Lecture 6- Genetics of Antigen Receptors (sorry this is really shit-edit if you understand it a bit better)

Question 1

How are innate immunity and adaptive immunity encoded for?

Answer 1

Innate= encoded in the germline (inherited)
Adaptive= Somatically generated (Rearrangement of multiple gene segments in a limited number of genes in developing B and T cells)

Question 2

How do innate and adaptive immunity achieve broad recognition?

Answer 2

Innate= pattern recognition receptors PRPs- Recognise PAMPS and DAMPS
Adaptive= BCRs (antibodies) and TCRs

Question 3

What are the advantages of the adaptive immunity?

Answer 3

Highly diverse random repertoire of potential specificities:
Great for achieving broad recognition
Needs no prior exposure to pathogens
Difficult for pathogens to predict and evolve to avoid
BUT/ potential for Autoimmunity!!

Question 4

Summarise clonal selection?

Answer 4

During development progenitor cells give rise to large numbers of NAÏVE circulating lymphocyteS each with a different specificity
When a lymphocyte recognises an epitope in a dangerous context then this useful clone is expanded to combat the threat. This also generates MEMORY cells, that will respond faster and better if the same threat is encountered again.

Question 5

How are B and T cell receptors similar?

Answer 5

Appear at cell surface as receptor complexes.
Have recognition regions and chains involved in signalling activation to the cell.
They have this antigen recognition region made up of complimentary determining region CDR.

Question 6

Structurally what do B and T cell receptors both have?

Answer 6

Complementary determining region (CDR)

Signal transducing molecules

Question 7

How do BCR and TCR recognise antigen?

Answer 7

B cell receptor recognises a native antigen whereas TCR needs antigen to be processed and peptide presented on MHC molecule.

Question 8

What are the different ways BCR and TCR bring about their effector functions?

Answer 8

B cells- secrete antibodies. These antibodies interact with effectors through these fc regions. Depending on binding properties of fc determines which type of effector mechanism you recruit in.
T cells- the cell itself is the machinery, effector function. By secreting different cytokines or by direct contact and killing. So you have no reason to ever want to secrete t cell receptor because want to keep it in the t cell to bring machinery with you

Question 9

What is an antibody made up of?

Answer 9

Made up of two identical heavy and light chains.

Light chains can be a kappa chain or a lambda chain. But which ever it is they will be identical in one antibody.

Question 10

What can the Kabat and Wu variability plot show us about the recognition sites of antibodies?

Answer 10

Kabat and wu variablity plot. Can see the variable and hypervariable regions.
They come together to form a tight beta barrel so they bring these 6 hyper variable loops together and that’s what makes these recognition site.

Question 11

What does Lineage specific developmentally regulated somatic recombination of multiple gene segments mean?

Answer 11

Lineage specific- only happens in b and t cells.
Developmentally regulated- As b and t cells go through development there are checkpoints before going on to next point.
Somatic recombination- don’t inherit it, it happens in body cells in this case b and t cells of multiple gene segments.

Question 12

Describe gene rearrangement in B cells?

Answer 12

b cells can choose different v and j segments. So end up with clonal b cells with light chains with different antigen binding properties.

Question 13

Even with his combinatorial diversity with gene segments joining differently, it doesnt add up to enough diversity. What else increases diversity?

Answer 13

The joining is an imprecise event so get junctional diversity.

Question 14

What are RSSs?

Answer 14

V, D and J segments are flanked by what we call recombination signal sequences (RSSs) made up of a conserved heptamer, a conserved nonamer and either a 12 or a 23 bp spacer. This is what is recognised by the recombination machinery that takes hold of them and brings together those segments so they can join together in this way.

Question 15

What is the 12/23 rule?

Answer 15

(relates to RSSs)
Only 12 can join with 23 which makes them link in the right order. V to a d to a J for example. Couldn’t do a V to a J directly on heavy chain.

Question 16

What does imprecise joining of gene segments generate?

Answer 16

Imprecise Joining of Gene Segments Generates Junctional Diversity

Question 17

Describe the imprecise joining of gene segments

Answer 17

(????) Rag binds to ends brings together. Cleavage at heptamer. So end up with hairpins.
As it comes to resolve the hairpin. Unfolds the nucleotides. This is how we get p nucleotides. Palindromic. Read same way back and forwards.
If theres terminal deoxytransferase here it will just add in some random bases.
Got p nucleotides and n nucleotides added. Extra diversity at cdr3. downside is that one in three of these will give you what you want. Got to maintain the reading frame. If you put in one extra nucleotide it will throw off the reading frame. Because ribosome read in threes. Two extra nucleotides throw it off. Three extra get an extra amino acid.

Question 18

What are the sources of diversity in the primary antibody repertoire?

Answer 18

Combinatorial Diversity =multiple gene segments, any H with any L
Junctional Diversity=P-nucleotide addition, exonuclease activity, N-nucleotide addition

Question 19

What are the two types of T cells that develop in the thymus?

Answer 19

Alpha/beta and gamma/delta

Question 20

Which are the most common type of T cells?

Answer 20

Alpha/beta are 95% of t cells.

They divide into CD4 and CD8 T cells.

Question 21

What are the functions of gamma/delta T cells?

Answer 21

gamma/delta T-cells:
play roles in immune responses at epithelial surfaces.
More innate in the way they recognise them

Question 22

What are the similarities and differences of how BCR and TCR genes are inherited?

Answer 22

Just like bcr genes, tcr are inherited as multiple gene segments.
Can see V, J and constant region. Similar to kappa light chain. Little difference is that delta locus is in middle of it. (If you find it where the V alpha is going to J alpha it means the delta has been deleted, important in some complicated way not in the unit I think).

Question 23

What are TCR genes surrounded by and when does recombination happen?

Answer 23

TCR Gene Segments are Flanked by RSSs. But in T cells, somatic recombination happens during development in the thymus

Question 24

Compare Sources and Distribution of

Diversity in Immunoglobulins and TCRs

Answer 24

> Both assembled by somatic recombination of multiple gene segments;

> Similar level of combinatorial diversity

> Greater junctional diversity in TcR;
 D segments read in all reading frames
 more J gene segments
 TdT activity at all junctions

Question 25

What is TCR diversity focused on?

Answer 25

TCR diversity is focused on CDR3 which contacts the antigenic peptide

Question 26

Explain Allelic and Isotypic Exclusion?

Answer 26

Clonality only one antigen expressed by one cell. One allele from each parents. By time make b cell must only express one allele from heavy chain. One from light chain. Can have kappa or lambda. Can only express one. Known as allelic or istopyic exclusion.

Question 27

Clonality requires what in B cells?

Answer 27

Clonality Requires Only One Antigen Specificity to be Expressed
Mature activated B cell;
1 productively rearranged and active H chain allele
1 productively rearranged and active L chain allele
Activity at all other light and heavy chain alleles is ‘excluded’

Question 28

How is allelic and isotypic exclusion achieved?

Answer 28

They are achieved because rearrangements occur in stepwise manner. As soon as you have a productive chain it feeds back to cell to stop any firther recombination at the other allel of that chain. And makes next bit that needs to be reaaranged become exposed.

Question 29

Gene Rearrangements Occur in a Regulated, Step-wise Manner During B Cell Development
Describe this…

Answer 29

(???)Early b cell get DJ rearrangement on both chromosomes
If v-dj is no productive rearrangement then goes onto next one. If its productive, get close down at other heavy chain locus. Get period of proliferation. Turn off your rags and turn them back on again. Get rearrangement at light chain genes. Follow this through, if you get rearrangement, shuts down the other one. In this case rearrangement of a chain makes fully functional chain to bind to heavy chain and goes up to surface.

Question 30

Gene Rearrangements Occur in a Regulated Manner During B and T Cell Development

Answer 30

???

Question 31

How do B cells recruit effector functions?

Answer 31

B cells recruit effector functions by expressing different isotypes. Any one b cell can make any one of these isotypes. Genes for isotypes are in particular order downstream of the j segment. At one particular time any one b cell only makes on isotype. Exception!!! Early on muew and delta can be expressed together on same cell!!

Question 32

Where are the C-region exons in B cells?

Answer 32

C-region Exons for the Different Antibody Isotypes Are Located 3’ of the JH Gene Segments

Question 33

What is the exception to the rule about B cells having one isotype?

Answer 33

At one particular time any one b cell only makes on isotype. Exception!!! Early on muew and delta can be expressed together on same cell!!
Only One Antibody Isotype is Expressed at Any One-time Except for IgM and IgD

Question 34

‘Isotype/Class Switching’ Occurs by Recombination Between Switch Regions
Describe this…

Answer 34

Isotype switching, Get recombination by switch sequences no switch sequence between meuw and delta. Which is why they are co-expressed. All others get one at a time.
Switching machinery brings these switch sequences together and deletes out everything in between so potential to express any isotype, once you’ve moved forwards down that chromosome. No going back. No chromosome left.

Question 35

How are secreted forms of antibodies generated?

Answer 35

Secreted Forms of Antibodies are Generated by Alternative RNA Processing

Question 36

Describe this:

Secreted Forms of Antibodies are Generated by Alternative RNA Processing

Answer 36

If you’ve got different C terminus then you an make transmembrane region. Tm one goes through to polA signal. So this is end of exon so you have the transmembrane region.
But if you use alternative polA signal these exons never get transcribed so gets secreted because doesn’t have transmembrane domain.
That happens to each antibody. You get a switch with b cells.

Question 37

Describe the second wave of diversification in antibodies?

Answer 37

In bone marrow primary repertoire.
When activated that can go to germinal centre. Secondary diversification(repertoire).
One= class switching gives you functional diversity.
the other way= The other is somatic hyper mutation- you get increased frequency of targeting of point mutations in v region. Allows you to undergo affinity maturation. might make binding worse, or better. Better ones get selected. Binding better selected.