Week 7 S - Immunogenetics

Focus on mechanisms generating antibody (Ab) and T-cell receptor (TCR) diversity.
Key processes include:
- Structure of immunoglobulin loci
- DNA rearrangement and loss
- V(D)J recombination mechanism
- Variability sources
- Isotype switching
- Antibody maturation

Three loci:
- kappa (k) light chain
- lambda (λ) light chain
- heavy chain (H)
Each locus contains gene segments:
- V (variable), D (diversity for heavy chain), J (joining), C (constant).
Locus structure differs in germline vs. B cells:
- In B cells, DNA is rearranged and some segments are lost.

V(D)J joining involves the loss of DNA during recombination:
- Recombination leads to the loss of loops of DNA.
- Randomness in joining contributes to diversity.

Recombination Signal Sequences (RSS):
- Comprised of nonamer and heptamer sequences separated by 12 or 23 bp.
- Important for aligning gene segments for recombination.
RAG1 and RAG2 Enzymes:
- Recognize RSS and initiate DNA breaks, forming hairpin structures.
Joining process can be either deletional or inversional.

Rejoining of segments is not precise, leading to:
- Non-productive gene arrangements.
- Additional variation through P-nucleotide addition (during hairpin cleavage) and N-nucleotide addition (by TdT).
Resulting diversity is concentrated in complementarity-determining regions (CDR) of both heavy and light chains.

Isotype switching allows B cells to change the type of antibody produced without altering the specificity for antigen:
- Initially, heavy chain transcripts contain both IgM and IgD.
- Selection of polyadenylation site determines which constant region is expressed (IgM vs. IgD).
- The process is facilitated by switch regions between C regions of heavy chain locus.
Enzyme AID (Activation-induced cytidine deaminase) plays a crucial role in deaminating cytosines, facilitating mutations and switch regions.

Antibody maturation includes:
- Isotype switching: Changing of heavy chain regions.
- Affinity maturation: Increased binding affinity for antigens through somatic hypermutation, focused primarily on CDR1 and CDR2 sequences.
- Transcription dependence: Both processes rely on transcriptional changes and are initiated by AID.

V(D)J Recombination: Process generating diverse antibodies and T-cell receptors.
RSS: Recombination signal sequences crucial for alignment of gene segments.
AID: Enzyme responsible for editing cytosines to uracils, critical to diversification processes.
Isotype switching: Mechanism enabling a B cell to produce different classes of heavy chain antibodies (IgM, IgD, etc.).
Affinity maturation: Process of increasing the binding strength of antibodies to antigens over repeated exposures.