Basic adaptive immunology Flashcards
Lectures: -Week 1, day 2, lecture 6: Antigen receptor diversity -Week 1, day 3, lecture 1: Adaptive immune response - organs
Of how many light and heavy chains does an immunoglobuline exist?
2 heavy chains + 2 light chains
Of how many light and heavy chains does a T-cell receptor (TCR) exist?
1 heavy chain + 1 light chain
Of how many constant (C)-domains does the Ig-heavy chain consist?
3 constant domains
Of how many constant (C)-domains does the Ig-light chain consist?
1 constant domain
Which kinds of regions can be found in the variable domain of heavy chains?
V-, D- and J-regions
Which kinds of regions can be found in the variable domain of light chains?
V- and J-regions (no D-regions!)
In which order are V, D and J combined?
First: D-J
Then: V-DJ
If no D is present, V and J are directly joined
In what way is indicated where DNA-breaks can be made in order to allow gene rearrangement?
The recombination signal sequences (RSS) indicate locations where breaks can be introduced
What does a recombination signal sequence (RSS) consist of?
- Nonamer (9 bases)
- One-turn (12 bp) or two-turn (23 bp) sequence
- Septamer (7 bases)
Which enzymes are responsible for introducing dsDNA breaks for gene rearrangement?
RAG-enzymes
What is the byproduct of gene rearrangement?
Circular excision products
How are byproducts of gene rearrangement distuinguished from the products of gene rearrangement?
These contain part of the RSS that can be recognized as being the byproduct
What are the steps of gene rearrangements, and which enzymes carry these steps out? (5)
- RAG1/RAG2 bind to RSS -> DNA cleavage
- Hairpin coding ends are closed by hairpins
- Hairpins are cleaved open by Artemis
- TdT performs addition of random nucleotides at the opened hairpins
- DNA ligase IV ligates the opened hairpins into a rearranged gene
What is the process of the addition of random nucleotides in the variable domain by TdT called?
N-nucleotide addition
Which three mechanisms ensure the high possible TCR/Ig diversity?
- The high number of possible V(D)J recombinations
- Combinations of two protein chains
- N-nucleotide addition (and: p-nucleotide addition)
What causes a significant amount of TCR’s that are generated through random nucleotide addition to be unviable?
- Number of added nucleotides is not a multiple of 3 -> frameshift
- Random additions of stop codons
What are the possible reasons of non-functional gene-rearrangements? (5)
- Rearrangements of truncated or non-functional genes
- Defects in regulator sequences (leader, splice-site)
- Out-of-frame junctional region (triplet violation)
- Introduction of stop codons in junctional regions
- Incorrect reading frame of D-gene (some cannot be read in all reading frames because they contain stop codons in certain frames)
What is special about the δ-gene of the TCR?
This gene can have multiple D-regions; further increases variability
Where does gene rearrangement of the B-cells take place?
Bone marrow
What is the process of B-cell gene rearrangement?
- Rearrangement of the heavy chain (first D-J, then V-DJ)
- The heavy chain is joined to the surrogate light chain, and the functionality of the heavy chain is checked (if succcesful: resumption to step 3)
- Rearrangement of the κ-light chain
- If κ-rearrangement is not succesful: rearrangement of λ-light chain
- Joining of heavy and light chain and testing of the BCR
Where does gene rearrangement of the T-cells take place?
Thymus
What is the process of T-cell gene rearrangement?
- γ- & δ-rearrangement, if successful development into a γδ-T-cell
- If δ-rearrangement is unsuccesfull: β-rearrangement (D-J, then V-DJ)
- Removal of the δ-gene from the α-gene, then α-rearrangement
Why does T-cell rearrangement always have to start with δ-rearrangement?
This is the gene locus that opens up first; because the δ-gene is located in the middle of the α-gene, the δ-gene needs to try a rearrangement first, because it has to be deleted to allow rearrangements of the other genes
Why does the δ-gene have to be removed before α-rearrangement?
Because the δ-gene is located in the middle of the α-gene; this causes the elements of the α-gene to be quite far apart, requiring them to be brought closer together before actual rearrangement can commence
Which of the chains of the TCR can be likened to heavy chains (V, D & J), and which are analogous to light chains (V & J)?
δ and β have V-, D- and J-regions, are are therefore analogous to heavy chains
γ and α have V- and J-regions, analogous to light chains
Which two processes take place during the germinal centre reaction?
- Somatic hypermutation
- Class switch recombination
Where does the germinal centre reaction take place?
Follicle centres of lymph nodes
What is somatic hypermutation, and what is its function?
Somatic hypermutation is the introduction of mutations (mainly) in the CDR-regions of the Ig-gene, possibly increasing the affinity of the Ig
In what way is made sure that somatic hypermutation always increases the affinity of Ig?
Posititive selection -> B-cells with a higher affinity will get a stronger stimulatory/survival signal and outcompete/outproliferate B-cells with a lower affinity
True or false: somatic hypermutation can only take once
False; a B-cell can undergo multiple germinal centre reactions and therefore multiple rounds of somatic hypermutation
Why are T-FH-cells (T-follicular helper cells) present during the germinal centre reaction?
These activate pathways and molecules in somatic hypermutation
Which molecule in B-cells is important for somatic hypermutation?
AID
What is the function of class switching of B-cells?
Changing the class of antibody, therefore altering its biological function
Which region of the Ig is changed during class switch recombination?
The C-domains of the Ig are changed in class switch recombination
True or false: class switch recombination can only take place once
False; class switch recombination can take multiple times, as long as there are classes downstream of the current region
What is the biological function of circular excision products?
These don’t have a biological function ;-)
What are circular excision products of T-cells called?
TREC
What are circular excision products of B-cells called?
BREC
How are circular excision products used in diagnostics?
They are included in perinatal screening for SCID, because the absence of these products indicate a dysfunction in gene rearrangement
What are lymphoid organs essential for? (4)
- T-cell activation
- Survival of naïve T-cells
- B-cell activation
- Germinal centre reaction
How is the organization of lymphoid organs in B- and T-cell compartments maintained?
Secretion of homeostatic chemokines by stromal cells, also known as mesenchymal cells/fibroblasts
What is the difference in function of the lymph node versus the spleen?
The lymph nodes are more tailored to respond to localized infections, whereas the spleen responds to systemic infections
What are primary lymphoid organs? Which organs are counted towards the primary lymphoid organs? (3)
Organs in which the immune system develops
1. Bone marrow
2. Thymus
3. Foetal liver
What are secondary lymphoid organs? Which ‘organs’ are counted towards the secondary lymphoid organs? (2)
Organs in which immune cells lie in a resting state, ready to react to infections
1. Lymphoid tissues (mainly lymph nodes, but also mucosa-associated lymphoid tissue (MALT))
2. Spleen (white pulp)
How do lymphocyte cells enter the secondary lymphoid organs?
Via the high endothelial venule (HEV, a blood vessel)
How do immune cells leave the secondary lymphoid organs?
Via efferent lymphatics, through which they end up in circulation
Where in the lymph nodes are T- and B-cells located?
T-cells: in the stroma
B-cells: in follicles
To which chemokine are T-cells attracted (in the lymph node), and by which cells is this chemokine produced?
CCL21, produced by T-zone reticular cells
How is efficient matching of dendritic cells and T-cells in the lymph node ensured?
Both T-cells and dendritic cells attach to the T-zone reticular cells and move around over them, increasing the chance of an encounter
To which chemokine are B-cells attracted (in the lymph node), and by which cells is this chemokine produced?
CXCL13, produced by follicular dendritic cells
Which cytokine, produced in the lymph node, ensures survival of naïve T-cells? By which cells is this cytokine produced?
IL-7, produced by stromal cells
Which two compartments can be identified in the spleen? What are their respective functions?
- Red pulp -> filters out old erythrocytes
- White pulp -> centres of lymphoid cells
How do dendritic cells and antigens reach the lymph nodes, and how do they reach the spleen?
Lymph node: via afferent lymphatics
Spleen: via the blood
Which cell population is unique to the spleen, as compared to the lymph nodes? What is the function of these cells?
Marginal zone B-cells, which recognize sugar structures different on many types of bacteria -> important for combating systemic bacterial infections
Where are the marginal B-cells located?
At the edge between the red and white pulp
Which class of antibodies is secreted by marginal zone B-cells if they encounter bacterial sugar structures in the bloodstream?
IgM
What is the function of the quick IgM-response by marginal zone B-cells in a systemic bacterial infection?
Rapid production of moderately effective IgM gives the rest of the immune system to kick in and produce more antibodies or antibodies with higher affinity/of a different class
What is the main immunological consequence of a removal of the spleen?
Loss of the marginal zone B-cells, increasing susceptibility to systemic bacterial infections
What is the result of disruption of the architecture of the lymph nodes or spleen?
Disrupts the adaptive immune response -> architecture is essential to function
In what way can the architecture of the lymph nodes or spleen be disrupted?
By wiping out the stromal cells that produce homeostatic chemokines
