Population dynamics in immunology Flashcards
Lectures: -L6 - T- & B-cell diversity & selection -L7 - Host diversity
How can T- & B-cell diversity occur on an intra-individual level? (2)
- IGR/TCR recombination
- Somatic hypermutation (B-cells only)
How can T- & B-cell diversity occur on an inter-individual level? (2)
- Antigen receptor gene polymorphisms
- HLA polymorphisms
What is the definition of ‘repertoire’ (as in B-cell or T-cell repertoire)?
All productive IG/TR rearrangements
What are two key aspects for productive IG/TR rearrangements?
- Triplet coding
- Reading frame
How many reading frames do the V-, J- & D-genes have?
V-genes: single reading frame
J-genes: single reading frame
D-genes: multiple reading frames
What part of IG/TR rearrangements is productive?
~1/3
What are reasons for non-productive gene rearrangements? (2)
- Use of non-functional gene regions
- Problematic junctions
What is often the problem in non-functional gene regions that cause non-productive rearrangements? Where are they often located?
They often contain stop codons
Often located in V-genes
What is an alternative name for non-functional gene regions that cause non-productive rearrangements?
Pseudogenes
Which 3 mechanisms can cause problematic junctions result in non-productive rearrangements?
- Out of frame (number of nucleotides addes was not 3 or a multiple thereof)
- Junctions carrying stop codons (introduced during nucleotide addition)
- Absent CDR3 anchors
What are CDR3 anchors? How can absent CDR3 anchors cause non-productive gene rearrangements?
Preserved sequences that produce amino acids on specific positions, which are needed for a correct receptor structure
When these amino acids are substituted, the receptor structure won’t be correct
After gene rearrangement, productive gene rearrangements can still become non-productive. How?
As a result of somatic hypermutation, the functional rearrangements could be changed in such a way that they do not produce a functional protein anymore
Productive rearrangements can be analyzed on DNA, RNA and protein level. What is the (approximate) ratio of functional vs. non-functional rearrangement on each of these three levels?
DNA-level: 1/3 productive, 2/3 non-productive
RNA-level: mostly productive
Protein level: almost exclusively productive
Productive rearrangements can be analyzed on DNA, RNA and protein level. How can the (approximate) ratio of productive vs. non-productive rearrangements on DNA-level be explained?
1/3 productive & 2/3 non-productive can be explained on the basis of triplet coding -> only introduction of (a multiple of) 3 nucleotides results in productive rearrangements -> chance of about 1/3
Productive rearrangements can be analyzed on DNA, RNA and protein level. How can the (approximate) ratio of productive vs. non-productive rearrangements on RNA-level be explained?
On RNA-level, we find mostly productive rearrangements
This is skewed towards productive rearrangements due to the preselection of transcription of productive gene rearrangements
Productive rearrangements can be analyzed on DNA, RNA and protein level. How can the (approximate) ratio of productive vs. non-productive rearrangements on a protein level be explained?
On protein level, we find almost exclusively productive rearrangements, because non-productive recombinations rarely make it into the protein stage
Some compartments will have a higher amount of productive vs. non-productive rearrangements. Which compartment contains a relatively high percentage of productive rearrangements? Why?
Lymph nodes/spleen -> only cells with productive rearrangements get to this stage
Some compartments will have a higher amount of productive vs. non-productive rearrangements. Which compartment contains a relatively low percentage of productive rearrangements? Why?
Bone marrow/thymus -> these contain B-/T-cells in early development
On which levels can antigen receptor diversity be studied? (2)
- DNA-/RNA-level, using molecular techniques
- Protein level, using (mostly) flow cytometry
Which resolutions of analysis of the antigen receptor diversity can be studies at DNA-/RNA-level? Which technique would be used?
- Low resolution using Sanger sequencing
- High resolution using NGS
Why would we use low resolution Sanger sequencing when studing antigen receptor diversity? What information does this technique give us?
To get an impression of antigen repertoire and its diversity
This technique can be used to check for size differences between gene sequences -> size differences represent differences in the length of the junctional region, as the other regions are preserved
Why would we use high resolution NGS when studing antigen receptor diversity? What information does this technique give us?
It can be used to study the whole region between the V- and J-sites of a large amount of cells -> gives a full picture of the diversity of combinations
Which two techniques are available to study antigen receptor diversity on a protein level?
- Antibody-based techniques
- Labelled antigens/tetramers aimed at specific receptors
What is the advantage of antibody-based techniques when studying antigen receptor diversity on a protein level? What causes this?
Recognize families of receptors
They do this because these antibodies are not specific enough to distinguish between individual receptors
What is the disadvantage of antibody-based techniques when studying antigen receptor diversity on a protein level?
They are mostly available for TCR’s, not so much for IGR’s
What is the advantage of using labelled antigens/tetramers when studying antigen receptor diversity on a protein level?
They have a high receptor specificity
When would we use labelled antigens, and when would we use tetramers when studying antigen receptor diversity on a protein level?
Labelled antigens for immunoglobulin receptors/antibodies
Tetramers for TCR
Which two dynamics can be seen in the B-/T-cells and their receptors?
- From naïve in the bone marrow to selected repertoire in the periphery due to maturation and differentiation
- Ontogeny -> during life the receptor repertoire gets skewed towards certain pathogens
Which 2 dynamics occur to B-cells at a cellular level during life?
- Changes in output from the bone marrow
- B-cell memory formation
How does the output of B-cells from the bone marrow change during life?
Higher at the start of life (first few years), lessens as the compartment gets filled
Which two ‘factors’ of B-cell memory formation can be described as dynamic?
- Phenotypic differences -> most are CD27+, some are CD27-
- Place of formation
Where can B-memory cells form? At which locations do/don’t they undergo class switch?
- Germinal centre -> undergo class switch
- Marginal zone -> do not undergo class switch
- Peripheral tissues -> do not undergo class switch
Which 2 dynamics occur to B-cells at a molecular level during life?
- Ig-repertoire selection
- Ig-repertoire maturation
What is Ig-repetoire selection? Towards which 2 characteristics is this selection?
Memory cells have a less diverse repetoire than naïve cells, causing a skewing/selection of the repertoire to occur
This skew is towards:
-Certain specificities/pathogens
-Towards shorter CDR3-regions
What two processes occur during Ig-repertoire maturation?
- Selection against some Ig-genes as memory cells develop
- Selection of advantageous SMH mutations
Which genes (V/D/J) are typically selected against during Ig-repetoire maturation & memory formation?
Certain V-genes
