Lecture 10 - Ag Processing

Question 1

What do the MHC polymorphisms affect?

Why?

Answer 1

• The different alleles have different peptide specificities

* Because the MHC binding cleft is affected by polymorphism

Question 2

Where do peptides bind to the MHC binding cleft?

Answer 2

• Anchor residues / side chains on peptide

* Binding pockets in the binding cleft of MHC

Question 3

Can one MHC product bind only one peptide?

Answer 3

No

Peptides that are presented in the same MHC product will have the same binding residues

Question 4

What can be said of non-anchor residues on the peptide?

Answer 4

These are normally involved in the TCR binding

Question 5

Compare, for example, HLA-A2 and HLA-A3, in terms of the binding pocket

Answer 5

HLA-A2: peptides w/ Leu and Val anchor residues

HLA-A3: peptide binding cleft w/ -ve charge → peptide anchor residue w/ +ve charge: Leu and Lys

Question 6

Which structure makes up the MHC peptide binding cleft?

Answer 6

• Two alpha helices (on the sides)

* Beta sheet floor

Question 7

What can be said of the CD4/CD8 binding sites on the various MHC alleles

Answer 7

Largely conserved

• CD4: binds β2 of MHC II
• CD8: binds α3 of MHC I

Question 8

Compare the MHC class I and II binding clefts

Answer 8

Class I: closed binding cleft
→ peptide tucked in

Class II: open binding cleft
→ peptide hangs out

Question 9

Describe the process that turns a protein into ‘peptide’ for presentation

Answer 9

• Protein: many antigens
• Proteolysis of protein into several peptides
• Individual peptides presented by MHC

Question 10

Why does it sometimes occur that there is no T cell response to an antigen?

Answer 10

The antigen could not be bound by MHC

Thus, T cells were not activated by APC’s, and there was no cellular response

Question 11

Compare the terms ‘polygeny’ and ‘polymorphism’, and describe the effect of them on the immune response

Answer 11

Polygeny: presence of different versions of a gene within a person; e.g. HLA-A, HLA-B, HLA-C

Polymorphism: presence of different alleles in the population

These different versions increase the likelihood that a peptide can be bound by MHC for activation of the cellular response

Question 12

Compare the types of antigens that Th and CTLs direct their responses against

Answer 12

CTLs
• ‘Endogenous antigens’
• virus, tumour, transplantation antigens

‘Helper’ T cells
• ‘Exogenous antigens’
• bacterial antigens, soluble protein antigens

Question 13

Outline the MHC Class II antigen processing pathway

Answer 13

• Antigen taken in by endocytosis
• Degradation in endolysosome
• Fuses with vesicle from ER that contains MHC II
• Binding of peptide to MHC II
• Trafficking of MIIC compartment to the cell surface

Question 14

Outline the MHC Class I antigen processing pathway

Answer 14

• MHC I made in ER, and is retained there until peptide binds
• Intracellular gene (host or virus)
• Intracellular antigen (IA)
• IA degraded by proteosome
• IA enters ER through TAP
• MHC I in ER binds the peptide

Question 15

What is the MIIC compartment?

Answer 15

Peptide-binding vesicle

Question 16

How is antigen ‘captured’ for processing in the MHC II pathway?

Answer 16

1. Receptors on cell surface
   • Surface bound Ab; Antibody-mediated endocytosis
   • Ab bound to FcR on cell surface
2. Simple endocytosis of antigen

Question 17

What are the benefits of antibody mediated endocytosis of antigen?

Answer 17

Better Th - B cell interaction

1. B cell; surface bound Ab binds antigen
2. Endocytosis, processing → presentation of antigen on MHC II
3. Th cells recognise antigen with TCR
4. T cell help for B cell

Question 18

Which molecules are really important for Ag presentation in MHC II?

Answer 18

• Invariant chain

* HLA-DM

Question 19

What is HLA-DM?

Answer 19

• A dimeric, MHC II-like molecule
• Present in MIIC compartment
• Important role in loading of peptide into MHC II
• through the removal of CLIP

NB it is not a surface MHC molecule, and thus does not actually present antigen itself

Question 20

What is Ii and what is its importance?

Answer 20

Invariant Chain
• Binds the peptide binding groove in MHC II in the ER
• Targets the MHC II to the endosomal compartment → MIIC compartment formation

NB In Ii KO mice, there is greatly reduced surface MHC II expression on APC’s

Question 21

What are MHC II peptide binding grooves predominantly occupied by before the peptide antigen is loaded?

Answer 21

CLIP:
• Class II associated Invariant chain Peptide
• It is the part of Ii that is left in the binding groove of MHC II after degradation of the Ii

Question 22

What is TAP?

Describe its function and some features

Answer 22

Transporter associated with Antigen Processing
• transports peptides from the cytosol into the ER
• binds ATP

• encoded by gene within MHC I region
• expression of different components upregulated by IFN-γ

Question 23

What is MHC restriction?

Answer 23

A given T cell will only be able to recognise one of the types of MHC

Question 24

Compare the length of peptides that are loaded into MHC I and MHC II

Answer 24

MHC I : length fairly uniform

MHC II: length is far more variable

Question 25

What is different about the different alleles of MHC molecules?

Answer 25

Different binding pockets

Question 26

Who is polygeny important for?

Answer 26

An individual

Question 27

What happens to Ii once the MHC II gets into the endosome?

Answer 27

It is degraded.

However, CLIP remains (HLA-DM needed to get rid of CLIP)

Question 28

Where are proteins degraded in the MHC I processing pathway?

Answer 28

In the cytosol, in a proteasome

Question 29

Describe some features of the proteasome

What changes occur during viral infection?

Answer 29

• Large, multi-subunit
• In the cytosol
• Highly conserved (also seen in bacteria)

Viral infection:
• There are alternate subunits that are used in immune responses whose expression is upregulated by IFN-γ
• These up-regulated subunits increase the activity of the proteasome, so that there is more antigen presentation

Question 30

What molecule is required for TAP function?

Answer 30

ATP

Question 31

Describe how B cells present exogenous antigen

What are the benefits of this?

Answer 31

1. Capture antigen w/ surface bound Ig
2. Receptor mediated endocytosis
3. Degradation of antigen into epitopes
4. Combination of MHC II from ER with epitope in MIIC
5. Trafficking to surface for presentation

Ig receptor mediated endocytosis facilitates:
• B cell-Th cell interaction

Question 32

Is HLA-DM a monomer or a dimer?

Answer 32

Dimer

Question 33

Describe the structure of TAP

Answer 33

Heterodimeric: TAP1 / TAP2

Question 34

Describe some features of peptides that TAP transports into the ER

Answer 34

• 8-16 aa in length

* Hydrophobic C-terminal residues

Question 35

Under what conditions is TAP expression upregulated?

Answer 35

IFN-γ

Viral infection

Question 36

What are Lmp2, Lmp7, MECL1 and PA28?

Answer 36

Alternate proteasome subunits

• Seem to have a role in antigen processing
• Not normally expressed in cells
• Expression upregulated by IFN-γ

• Preferentially generate peptides ideal for transport into ER with TAP:

• 8-16 aa in length
• C-terminal hydrophobic residues

Question 37

What can interference with antigen processing lead to, in terms of MHC I expression?

Answer 37

MHC I is retained in the ER until peptide is bound to it

If there is interference with antigen processing, peptides are not being loaded onto MHC I, and thus, there is a reduced presence of MHC I on the cell surface

Question 38

Which pathway of antigen processing is ‘endosomal’ and which is ‘cytosolic’?

Answer 38

MHC class I: cytosolic

MHC class II: endosomal