T Cell Development and Generation of Repertoire Diversity Flashcards
After the commitment stage (commitment to lymhoid lineage then commitment to T cell lineage) what is the next event in the development of the T cell?
Proliferation - there is vigorous proliferation of the precurrosors and at later stages (red circles)
After the stages of Commitment and Proliferation there is a {?} stage
Selection
What is meant by selection in the context of T cell hematopoiesis?
Towards the final stages there is selection by the type of T cell receptor they produce
What is an effector cell in the context of T cell hematopoiesis?
A mature cell that has finished maturation and can now perform a particular immune function
What are the roles of stem cell factors (c-KIT), cytokines (IL7 and IL3) and tissue specific signals such as notch in T cell hematopoiesis?
- early maintenance of progenitors (c-KIT)
- commitment to T cell lineage so common lymphoid progenitor → T cell progenitor (notch)
How is the development of ILC cells slightly different than that of αβ or γδ \T cells
- They branch off from the T cell lineage earlier
- ILCs = innat lymphoid cells
Describe the stages of T cell maturation (development)
At what point in the development (maturation) of a T cell or B cell is a receptor present?
- At a pre-lymphocyte.
- Note that this receptor changes!
Name the 3 major events in lymphocyte development regarding the formation of the receptor on a mature cell
- (As a stem cell and pro-lymohocyte) Initiation of T/B cell receptor gene rearrangement
- (As a pre-lymphocyte) Selection of cells that express a T/B cell pre-antigen receptor
- (As an immature lymphocyte) Selection of repetoire and acquisition of functional confidence (selected for it to work and also to not detect self antigens)
Where do the 2 types of selection a T cell undergoes in development (maturation) happen?
Thymus
What is meant by late development and mature T cells being antigen dependent?
Their survival is dependant on self antigen (not exogenous antigens from infection)
Do T cell progenitors commit to the T cell lineage before or after migrating to the Thymus?
After (so in the thymus)
Name the 2 layers of the Thymus
Cortex and Medulla
Within the thymus, what cells are found mostly?
A dense network of stromal cells (mostly epithelial)
- many dark purple small lymphocytes
Which 2 places can lymphocytes begin their development?
- Bone marrow
- Foetal liver
{?} and {?} are released by {?} to induce committment to the T cell lineage
Notch 1 and GATA3 are released by the thymic stromal cells to induce committment to the T cell lineage
{?} is a transcription factor induced by Notch signals essential for T cell commitment and early T cell precurosors
GATA3 is a transcription factor induced by Notch signals essential for T cell commitment and early T cell precurosors
Why is it that even though there is many waves of T cells undergoing intense proliferation in the Thymus, it does not change size?
As around 98% of T cells die as once they commit to the T cell lineage and proliferate, they may fail the production of a T cell receptor or the T cell receptor fails selection (so would fail one of the 2 selections)
How do we define successive stages in T cell development (how do we work out what stage a cell is in)?
- By the surface markers expressed/not expressed
early markers of T cell lineage is CD2 with NO expression of later markers such as CD3/4/8
Why are developing T cells called DN (double negative)?
Because of the lack of CD4 and CD8 markers (but will express CD2)
What are thymocytes and what do they do?
Thymocytes = DN (double negative) stage T cell progenitors.
They rearrange their T cell locus
Describe the expression of CD4 and CD8 in late stage T cells in development
- First are double negative
- Then express both (double positives)
- Then express one or the other
Name a mature T cell that is not positive for CD4 or CD8
- gamma delta T cell
Name the 2 components of the T cell receptor
α chain and β chain
What holds together the 2 components of a TCR?
Covalent bonds (disulphide bridges) - heterodimer
Name the 2 types of TCRs
2 types: Alpha-beta and Gamma-delta
Name the 2 domains on each of the components (so 4 in total) on a TCR
Each chain has one lg-like N terminal variable domain (V) and one lg-like constant domain (C), a hydrophobic transmembrane region and a short signaling cytoplasmic
Explain what complimentary determining regions (CDRs) are
- These are in the V (variable) domains of both chains
- Are regions stretches of amino acid sequence that is highly variable between receptors
How many CDRs does each TCR have in total?
TCR has 2 chains (alpha and beta)
- each chain has one V (variable) domain
- each V domain has 3 CDRs
- so 6 in total
What do all of the CDRs together form on a TCR?
The peptide-MHC binding site
Compare the structure of TCR to Ig (immunoglobulin)
Which, Ig or TCR can bind soluble antigens?
ONLY Ig (TCR has to bind membrane bound antigens)
What allows TCR to interact with other molecules/complexes? (Not what receptor, but what property of the TCR)
Charged amino acids in the transmembrane domain
The TCR complex is formed by TCR interacting with {?} and {?}, these 2 accessory complexes allow for the transduction of signals upon MHC-peptide binding
The TCR complex is formed by TCR interacting with CD3 and ζ chain, these 2 accessory complexes allow for the transduction of signals upon MHC-peptide binding
Most T cells recognise {?} and no other molecules
Most T cells recognise peptides and no other molecules
Explain why TCRs recongise only membrane bound antigens and not soluble
Because they need MHC
CD4+ T cells preferentially recognise antigens sampled from the {?} as opposed to CD8+ T cells that recognise antigens from the {?}
CD4+ T cells preferentially recognise antigens sampled from the extracellular space as opposed to CD8+ T cells that recognise antigens from the {intracellular (cytosolic) space
TCR interacts both with the {?} and also {?} exteremly specifically
TCR interacts both with the antigen presented by MHC and also the MHC itself exteremly specifically
Describe the difference between the antigens Presented by MHC class 1 and class 2
- MHC class | molecules present peptide antigens derived from pathogens that replicate inside the cell, such as viruses
- MHC class II molecules present peptides from pathogens and antigens that are present outside the cell taken up by endocytic vesicles of phagocytic cells.
Describe the structure of MHC class 2
Has an alpha and a beta chain, each has 2 chains within it (alpha 1, alpha 2 …)
- Is similar to Ig
MHC class 2 has a conserved binding site for {?}
MHC class 2 has a conserved binding site for CD4
MHC class 1 has a conserved binding site for {?}
MHC class 1 has a conserved binding site for CD8
MHC molecules are poly{?} and poly{?}
MHC molecules are polymorphic and polygenic
- Polymorphic = Multiple genes/forms
- Polygenic = A polygenic trait is one whose phenotype is influenced by more than one gene.
Can MHC bind multiple peptides or only 1?
Can bind multiple, but this is all in one celft
- binds a group of structurally similar peptides
Can MHC molecules bind and display foreign and self peptides or only one or the other?
Can bind and display BOTH self and foreign peptides
MHC class 2 binds to {?} peptides than class 1
MHC class 2 binds to longer peptides than class 1
All cells apart from {?} express MHC class 1, only {?} cells express MHC class 2
All cells apart from erythrocytes express MHC class 1
only antigen presenting cells express MHC class 2
So if we know which cells (CD8/CD4) sample the intracellular or extracellular space, which cell will bind to MHC class {?} to bind a viral antigen
So if we know which cells (CD8/CD4) sample the intracellular or extracellular space, which cell will bind to MHC class 1 to bind a viral antigen
Describe the whole process leading up to the presentation of an antigen by MHC2
Explain what the different components are in the image below and what is meant by germ-line alpha/beta chain DNA?
Germ line ___ DNA: is simply the inherited DNA, so how the DNA is in the cell
V is variable region
J is joint region
C is constant region
Explain overall how TCR rearrangement works with the help of the image below
There are many V fragments of DNA in the germ line that the cell can chose to make a V domain, also many J fragments.
- First step is the cell joins a D fragment with a J fragment (what is a D fragment?) are chosen at random
- second step is to join a V fragment with this DJ fragment
- this will be joined to a C fragment to make a chain
Does one T cell progenitor make one mature T cell? And do they all have the same TCR?
- No, makes many
- NOOOOO! Each mature T cell would have a different receptor
Which of the two TCR chains has no D segments in the locus?
Alpha
What chromosomes are the alpha and beta TCR chains on?
Alpha (and delta)- 14
Beta (and gamma) - 7
T cell receptor gene segments are arranged into a similar pattern to Ig gene segments and are rearranged by the same enzymes: {?}
T cell receptor gene segments are arranged into a similar pattern to Ig gene segments and are rearranged by the same enzymes: Rag1 and Rag 2
The most variable of the hypervariable regions in a TCR is CDR{?} (??)
The most variable of the hypervariable regions in a TCR is CDR3
In the process of gene rearrangement in the biosynthesis of a TCR, what is meant by the checkpoint
This is a checkpoint where if there is successful rearrangement of the beta chain, then the alpha chain can be rearranged
Which of the two chains, alpha or beta, in a TCR undergoes D-J joining?
- Beta
- Alpha undergoes V-J joining
Is the biosynthesis of a TCR antigen dependant or independant?
Antigen independant
Which chain on a TCR receptor does not have D segments in its gene?
α (but also γ?)
Describe the 2 mechanisms that TCR receptors create diversity in their structure (not too sure about this)
TCR receptor diversity (localised mostly in CDRs) is achieved by the selection of different segments (gene rearrangement) but also by modification in the junctional areas between those segments
- He says that we do not need to know this mechanism of recombination super well as we will be taught it in B cell receptor formation which is basically the same
Example of a formation of β chain of a TCR
Which chain in a TCR (α or β) is rearranged first?
β
{?} chain rearangement in a TCR can happen multiple times in order to pair a good α chain with a {?} chain.
α chain rearangement in a TCR can happen multiple times in order to pair a good α chain with a beta chain.
Explain what junctional diversity is
- This is a second way for the TCR to add specificitiy/diversity in its TCR as well as gene rearrangement.
- Is where during the joining of different gene segments, addition or removal of nucleotides may create new sequences at junctions
What enzyme mediates junctional diversity?
Mediated by TdT terminal deoxyneucleotidyl transferase
Compare which TCR chains show the most variability and compare with Ig
In total, does Ig or TCR αβ have more potential for diversity?
TCR αβ (has 1016 but Ig has 1011)
Name the 2 T cell markers that we can use to further characterise double negative T cells into 4 distinct categories of DN1-DN4
CD44 and CD25
DN1 (double negative 1) T cells {?} begun TCR rearrangment
DN1 (double negative 1) T cells have/have not begun TCR rearrangment
Describe the characteristics of the TCR in DN2 and DN3 cells
Are both undergoing TCR gene Beta chain rearrangement
- alpha chain will come later
Describe the status of development of the TCR at DN4 stage
These cells have undergone successful TCR rearrangment in the beta chain only (remeber that alpha chain comes later)
When is the first major checkpoint in T cell development in the thymus? What does it check?
Just after TCR β chain gene rearrangement, the DN4 cells need to go through the checkpoint
- checkpoint tells the body that the cell has undergone successful gene rearrangement
Describe the mechanism of the first checkpoint in the thymus (is to check for TCR gene rearrangement)
The DN4 cell will export the beta chain and a temporary alpha chain to its surface
What is the name of the temprary alpha chain exported to the surface of a DN4 T cell when undergoing the first checkpoint in the thymus?
pre T α
Describe what happens when the molecules are exported to the surface of a DN4 cell in the first checkpoint for T cell development in the thymus - Explain how T cells only form one TCR
- what is allelic exclusion?
- When the temporary alpha chain and the beta chain (forming the pre-TCR?) are exported to the surface of the DN4, signalling suppresses the expression of RAG genes so there is no more rearrangement of the Beta chain so the T cell can only form one specific TCR (so this is how T cells have one specificity)
- This is allelic exclusion
- The alpha chain still needs to be re-arranged
Describe the process of how the T cell triggers rearragement of the alpha chain
After successful signalling of a pre-TCR, this
- halts further b chain rearrangements
- induces expression of CD4 and CD8 (so is now double positive instead of double negative)
- initiates alpha chain rearrangement
So when (after what event) does the T cell become double positive?
After successful rearrangement of the β chain of the TCR
Summary of TCR and T cell development
