Chapter 5

Antigen Presentation to T Lymphocytes

Review:�Two antigen-specific receptors: the TCR and the BCR.

TCR “sees” antigens that were inside cells and that are displayed on the surface by MHC molecules.

*Antigen Processing is the modification of native proteins into peptides for presentation by MHC

MHC class I presents processed proteins* that were in the cytosol.�MHC class II presents processed proteins* that were in endocytic vesicles.

MHC class I presented-antigens are recognized by CD8⁺ T cells (CTL).�MHC class II presented-antigens are recognized by CD4⁺ T cells (T_H).

Basic cell structure

(ER)

Inside of a cell, pathogens and their products are found in either the cytosol or in vesicles

Mostly viruses but some bacteria

Mostly bacteria, common bacterial products (less likely to be toxins and viruses), self junk

Bacteria, bacterial products, viruses (anything that is antigenic)

and more (see chpt. 2)

after recognition by an appropriate T cell

Dendritic cell

This slide is missing the very important antigen presentation by dendritic cells: Degrade in vesicles; peptides bind to MHC II, presented to naïve CD4 T cells, activates naïve CD4 T cells

How do cytosol peptides get associated with MHC class I (and not with MHC class II)?

Peptides (made from proteins by proteosomes; next slide) are pumped from the cytosol into the endoplasmic reticulum (ER) by transporters associated with antigen processing (TAP) molecules

In the cytosol, proteins are degraded into peptides by proteasomes

Proteasomes are multicatalytic protease complexes made of ~28 subunits

2004 Nobel Prize in chemistry for the role of ubiquitin in protein recycling

Peptides are made from proteins in the cytosol, transported into the ER, loaded into MHC class I and transported to the surface of the cell

Which cells do this?

peptide

MHC class I

Some viruses evade the immune system by inhibiting or blocking antigen presentation by MHC class I

Peptides that are destine for MHC class II are taken up from the outside of the cell and are degraded into peptides in acidified endocytic vesicles

Class II-associated invariant-chain peptide (CLIP)

The invariant chain

The invariant chain prevents MHC class II from acquiring peptides too soon

Which cells do this?

Endosome containing degraded protein (i.e., peptides) fuses with endosome containing MHC class II

Peptides binds to MHC class II. MHC class II + peptide are displayed on the cell surface

More on the Major Histocompatibility Complex Genetics and Function

MHC class I

MHC class II

MHC class I and class II are polygenic �(several loci encoding products with essentially the same function)

α chain

α chain

α chain

Class II

β₂ microglobulin is not encoded in MHC

Class I

A more detailed look at MHC

More DNA than most bacterial genomes

kb

MHC class I and class II are polymorphic [variability at a gene locus at a frequency higher than predicted by chance (i.e., variability of alleles in the species)]

The number of known alleles at various MHC loci seems to increases over time (why?)

MHC class I

MHC I α chain

DPB, DQB and DRB are the MHC II β chain

DPA, DQA and DRA� are the MHC II α chain

MHC is polymorphic and expression is co-dominant

What does this mean�for you and your species?

for example, here is HLA class I A gene expression

Although there are thousands of combinations in the population*, there are only 4 combinations among siblings

414 known HLA-A alleles in humans (previous slide) but a maximum of 2 per person

A^b/r

A^y/g

A^b/g

A^r/y

A^b/y

A^r/g

*At A there are 414 known alleles so there are (414)² = 171,396 pair combinations possible in the species (although not all combinations exist)

Because MHC loci are polymorphic, individuals are rarely homozygous at any of the (polygenic) MHC class I and II loci

Lots of alleles in the species

In an individual, several non-allelic genes with essentially the same function (B, C and A are all MHC class I and present peptides to CTLs)

A^r

A^y

B^r C^y A^p

B^r C^y A^p

All expressed on all nucleated cells (co-dominant)

Why Polymorphism and Polygenism in MHC?

Polymorphism and polygenism in MHC make it impossible for a pathogen to alter its antigenic epitopes so that the epitopes cannot be presented by a majority of the individuals in a population.

Most individuals have six MHC class I proteins (and at least 6 MHC class II) so if one MHC protein cannot present a pathogen’s antigens, another MHC protein probably can.

Each species has thousands of way to present antigens from a pathogen so, even if some individuals (or small populations) cannot efficiently present some antigens, the species is not at risk.

Haplotype: a linked set of genes associated with one haploid genome

Common mouse MHC haplotypes

We will commonly use the term MHC^a or MHC^axb.

H-2^a

H-2^b

H-2^d

H-2^f

MHC^a when both MHC haplotypes in an individual are exactly the same (MHC^a/a). MHC^axb as the offspring when a MHC^a individual is crossed with an MHC^b individual (MHC^a/b)

K^k

K^d

Skip this slide

DP DQ DR B C A

HLA^a a/a a/a a/a a/a a/a a/a�HLA^b b/b b/b b/b b/b b/b b/b�HLA^a/b a/b a/b a/b a/b a/b a/b

Class II Class I

If written as MHC^a or HLA^a, it is to be assumed that the other allele is identical (i.e., MHC^a/a or HLA^a/a and

MHC^a or^�MHC^b or^�MHC^a/b or

MHC^axb = MHC^{a/b =} MHC^(axb)F1

Generic term

Human specific term

Haplotype: a linked set of genes associated with one haploid genome

MHC^a/a = MHC^a )

(MHC Restriction)

Yes

MHC^a

No

MHC^a

Yes

MHC^b

No

MHC^b

MHC Restricted Recognition of Antigen by T cells

Zinkernagal and Doherty, 1974

This figure is not in the text

Target Cell used in In Vitro Killing Assay

(MHC Restriction)

Source of CTLs

H-2^a

H-2^d

H-2^k

H-2

Mapping the MHC restricted recognition of antigens by CTLs

Experiment: Take CTLs from a virus-immunized H-2^d mouse and test on virus infected targets of the H-2^d, H-2^a and H-2^k haplotypes*.

Result: H-2^d and H-2^a cells are killed. H-2^k cells are not killed.

Conclusion: Killing maps to the right of Ea (blue line).��Other experiments show that CTL killing is restricted to MHC class I�

* All mice in this experiment have the same background (non MHC) genes

Killed by H-2^d CTLs

Killed by H-2^d CTLs

Not killed by H-2^d CTLs

Results of killing assay

targets

It is okay to skip this slide

The Zinkernagel & Doherty experiment showed that CTL killing is not only antigen specific, it is specific for the MHC haplotypes of the individual. Later experiments mapped killing into MHC class I and T_H activity into MHC class II*. �Thus, TCRs are specific for the antigen AND for allele-specific determinants of MHC class I OR class II�(i.e., MHC restricted-recognition of antigen)

[Dual recognition vs. altered self (new antigenic determinants; NAD)]

MHC polymorphism affects which antigens can be presented and which T cells can recognize antigen

*Although we have not shown experiments demonstrating MHC restricted recognition of antigens by T_H1 and T_H2 cells, T_H recognition of antigens is also MHC restricted (restricted to allele-specific determinants of MHC class II)

determinants

allele-specific

This shows one of an individuals two HLA (MHC) loci

This shows both of an individual’s two HLA class I (MHC class I) loci and shows different alleles at each of the three class I genes. The uppercase letter is the gene the lowercase superscript is the allele. HLA is on chromosome 6. Each of us has one chromosome 6 from mother and another from father.

This slide deals only with class I but essentially everything is the same for T cells that bind antigen presented by class II.

There will be some T cells that bind antigen only when it is presented in association with B^x. Other T cells will bind antigen only when present in association with A^w. In all, there are 6 different MHC class I proteins in an individual and thus 6 ways to present antigen. An individual T cell can bind antigen only when it is presented by one of the 6 MHC proteins (the T cell are restricted to allele-specific determinants of MHC). The T cell are, of course, also specific for the antigenic peptide. A T cell receptor has 2 specificities, antigenic peptide and allele-specific determinants of MHC.� Since MHC is polymorphic, how do the T cell know what MHC type is expressed by self? The answer to this question is yet to come.

How is genetic polymorphism generated?

Gene conversion in the germ line

High crossover rate

When compared to similar events at other loci, these germ line events are relatively common in MHC: however, they are still quite rare. Somatic rearrangements are of no consequence

Over evolutionary time, many gene conversion events to generate polymorphism in the species

MHC polymorphism in the peptide binding groove explain the preference of different MHC proteins for different sequence motifs.

Polymorphisms on the top of MHC show how TCRs recognize MHC- allele-specific epitopes for restricted recognition of antigens

For MHC class I, α1 and α2 domains are polymorphic; � the α3 domain has relatively low polymorphism; β₂microglobin is not polymorphic�For MHC class II, α1 and β1 domains are polymorphic;� α2 and β2 domains have relative low polymorphism

Allelic variation in MHC occurs at the peptide binding site and on the top/sides of the binding cleft

How do you explain alloreactivity? Why?

There is extraordinary high immune reactivity to allogeneic (same species, non-self) MHC. (thus the name MHC). 1-10% of T cells will react to any given allogeneic MHC (alloMHC).

Superantigens

TCR

MHC

superantigen