L3 - Genetics of antigen recognition receptors (TCR & MHC)

Question 1

How are TCR polypeptides encoded?

Answer 1

By rearranging genes

Variable regions encoded by V, (D) & J segments

Gene segments rearrange during T cell development in the thymus (not bone marrow)

Question 2

Gene segment rearrangement during T cell development in the thymus

Answer 2

Once they get into the thymus they turn on RAG1 & RAG2 genes & start doing this process in the thymus

Question 3

What happens if you have mutations in RAG genes?

Answer 3

Patients with mutations in RAG1&2 will have no T cells as well as no B cells – so will have no acquired immune system – SCID

Question 4

Generation of diversity in TCR

Answer 4

Similar mechanisms to Ig

Multiple V, (D) & J gene segments
Combinational diversity
Junctional diversity

However, no somatic hypermutation occurs in TCR genes

Question 5

TCR generation

Answer 5

The different components of the variable regions are spaced out in the genome

The genes get closer together by breaking & repairing

There are no D regions in the alpha – only V & J

Alpha chain can then bind to the beta chain

Beta chain has a D region

End up with a receptor that has a high variability in the antigen recognition site

Recognises peptides displayed my MHC molecules

Question 6

What other chains can T cells express other than alpha & beta?

Answer 6

Can also be gamma or delta – from the same chromosomes

They either express one or the other sets

Question 7

MHC diversity

Answer 7

No gene rearrangement occurs

Genes located within MHC (HLA in humans on chromosome 6)

Don’t have allelic exclusion on MHC molecules – MHC molecules can be made from each chromosome & can be co-dominant (heterozygous)

Question 8

MHC expression on class I & II

Answer 8

Class I expressed by all nucleated cells

Class II expressed on particular cell types – APCs (B cells, macrophages & dendritic cells)
– Up-regulated & induced by interferon

Question 9

Gene structure of the human MHC

Answer 9

Class I region – where class I genes live

Class II region – where class II genes live 
– Are dimers – HLA:DP-DQ-DR: have an alpha & beta chain gene for each 

Class III region – other genes that are related to the immune system but not related to MHC

Question 10

Dimers that make up class II MHC

Answer 10

DP has alpha & beta gene
DQ has alpha & beta gene
DR has an alpha & 2 beta genes

Question 11

Whats the most MHC an individual can have?

Answer 11

A single individual will have up to 12 different MHC molecules (if they’re heterozygous for all 6 MHC loci)

Question 12

What are polymorphic genes?

Answer 12

Can be a single base pair different

MHC molecules are the most polymorphic genes known

Question 13

Co-dominant expression of MHC molecules

Answer 13

3 MHC class I molecules (HLA-A, HLA-B and HLA-C)

If heterozygous at each loci, one person can express six different class I molecules

Similarly, for class II (HLA-DP, HLA-DQ and HLA-DR)

Question 14

Where are polymorphic residues within MHCs located?

Answer 14

Polymorphisms are within the peptide binding groove – affects the ability to bind peptides

Question 15

Reason for such high levels of MHC polymorphism

Answer 15

Allows the binding if a vast range of peptides that can be presented to T cells – provides a clear evolutionary advantage to the population

Question 16

Disadvantages of high levels of MHC polymorphism

Answer 16

Increases risk of many immune-mediated diseases

Makes selection of suitable donor organs for transplantation very complex & inefficient

Question 17

How do peptides end up on the surface of cells bound to MHC molecules?

Answer 17

ANTIGEN PROCESSING & PRESENTATION

Question 18

Antigen processing and presentation in MHC

Answer 18

MHC molecules present the peptides

Before they do that the cells that express the MHC have to process the antigen to allow the peptides to fit in the groove of the MHC molecules

Question 19

Endogenous antigens

Answer 19

If a cell makes a protein that’s going to be put on a MHC it goes onto a MHC I molecule

If a cell is infected with a virus, the cell starts to make the viral proteins – proteins will be loaded onto the class I as its made within the cell

When the cells not infected, the proteins are from its own proteins – class I

Question 20

Exogenous antigens

Answer 20

APCs take things up from the outside of cells – generate peptides from wheat they’ve taken up

Load peptides onto MHC II molecules

APCs capture antigens & express them

Question 21

Presentation of Ag by MHC I molecules

Answer 21

1. Ag (eg. viral protein) synthesised in cytoplasm
2. Protein cleaved to peptides by proteasome
3. Peptides transported to endoplasmic reticulum by TAP transporter
4. Peptides bind to MHC I molecules
5. MHC-I/peptide complex then transported to cell surface

Question 22

Where are class I MHC when theres no peptides?

Answer 22

Stays in the ER

Question 23

Where are class I MHC where there are peptides present?

Answer 23

Peptides go through the TAP transporter & binds to class I

Once it binds it changes its shape & releases these chaperones & class I can leave via a vesicle to go to the cell surface

Question 24

Presentation of Ag by MHC II molecules

Answer 24

1. Ag endocytosed into intracellular vesicles inside the cell
2. Protein cleaved to peptides by acid proteases in vesicles in the endocytic pathway
3. Vesicles fuse with vesicles containing MHC II molecules
4. Peptides bind MHC II molecules
5. MHC-II/peptide complex then transported inside vesicle to cell surface in the endocytic pathway

Question 25

Why doesn’t class II bind peptides in the ER??

Answer 25

Has an invariant chain bound in its binding cleft which stops peptides getting into the cleft while still in the ER - stops class II going to the cell surface

Invariant chain has a sequence in its cytoplasmic tail which takes it into the endocytic pathway where enzymes can chop up the invariant chain – leaves the CLIP peptide associated with the binding groove

Peptides from antigen displace CLIP when they bind

HLA-DM, a class II-like molecule, is required for loading of peptides into the groove

Question 26

Function of the invariant chain?

Answer 26

Invariant chain protects the class II MHC from picking up peptides that are expressed by MHC I

Question 27

What molecule is required for loading of peptides into groove of class II MHC?

Answer 27

HLA-DM
A class II-like molecule

Question 28

What happens with MHC in normal healthy uninfected cells?

Answer 28

MHC I & II molecules will bind & present peptides from self-proteins

Question 29

What are the accessory molecules in antigen processing & presentation?

Answer 29

DM (alpha&beta) – takes invariant chain off class II & puts peptides on

TAP – delivers peptides to the ER for class I MHC

LMP – encodes subunits for the proteasome

Question 30

Where are the accessory molecules encoded?

Answer 30

Encoded within the MHC

Kept evolutionary together – all involved in antigen processing

Question 31

APCs

Answer 31

As all nucleated cells express MHC I, any cell infected with a virus can present viral peptides on the MHC I & be recognised & killed by cytotoxic CD8+ T cells

Only APCs express MHC II which take up & present extracellular Ag to activate helper CD4+ T cells