in a MCH gene cluster.

Question 7

The MHC locus encodes the three major classes of MHC

Answer 7

chromosome 6 in humans.

MHC is aka HLA (human leukocyte antigen)

two main types: classical and nonclassical MHC genes

Question 8

Classical MHC genes

Answer 8

3 groups/classes:

MHC class I genes encode glycoproteins expressed on the surface of nearly all nucleated cells; the major function of these gene products is the presentation of endogenous peptide Ags to CD8+ cells.

MHC class II genes encode glycoproteins expressed predominantly on APCs, where they primarily present exogenous peptide Ags to CD4+ cells.

MCH class III encode a diverse set of proteins, some of which have immune functions, but that do not play a direct role in presenting Ags to T cells.

The class I was first discovered, are expressed on the wides range of cells. Protein products can be found in virtually every nucleated cell in humans and mice. human gene region = continous. In humans, the HLA-A, -B and -C loci encode the MHC I genes. β2-microglobulin is encoded outside of the MHC locus, on another chromosome (15 in humans). the α-chains are reffered to as classical class I molecules; all possess the functional capability of presenting protein fragments of Ag to CD8+ cells.

MCH II shows lesser tissue variation, and more varied expression levels. primarily on the pAPCs. Encoded in HLA-DP, -DQ and -DR loci in humans. All three loci have a coding seq for α and β chain (sometimes multiple). Can have more than one DR β-chain gene on one or both chromosomes, all expressed at the same time. Any DR α-chain gene product can pair with any of these, giving many possible combinatons, allowing for several unique MHC class II DR molecules on the cell.

class III has no structural or functional similarities to the other tow classes. these proteins are involved in other immune functions. Includes C2, C4, fabtor B, cytokines, and more.

Question 9

Nonclassical MHC genes

Answer 9

nonclassical class I proteins are only expressed on some cell types, but seem to be important in distinguishing self/nonself.

class II: 
DO and DM. DO are invilved in Ag processing and presenting. DM encode a class II-like moelecule that facillitates the intracellular loading of antigenic peptides into MHC class II molecules.

Question 10

Allelic forms of MHC genes are inherited in linked groups

Answer 10

MCH genes are both highly polymorphic and tightly linked, so that the set of alleles within the entire MHC locus is generally passed down as one unit; one such linked set of MHC alleles inherited from a parent is called a haplotype

Question 11

MHC molecules are codominantly expressed

Answer 11

both haplotypes are expressed at the same time in the same cell.

Question 12

Class I and class II molecules exhibit diversity at both the individual and species level

Answer 12

MHC region is polygenic (has HLA-A -> -C in class I and -DP, DQ and DR in class II), as it contains multiple genes with the same function but with slightly different structures.

In an individual that is fulle heterozygous, the codominance will enable the expression of six unique classical class I molecules on each nucleated cell, allowing for the presentation of many peptides.

Class II has even greater potential for diversity, as each is made up by one α and one β chain, which can combine in different ways. 12 different class II combinations.

Species diversity at the MHC locus imparts an evolutionary survival advantage against mortality from infectious disease.

Question 13

MHC polymorphism is primarily limited to the Ag-binding groove

Answer 13

Polymorphic residues in MHC alleles cluster in the peptide-binding pocket, influencing the fragments of Ag that are presented to the IS, and thereby influencing susceptibility to a number of diseases.

Question 14

MHC class I expression is found throughout the body

Answer 14

level of expression varies between cell types. Highest: lymphocytes. lowest: fibroblasts, mucle cells, liver hepatycytes, and some neural cells. liver transplants are very successful, probs bc of this. red blood cells (nonnucleated) do not have MHC. Normally, MHC class I present self-peptides to signal that all is well. If virus infected, some viral proteins will also be presented here. Altered self cells like cancer cells, aging cells or cells from an allogenic graft (tissue from a genetically different individual) can also have defect or foreign proteins in the MHC I.

Question 15

Expression of MHC class II

Answer 15

primarily pAPCs. non-pAPCs can also be stimulated to express.

DCs constitutively express MHC II, and have costimulatory activity so they can activate naïve TH cells

Macrophages must be activated before they express MHC II or costimulatory molecules such as CD80/60.

B cells constitutively express MHC class II molecules, although at low levels, and posess Ag-specific surface receptors. This makes them aprticularly efficient at capturing and presenting their cognate Ag, or the specidic epitope recognized by their BCR.

Question 16

MHC expression can change with changing conditions

Answer 16

class I constitutively expressed in most cells. class II not so much. Mechanisms for changes in MHC expression:

1) genetic regulatory components
the presence of internal or external triggers (invaders or cytokines) can induce a signal cascade leading to changes in MHC gene expression. both MHC class I and II genes are flanked by 5' promoter seq that bind seq-specific TFs. regulation can be mediated by both positive and negative elements. NLRs function as core components of the MHC transcriptional activators (CITA) for both I and II. defects in these TFs can cause bare lymphocyte syndrome, causing lack of MHC II and severe immunodeficiency. 

2) viral interference
certain viruses interfere with MHC I expression, and thus avoid detection by CD8+. F:ex. hepB and adenovirus 12, cytomegalovirus. in the latter case, a viral protein binds to β2-microglobulin, preventing assembly of the MHC. adenovirus 12 decreases expression of the transporter genes TAP1 and TAP2 (important for Ag processing and presenting.

lack of changes in MHC I will lead to the immune system not realizing that something is wrong in a cell.

3) Cytokine-mediated signaling
IFN-α,β, γ + TNF increase MHC class I . IFNα + TNF are often first. 

Binding of these cytokines can also increasing MHC II on cells, including non-pAPCs. Happens via signalling cascades (du kan dette, orker ikke skrive det).

Other cytokines influence MHC expression in only some cell types. IL-4 increases class II in resting B cells. IFN-γ downregulates MHC II in B cells, along with corticosteroids and prostaglandins.

Question 17

MHC alleles play a critical role in immune responsiveness

Answer 17

MHC haplotype plays a strong role in the outcome on an immune response, as these determine which fragment of the protein will be presented. MHC class II activate TH cells, which in turn stimulate B cells to produce Abs.

The immune responsiveness to MHC class II genes reflects the central role of determining which specific peptide fragments of a foreign protein will be presented as an Ag to TH cells.

Two main explanations for the variability in immune responsiveness between different haplotypes:
1) determinant selection model.
Different MHC II differ in their ability to bind particular processed Ags. In the end, some peptides may be more cruical for the eleimiation of a pathogen than others. The ability of an organism to present these cruicial fragments would give them an advantage

2) holes-in-the-repertoire model
postulates that T cells bearing receptors thar rec certain foreign agents, which happen to closely resemble self-antigens, may be eliminated during T cell maturation, leaving the organism without these cells/receptors that may be important for future responses to particular foreign molecules.

These models are not mutually exclusive, and in fact both appear to be correct.

Question 18

Studies demonstrate that T cells recognize peptides presented in the context of self-MHC alleles

Answer 18

1) both CD4+ and CD8+ T cells can rec Ags only when presented in the groove of an MHC.
2) the MHC haplotype of the APC and T cell must match. This happens naturally in the host, where T cells develop alongside APCs, and express the host MHCs. T cells are also tested against host cells, where they must interact with MHCs to be able to live.

Question 19

The endogenous pathway: peptide generation

Answer 19

Peptides are generated by proteasomes
intracellular proteins are degraded into short peptides by the proteasome (present in all cells). The lareg (20S) proteaseome is composed of multiple α and β subunits. Ubiquitin is a small protein that marks other proteins for proteolysis. these enter the proteasome complex (20S base + 19S regulatory component) through a narrow channel at the 19S end. the complex cleaves peptide bonds in an ATP-dependent process.

pAPCs or infected cells can temporarily express immunoproteasemes, which generate peptide fragments that are optimized for MHC class I binding. replacement catalytic protein subunits convert proteasomes into immunoproteasomes.

Question 20

The endogenous pathway : peptide-MHC association

Answer 20

a transmembrane protein in the ER called TAP (transporter associated with antigen processing) is required to transport the peptides of approximately the right size into the lumen of the rough endoplasmatic reticulum (RER), where they can associate with newly formed MHC class I molecules.

The translocation requires hydrolysis of ATP. TAP has affinity of peptides 8-16 AA long, but the MHC wants 8-10 (mostly 9). ERAP (ER aminopeptidase) trimmes the longer peptides. TAP also favors peptides with hydrophobic or basic C-terminal ends, the preferred anchor residues.

Question 21

the endogenous pathway: peptide assembly with MHC class I molecules

Answer 21

In the RER, chaperone proteins and proteases assist with the loading and processing of peptide fragments as they associate with MHC class I molecules, stabilizing this protein complex and allowing peptide-loaded MHC class I molecules to move out of the RER and toward the cell surface.

The α and β chains of the MHC I molecule is synthetized in ribosomes, and needs to be presented with a peptide in the binding groove before it can exit the RER to the membrane. This requires several chaperones

calnexin (resident membrane protein of the RER). associates with ERp57 (protein with enzymatic activity), and then associate with the alpha chain to promote proper folding. when beta binds to the alpha chain, calnexin is released and the complex (class I + ERp57) binds calreticulin and tapasin (TAP-associated protein). Tapasin brings TAP into proximity with the class I molecule before the peptides are exposed to the luminal environment of the RER. if the peptide is too long, exoproteases step in (like ERAP1).

Question 22

The exogenous pathway: entry

Answer 22

multiple possibilites:

• phagocytosis
• receptor-mediated endocytosis
• pinocytosis (nonspecific “cell-drinking”)

One thing in common: the internalized components gain acces to the cell but remain bound by a phospholipid bilayer structure.

Question 23

The exogenous pathway: peptide generation

Answer 23

typically degraded within the compartments that make up the endocytic processing pathway. The endocytic Ag-processing and presentation pathway appears to involve several increasingly acidic compartments: early endosomes (pH 6,0-6,5), late endosomes (4,5-5) and lysosomes (4,5). Each of these compartments contains proteases, and degrade the proteins into peptides 13-18 AA.

not really clear how it moves between these compartments.

Question 24

The exogenous pathway: transport of MHC II to endocytic vesicles

Question 24

The exogenous pathway: transport of MHC II to endocytic vesicles

Answer 24

APCs have both class I and class II, so there must be a mechanism to prevent them bidnign to each others peptides. when MHC II are synthetized in the RER, they associate with a protein calles invarian chain (Ii). this interacts with the peptide-binding groove of MHC II, thus blocking it from accepting peptides while in the RER. Ii also helps the transport of MHC class II to late endosomes, where they encounter their peptides.

Question 25

The exogenous pathway: MHC class II-peptide assembly

Answer 25

The Ii is gradually processed into a smaller fragment called CLIP, that blocks the peptide-binding groove of classical class II molecules in the late endosomes, where HLA-DM (nonclassical class II molecule) mediates exchange of CLIP for antigen fragments

the presence of HLA-DO another nonclassical class II molecule, in some pAPCs (specifically DCs) may regulate the activity of HLA-DM and encourage class II presentation of self-peptides in a manner than encourages self-tolerance.

Question 26

Unconventional Ag processing and presentation

Answer 26

exogenous peptides can be presented on MHC I. cytosolic protein fragments can be associated with MHC II (via autophagy).

cross-presentation = blending the exo- and endogenous pathways. The phenomenon of cross-presentation requires that antigens acquired from extracellular sources, normally handled by the exogenous pathway leading to MHC II presentation, are redirected to a class I peptide loading pathway. WHen this form of Ag-presentation leads to the activation of a naïve CD8+ cell, it is called cross-priming. when it lead sto the induction of tolerance in a CD8+ cell (like when the APCs are not activated), it is called cross-tolerance.

Cross-presentation by APCs (especially DCs) is essential for the activation of naïve CD8+ cells
two possible models for how DCs accomplish cross-presentation. 
1) cross-presenting cells possess special Ag-processing machinety that allows loadingn of exogenously derived peptides onto MHC class I molecules. 
2) specialized endocytosis machinery that can send internalized Ag directly to an organelle (phagosome or endosome), where peptides from those AGs are then loaded onto MHC class I molecules.

Cross-presentation = process by which pAPCs, particularly DCs that have been activated and licensed by Ag-specific TH cells, divert exogenously acquired Ags into class I molecules (crossing endogenous and exogenous pathways), allowing acgivation of CD8+ TC cells; the responses of these cells are responsible for destroying other virally infected target cells that express this same peptide-MHC combination.

Great advantage - activates cytotoxic T cells. Not all APCs do it however, as the ones that do become targets for lysis.

Question 27

“licencing” of DCs for cross-presentation

Answer 27

classical exogenous pathway of Ag processing in DCs leads to the presentation of Ag to CD4+ T cells via class II, leading to activation of these cells. The activated TH cells can also return the favor by inducing costimulatory expression in the DC and by secreting stimulatory cytokines (IL-2). this results in a “licenced” DC.

If unactivated and unlicenced DCs cross-present, it may induce tolerance (dampen reactivity to self-Ags and maintain self-tolerance).

Question 28

Presentation of non-peptide Ags

Answer 28

mycolitic acid and other small lipid-containing Ags are presented by CD1 family and MHC class I-related protein (MR1). these are encoded outside the MHC clusters.

CD1 and MR1 share structural similarity with MHC class I but have more of a functional overlap with class II. They present to αβ and γδ T cells, and NK cells.

CD1 and MR1 have limited variability, and serve to regulate immune homeostasis as well as control some infectous agents at mucosal surfaces.