L7 - Genetics of antigen receptors Flashcards
Recognition of pathogens: what two types are there and what do they produce?
Pattern recognition - PAMPS/MAMPS/DAMPS
* receptors are encoded in the germline (inherited)
BCR/TCR - rearrangement of genes within B-cells and T-cells to recognise more specific epitopes
* Somatically generated
* Needs no prior exposure to pathogens
* Great for achieving broad recognition
* Difficult for pathogens to predict and evolve to avoid
* potential for Autoimmunity
B-cell receptor: how is it???
Recruited by FcR interactions of different soluble antibody isotypes
(“whatever that means”)
T-cell receptor: how is it????
Mediated by cell-cell contact or local secretion of cytokines
(“whatever that means”)
T-helper cell 1: what is it used for and what example is there?
Th1 Intracellular pathogens
- Increase macrophage killing
T-helper cell 2: what is it used for and what example is there?
Th2 Extracellular parasites
- Eosinophils, mast cells, IgE (activation (??))
T-helper cell 17: what is it used for and what example is there?
Th17 (Inflammatory) extracellular bacteria/fungi
- Recruit neutrophils
T-follicular helper cell 1: what is it used for?
Localise to B cell follicles to support them
T-regulatory cell: what is it used for?
Tolerance/Immune regulation
T-cytotoxic cell 1: what is it used for?
Killer T cells
Antibody typical structure
2 heavy chains and 2 light chains
Each heavy site forms both the constant region and the hypervariable region, with the two regions separated by a hinge and the two chains joined by disulfide bridges
The light chains only form the hypervariable region and work with the heavy chain to form antigen-binding sites
Antibody/TCR/BCR genes: why are they strange?
They contain V-gene segments and J-gene segments which can recombine to give rise to various manufactured proteins
A typical protein contains a Vₗ chain and a Cₗ chain
Light chains of antibodies: what type of segments in their genes do they have?
- V-segments
- J-segments
Heavy chains of antibodies: what type of segments in their genes do they have, how does rearranging occur, what is the exon, where are CDR1/2/3 located, and what gene is the extra gene segment found?
V, D, and J segments
Two gene arrangements occur sequentially,
D → J and then V → DJ
VDJ = V exon
CDR1 and CDR2 are contained in V and V, D and J all contribute to CDR3
IgH gene
Combinatorial diversity: how are the high levels of diversity established?
V/D/J (and sometimes H) differential joining results in some of the diversity
Junctional diversity - imprecise joining of gene segments causes lots more diversity
RSS: what are they, what do they do, and what use do they have?
Recognition signal sequences
Border gene segments and enforce the 12/23 rule (recombination can only occur between segments with different spacer lengths - only either 12/23 or 23/12 may be formed)
Allows controlled diversity - helps keep the immune system functional
Molecular mechanics of V(D)J recombination
1 - Initiation:
* RAG1/RAG2 - bind to RSS and initiate a cleavage event, generating a DSB in the DNA, and allowing recombination to occur
2 - DNA-damage recognition and hairpin opening:
* The cleavage results in hairpin structures at the ends of the gene segments which are opened by enzymes and other cellular components and generate free ends which can be ligated
3 - DNA repair:
* TdT and ligase activity repair DNA and finish the recombination
TdT: what is it and what does it do?
Terminal deoxynucleotidyl transferase
Adds nucleotides to hairpins on VDJ recombinations
Combinatorial and junctional diversity: the difference between the two?
Combinatorial Diversity multiple gene segments
any H with any L
Junctional Diversity P-nucleotide addition
N-nucleotide addition exonuclease activity
T cells: what types are there?
Gamma/delta - play roles in immune responses at epithelial surfaces (innate)
Alpha/beta - most abundant (~95%)
B cells/T cells: where do they develop?
B cells - bone marrow
T cells - thymus
T cells
Follow the same recombinant machinery as BCRs
Immunoglobulin vs TCR recombination diversity
Both are assembled by somatic recombination of multiple gene segments - Similar levels of combinatorial diversity
> Greater junctional diversity in TcR;
- D segments read in all reading frames
- TdT activity at all junctions
- TCR diversity is focused on CDR3, which contacts the antigenic peptide
> More J gene segments
- Footprint of αβTCRs docking down onto MHC class I and II peptide complexes
Mature activated b cell gene expression
Only productively rearranged genes are expressed, everything else is excluded
Clonality: what is required?
- Only one antigen specificity to be expressed
Gene rearrangements: which steps occur at which time?
Early pro b-cell:
* H-chain gene rearrangement
* D-J rearrangements on both chromosomes
Late pro b-cell:
* H-chain gene rearrangement
* D-J rearrangements on first chromosomes
* D-J rearrangements on second chromosomes
* Cell loss
Pre-b cell:
* L-chain gene rearrangement
* Rearrange the k gene on the first chromosome
* Rearrange the k gene on the second chromosome
* D-J rearrangements on second chromosomes
* Cell loss
Immature b-cell:
* Rearrangement ceases
Are secreted forms of antibodies the same as their forms expressed at the transmembrane?
They differ by the secreted forms having a reduced carboxy terminus
AAA region is cut off
Google or ask whatever the TM forms of antibodies are (and AAA region.)
Antibody expression: is only one antibody expressed by a cell at one time?
Yes, mostly
IgM and IgD may be co-expressed and this is regulated by alternative RNA processing
How does class switching occur?
Isotypes are formed by recombinations between switch regions
Are the antibodies produced in the bone marrow (primary repertoire) the only antibodies produced throughout their cell’s lifespan?
Not usually, as the cells move from the BM to the germinal centre in lymph nodes, they first have somatic hypermutation for affinity maturation, and then may later class switch
V-region assembly: what does it result in, is it reversible and does it occur in T/B-cells?
Somatic recombination of DNA
No
Both
Junctional diversity: what does it result in, is it reversible and does it occur in T/B-cells?
Imprecise joining, N-sequence insertion
No
Both
Transcriptional activation: what does it result in, is it reversible and does it occur in T/B-cells?
Activation of promoter by proximity to the enhancer
No but regulated
Both
Switch recombination: what does it result in, is it reversible and does it occur in T/B-cells?
Somatic recombination of DNA
No
B-cells
Somatic hypermutation: what does it result in, is it reversible and does it occur in T/B-cells?
DNA point mutation
No
B-cells
IgM/IgD expression on cell surface: how is it formed, is it reversible and does it occur in T/B-cells?
Differential splicing of DNA
Reversible, regulated
B-cells
Membrane/secreted antibody form: how is it formed, is it reversible and does it occur in T/B-cells?
Differential splicing of DNA
Reversible, regulated
B-cells
