Basic adaptive immunology

Question 1

Of how many light and heavy chains does an immunoglobuline exist?

Answer 1

2 heavy chains + 2 light chains

Question 2

Of how many light and heavy chains does a T-cell receptor (TCR) exist?

Answer 2

1 heavy chain + 1 light chain

Question 3

Of how many constant (C)-domains does the Ig-heavy chain consist?

Answer 3

3 constant domains

Question 4

Of how many constant (C)-domains does the Ig-light chain consist?

Answer 4

1 constant domain

Question 5

Which kinds of regions can be found in the variable domain of heavy chains?

Answer 5

V-, D- and J-regions

Question 6

Which kinds of regions can be found in the variable domain of light chains?

Answer 6

V- and J-regions (no D-regions!)

Question 7

In which order are V, D and J combined?

Answer 7

First: D-J
Then: V-DJ
If no D is present, V and J are directly joined

Question 8

In what way is indicated where DNA-breaks can be made in order to allow gene rearrangement?

Answer 8

The recombination signal sequences (RSS) indicate locations where breaks can be introduced

Question 9

What does a recombination signal sequence (RSS) consist of?

Answer 9

1. Nonamer (9 bases)
2. One-turn (12 bp) or two-turn (23 bp) sequence
3. Septamer (7 bases)

Question 10

Which enzymes are responsible for introducing dsDNA breaks for gene rearrangement?

Answer 10

RAG-enzymes

Question 11

What is the byproduct of gene rearrangement?

Answer 11

Circular excision products

Question 12

How are byproducts of gene rearrangement distuinguished from the products of gene rearrangement?

Answer 12

These contain part of the RSS that can be recognized as being the byproduct

Question 13

What are the steps of gene rearrangements, and which enzymes carry these steps out? (5)

Answer 13

1. RAG1/RAG2 bind to RSS -> DNA cleavage
2. Hairpin coding ends are closed by hairpins
3. Hairpins are cleaved open by Artemis
4. TdT performs addition of random nucleotides at the opened hairpins
5. DNA ligase IV ligates the opened hairpins into a rearranged gene

Question 14

What is the process of the addition of random nucleotides in the variable domain by TdT called?

Answer 14

N-nucleotide addition

Question 15

Which three mechanisms ensure the high possible TCR/Ig diversity?

Answer 15

1. The high number of possible V(D)J recombinations
2. Combinations of two protein chains
3. N-nucleotide addition (and: p-nucleotide addition)

Question 16

What causes a significant amount of TCR’s that are generated through random nucleotide addition to be unviable?

Answer 16

1. Number of added nucleotides is not a multiple of 3 -> frameshift
2. Random additions of stop codons

Question 17

What are the possible reasons of non-functional gene-rearrangements? (5)

Answer 17

1. Rearrangements of truncated or non-functional genes
2. Defects in regulator sequences (leader, splice-site)
3. Out-of-frame junctional region (triplet violation)
4. Introduction of stop codons in junctional regions
5. Incorrect reading frame of D-gene (some cannot be read in all reading frames because they contain stop codons in certain frames)

Question 18

What is special about the δ-gene of the TCR?

Answer 18

This gene can have multiple D-regions; further increases variability

Question 19

Where does gene rearrangement of the B-cells take place?

Answer 19

Bone marrow

Question 20

What is the process of B-cell gene rearrangement?

Answer 20

1. Rearrangement of the heavy chain (first D-J, then V-DJ)
2. 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)
3. Rearrangement of the κ-light chain
4. If κ-rearrangement is not succesful: rearrangement of λ-light chain
5. Joining of heavy and light chain and testing of the BCR

Question 21

Where does gene rearrangement of the T-cells take place?

Answer 21

Thymus

Question 22

What is the process of T-cell gene rearrangement?

Answer 22

1. γ- & δ-rearrangement, if successful  development into a γδ-T-cell
2. If δ-rearrangement is unsuccesfull: β-rearrangement (D-J, then V-DJ)
3. Removal of the δ-gene from the α-gene, then α-rearrangement

Question 23

Why does T-cell rearrangement always have to start with δ-rearrangement?

Answer 23

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

Question 24

Why does the δ-gene have to be removed before α-rearrangement?

Answer 24

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

Question 25

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)?

Answer 25

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

Question 26

Which two processes take place during the germinal centre reaction?

Answer 26

1. Somatic hypermutation 2. Class switch recombination

Question 27

Where does the germinal centre reaction take place?

Answer 27

Follicle centres of lymph nodes

Question 28

What is somatic hypermutation, and what is its function?

Answer 28

Somatic hypermutation is the introduction of mutations (mainly) in the CDR-regions of the Ig-gene, possibly increasing the affinity of the Ig

Question 29

In what way is made sure that somatic hypermutation always increases the affinity of Ig?

Answer 29

Posititive selection -> B-cells with a higher affinity will get a stronger stimulatory/survival signal and outcompete/outproliferate B-cells with a lower affinity

Question 30

True or false: somatic hypermutation can only take once

Answer 30

False; a B-cell can undergo multiple germinal centre reactions and therefore multiple rounds of somatic hypermutation

Question 31

Why are T-FH-cells (T-follicular helper cells) present during the germinal centre reaction?

Answer 31

These activate pathways and molecules in somatic hypermutation

Question 32

Which molecule in B-cells is important for somatic hypermutation?

Answer 32

AID

Question 33

What is the function of class switching of B-cells?

Answer 33

Changing the class of antibody, therefore altering its biological function

Question 34

Which region of the Ig is changed during class switch recombination?

Answer 34

The C-domains of the Ig are changed in class switch recombination

Question 35

True or false: class switch recombination can only take place once

Answer 35

False; class switch recombination can take multiple times, as long as there are classes downstream of the current region

Question 36

What is the biological function of circular excision products?

Answer 36

These don't have a biological function ;-)

Question 37

What are circular excision products of T-cells called?

Answer 37

TREC

Question 38

What are circular excision products of B-cells called?

Answer 38

BREC

Question 39

How are circular excision products used in diagnostics?

Answer 39

They are included in perinatal screening for SCID, because the absence of these products indicate a dysfunction in gene rearrangement

Question 40

What are lymphoid organs essential for? (4)

Answer 40

1. T-cell activation 2. Survival of naïve T-cells 3. B-cell activation 4. Germinal centre reaction

Question 41

How is the organization of lymphoid organs in B- and T-cell compartments maintained?

Answer 41

Secretion of homeostatic chemokines by stromal cells, also known as mesenchymal cells/fibroblasts

Question 42

What is the difference in function of the lymph node versus the spleen?

Answer 42

The lymph nodes are more tailored to respond to localized infections, whereas the spleen responds to systemic infections

Question 43

What are primary lymphoid organs? Which organs are counted towards the primary lymphoid organs? (3)

Answer 43

Organs in which the immune system develops 1. Bone marrow 2. Thymus 3. Foetal liver

Question 44

What are secondary lymphoid organs? Which 'organs' are counted towards the secondary lymphoid organs? (2)

Answer 44

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)

Question 45

How do lymphocyte cells enter the secondary lymphoid organs?

Answer 45

Via the high endothelial venule (HEV, a blood vessel)

Question 46

How do immune cells leave the secondary lymphoid organs?

Answer 46

Via efferent lymphatics, through which they end up in circulation

Question 47

Where in the lymph nodes are T- and B-cells located?

Answer 47

T-cells: in the stroma B-cells: in follicles

Question 48

To which chemokine are T-cells attracted (in the lymph node), and by which cells is this chemokine produced?

Answer 48

CCL21, produced by T-zone reticular cells

Question 49

How is efficient matching of dendritic cells and T-cells in the lymph node ensured?

Answer 49

Both T-cells and dendritic cells attach to the T-zone reticular cells and move around over them, increasing the chance of an encounter

Question 50

To which chemokine are B-cells attracted (in the lymph node), and by which cells is this chemokine produced?

Answer 50

CXCL13, produced by follicular dendritic cells

Question 51

Which cytokine, produced in the lymph node, ensures survival of naïve T-cells? By which cells is this cytokine produced?

Answer 51

IL-7, produced by stromal cells

Question 52

Which two compartments can be identified in the spleen? What are their respective functions?

Answer 52

1. Red pulp -> filters out old erythrocytes 2. White pulp -> centres of lymphoid cells

Question 53

How do dendritic cells and antigens reach the lymph nodes, and how do they reach the spleen?

Answer 53

Lymph node: via afferent lymphatics Spleen: via the blood

Question 54

Which cell population is unique to the spleen, as compared to the lymph nodes? What is the function of these cells?

Answer 54

Marginal zone B-cells, which recognize sugar structures different on many types of bacteria -> important for combating systemic bacterial infections

Question 55

Where are the marginal B-cells located?

Answer 55

At the edge between the red and white pulp

Question 56

Which class of antibodies is secreted by marginal zone B-cells if they encounter bacterial sugar structures in the bloodstream?

Answer 56

IgM

Question 57

What is the function of the quick IgM-response by marginal zone B-cells in a systemic bacterial infection?

Answer 57

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

Question 58

What is the main immunological consequence of a removal of the spleen?

Answer 58

Loss of the marginal zone B-cells, increasing susceptibility to systemic bacterial infections

Question 59

What is the result of disruption of the architecture of the lymph nodes or spleen?

Answer 59

Disrupts the adaptive immune response -> architecture is essential to function

Question 60

In what way can the architecture of the lymph nodes or spleen be disrupted?

Answer 60

By wiping out the stromal cells that produce homeostatic chemokines