Fundamental immunology Flashcards
From which stem cells to T-cells derive, and where are these located?
Pluripotent haematopoietic stem cells in the bone marrow
What is the progenitor cell of T-cells?
Common lymphoid progenitor
Which two processes in T-cells take place in the thymus?
- Turning off non-T-cell lineage genes
- TCR gene rearrangement + selection based on TCR
Which chains make up the αβ-TCR?
- α-light chain
- β-heavy chain
Which regions comprise the α-light chain of the TCR?
V + J
Which regions comprise the β-heavy chain of the TCR?
V + D + J
Which processes lead to high TCR diversity? (2)
- VDJ recombination
- Junctional diversity
Which two forms of junctional diversity are there, and which is most important?
- n-nucleotide addition = most important
- p-nucleotide addition
How many % of T-cells is deleted during selection? Why?
90-98% are deleted, due to:
1. Negative selection
2. Non-productive rearrangements
On which cell types can MHCI be found?
Most nucleated cells
To which type of T-cell does MHCI present?
CD8+ T-cells
What is the structural makeup of MHCI?
- α heavy chain, consisting of 3 domains
- β2-microglobulin
Where is the antigen binding cleft of MHCI located?
Between domains 1 and 2 of the α heavy chain
What is the function of β2-microglobulin in MHCI?
Stabilization of the complex on the cell surface
On which cell types can MHCII be found?
Professional antigen-presenting cells
To which type of T-cell does MHCII present?
CD4+ T-cells
What is the structural makeup of MHCII?
α and β chains, each consisting of two domains
Where is the antigen binding cleft of MHCII located?
Between the α1 and β1 domains
What is the advantage of the MHC locus being highly polymorphic?
Population protection against pathogens
Which two forms of T-cell selection take place in the thymus?
- Positive selection
- Negative selection
In which part of the thymus does positive selection of T-cells take place?
Cortex
Which cell type is responsible for positive selection of T-cells in the thymus?
Cortical thymic epithelial cells = cTEC
What are T-cells selected for during positive selection? How does this work?
Their ability to bind self-MHC -> gives necessary survival signal
If the T-cell is unable to bind to self-MHC -> no survival signal -> death by neglect
What kind of antigen is presented to T-cells during positive selection in the thymus? What may one conclude from this?
Self-antigen is presented in the context of self-MHC
Conclusion: all T-cells are somewhat auto-reactive, for they are triggered by self-antigen presented in self-MHC
In which part of the thymus does negative selection of T-cells take place?
Medulla
Which cell types are responsible for negative selection of T-cells in the thymus? (2)
- Dendritic cells
- Medullary thymic epithelial cells = mTEC
What are T-cells selected for during negative selection? How does this work?
A wide variety of self-antigens is presented to T-cells -> if they react too strongly to this, they will be deleted by clonal deletion, preventing auto-reactive T-cell clones
Which two options are allowed to survive by the combination of positive and negative selection of T-cells in the thymus? Into which cell types will they develop?
- TCR with medium recognition of self-MHC and self-peptide -> Tregs
- TCR with weak recognition of self-MHC and self-peptide -> regular T-cells
How many % of T-cells survive negative selection in the thymus?
1-10%
What determines the total amount of T-cells in the body? (2)
- Thymic output
- Homeostatic proliferation
What determines the thymic output of T-cells?
Input of bone marrow-derived progenitor cells into the thymus
What is the approximate/average output of a human thymus in a young person? (CD4+ / CD8+)
CD4+ = ~17 million/day
CD8+ = ~8 million/day
How many antigen-specific T-cells/million are there to any specific antigen? (CD4+/CD8+)
CD4+ = 0,2-20/million
CD8+ = 0,6-60/million
Why doe higher frequencies of antigen-specific T-cells offer better protection?
Higher chance of encountering their antigen sooner upon infection
What are recent thymic emigrants (RTEs)? Why are they useful?
T-cells that have recently left the thymus -> can be used to reliably measure thymic function
In which situations is it especially useful to measure thymic output of T-cells? (2)
- After bone marrow transplantation
- During/after chemotherapy
Which three methods are available to measure thymic output?
- T-cell receptor excision circles (TRECs)
- Antigen expression
- In vivo labelling
What are T-cell receptor excision circles (TRECs)?
Circular DNA fragments, left behind after VDJ-recombination
Why are TRECs useful to measure thymic output?
TRECs do not replicate during mitosis -> frequency is stable, even is daughter cells divide. Therefore, TREC concentrations directly correlate with thymic output.
What is the TREC concentration in
1. Childhood
2. Elderly people
Childhood = high
Elderly = strongly decreased
In which clinical applications are TRECs mesured? (3)
- Newborn screening for SCID
- T-cell reconstitution for AIDS patients on cART
- T-cell reconstitution after bone marrow transplant
The total number of T-cells in the body of children and elderly people is roughly equal, despite a strongly decreased thymic output in elderly. How is this possible?
Proliferation of T-cells in the periphery
Which two mechanisms can lead to a reduction of TRECs?
- Cell division -> natural dilution
- Intracellular degradation of TRECs
How can antigen expression be used to measure thymic output? What is the weakness of this?
Certain antigens are enriched on naïve T-cells -> can be counted using flow cytometry
Weakness: while these antigens are enriched on naïve T-cells, they are not exclusive to them
Which two methods of in vivo labelling are available to measure thymic output? Which can be used in humans?
- Deuterated water labelling
- Bromodeoxyuridine labelling
Deuterated water labelling can be used in humans
How does deuterated water labelling to measure thymic output work?
Deuterated water is incorporated into macromolecules -> total uptake can be measured
What is the half-life of naïve T-cells in humans? (CD4+/CD8+?
CD4+ = ~6 years
CD8+ = ~9 years
How many % of human T-cells is produced in the thymus during their lifetime, and how many % is produced through homeostatic proliferation?
How does this differ from mice?
10-20% = produced in thymus
80-90% = produced using homeostatic proliferation in the periphery
In mice, near to 100% of T-cells is produced in the thymus
Which T-cell subset is largest in young individuals?
Naïve T-cells
Which T-cell subset is largest in elderly individuals?
Memory T-cells
What is the disadvantage of a reduced thymic output in elderly individuals?
While total numbers of T-cells remain the same, T-cell diversity declines -> less protected against new antigens
What is the difference in homeostatic proliferation between naïve and memory T-cells?
- Naïve T-cells: dependent on self-peptide-MHC complexes presented by DCs
- Memory T-cells: proliferation largely independent on self-peptide-MHC complex presentation by DCs
Which cytokines are important for homeostatic proliferation of T-cells?
- IL-7
- IL-15
What happens to the total number of T-cells when the CD4+ T-cell subset is depleted, for instance due to HIV?
Expansion of the CD8+ T-cell subset -> total number of T-cells stays the same
Upon encountering an antigen, the antigen-specific T-cell expands. After clearning the antigen, a memory T-cell subset remains. How much is this memory subset expanded, compared to the the starting subset of naïve, antigen-specific T-cells?
~1000-fold expansion (1/100.000 -> 1/100)
Upon encountering an antigen, the antigen-specific T-cell expands. How many times does the antigen-specific T-cell subset expand?
~10.000-100.000 fold expansion
What is the advantage of the expanded memory T-cell subset after infection? (2)
- Higher amount of antigen-specific cells -> better immune surveillance
- Pre-activated state of memory T-cells -> swift reaction upon encountering antigen
How do memory T-cell subsets stay around, even decades after encountering their antigen? Does their number stay similar?
Homeostatic proliferation; their number slowly drops as time passes without encountering their antigen
What is the result of a thymectomy upon birth in mice?
As mice are wholly dependent on their thymic output for T-cells, no T-cell repertoire forms -> immunodeficiency
What is the result of a thymectomy in adult mice?
T-cell subset has had the chance to establish -> no immunodeficiency, but lower T-cell numbers = more prone to infection
When does the human T-cell repertoire start to form? What is the result of this?
~12-13 weeks post-conception
Result: full T-cell repertoire present upon birth
What is the acute result of thymectomy upon birth in humans?
No acute clinical manifestation -> T-cell repertoire develops long before birth
What is the result of thymectomy in humans in their later life? (3)
Premature immunosenescence:
1. Infectious diseases
2. Poor response to vaccinations
3. Increased malignancies
What is DiGeorge syndrome, and what are its three main hallmarks?
22q11.2 deletion, resulting in:
1. Primary immunodeficiency
2. T-cell defects
3. Antibody isotype abnormalities
What causes high phenotypic variability in DiGeorge syndrome?
30-50 genes can be deleted -> exactly which genes are deleted determines the clinical manifestation
After a haematopoietic stem cell transplant, there is a transient altering of T-cell dynamics. What is the main determinant of how quickly T-cells repopulate?
Patient age
Which T-cell subset is quickest to recover after chemotherapy?
CD8+ T-cells
What determines the speed and ‘completeness’ of CD4+ recovery after chemotherapy?
Patient age
Which solution is being investigated to improve CD4+ recovery after chemotherapy?
Thymic rejuvination -> boosting the thymus output to improve T-cell recovery in elderly patients
Through which mechanisms can B-cells mediate auto-immune disease? (6)
- Antibody-mediated cytotoxicity
- Complement-mediated inflammation
- Ig-mediated antigen uptake
- FcγR-mediated antigen-antibody uptake
- Antigen (cross)presentation
- FcγR-mediated activation
Which two strategies can be used to specifically reduce B-cell function?
- Biologicals that deplete (subsets of) B-cells
- Small molecule inhibitors that interfere with downstream BCR signaling
Which surface marker is often targeted using B-cell depleting biologicals?
CD20 (rituximab)
For which processes is BCR signalling in B-cells important? (4)
- Activation
- Survival
- Proliferation
- Differentiation
What is are critical conditions for small molecule aiming to interfere with downstream BCR signalling?
- Must be specific for BCR downstream signalling -> no off-target effects
- Must target a part of BCR downstream signalling that does not have redundancy to prevent signalling via other parts of the pathway
What is an important target of small molecule inhibitors used to target B-cell function?
BTK
What is an often-used compound to interfere with BTK? How does it work?
Ibrutinib -> specifically targets the kinase domain of BTK, without interfering with other kinases
What is XLA? How does it occur?
X-linked agammaglobulinaemia
Occurs in case of BTK deficiency -> obstructed pre-BCR signalling after heavy chain rearrangements completely prevents B-cell development
What happens when BTK is deficient?
No pre-BCR signalling after heavy chain rearrangement -> complete developmental stop for all B-cells
Results in XLA
How do BTK-negative mice differ from humans with complete BTK deficiency?
Mice are still able to produce some B-cells, but these have reduced survival & proliferaton
In humans, B-cells are alltogether absent
What happens when the BCR of B-cells in BTK-negative mice is stimulated? What are the downstream effects of this? (2)
Reduced Ca2+ influx = lower activation of B-cells, leading to:
1. Lower NF-κB activation
2. Reduced expression of proliferation factors
What is a way to stimulate BCRs, regardless of their antigen-specificity?
Using anti-BCR antibodies (anti-IgM, -IgG, -IgA)
How does ibrutinib (and other small molecule inhibitors) interfere with BTK function?
Covalent binding to the ATP-binding site in the BTK kinase domain -> prevents kinase activity
Is ibrutinib activity reversible or permanent? Why?
Permanent -> covalent binding of ibrutinib to BTK kinase domain
Why does ibrutinib have limited adverse effects?
High specificity to BTK -> little interference with other pathways
True or false: ibrutinib is currently the only BTK inhibitor
False; since the introduction of ibrutinib, many even more specific BTK inhibitors have been introduced
What are the hypothesized mechanisms of action of BTK inhibitors? (4)
- Reduced BCR signalling
- Inhibition of B-cell integrin signalling
- Interference with chemokine signalling
- Interference in signalling from the microenvironment
For what type of disease have BTK inhibitors been approved?
Haematological malignancies involving B-cells
In which haematological malignancies can BTK inhibition currently be used? (6)
- Chronic lymphocytic leukaemia (CLL)
- Mantle cell lymphoma (MCL)
- Waldenström macroglobulinaemia
- Primary CNS lymphoma
- Marginal cell lymphoma
- Follicular lymphoma
Why do BTK inhibitors likely have limited effect on pre-B-cell tmours?
Pharamcokinetics -> not enough inhibitor to block rapidly dividing B-cells
Through which mechanisms can resistance to BTK inhibitors occur? (2)
- Spontaneous mutation of Cys481 = BTK inhibitor attachment site
- Gain of function of PLCγ
How does a gain of function of PLCγ lead to BTK inhibitor resistance?
PLCγ = downstream of BCL -> if it is constitutively active, inhibiting BTK no longer has any effect
What is the solution to prevent resistance to BTK inhibitors? (3)
- Increasing dosage
- Combining BTK inhibition with a compound that interferes in the same pathway
- Combining BTK inhibition with a therapy interfering with another pathway
Which pathways are often targeted in concert with BTK inhibition to prevent resistance? (2)
- Bcl2-inhibitors
OR - Anti-CD20 (rituximab)
What is unique to B-cell activation via the BCR, when compared with other activatory mechanisms (such as TLR signalling)?
Only signalling via the BCR causes a slight increase in BTK expression in the B-cell
What happens when BTK expression is constitutively slightly increased to the levels of activated B-cells in mice? What does this imply?
Development of auto-immune diseases
This implies that BTK is involved in auto-immunity
Which changes are observed in B-cells with constitutively increased BTK expression in mice? (3)
- Increased BCR signalling
- Increased NF-κB activation
- Spontaneous germinal centre formation in the spleen
What is the result of the changes observed in B-cells of mice with constitutively increased BTK expression?
Production of anti-nuclear auto-antibodies -> triggers auto-immune phenomena
What is the result of the use of BTK inhibitors in mice experiencing auto-immune disease due to constitutively increased BTK expression? What can be concluded from this?
Lower disease score -> conclusion: BTK inhibition might be useful in auto-immmune disease
BTK expression in memory B-cells is [decreased/increased] as opposed to naïve B-cells
Increased -> more easily activated
True or false: BTK only plays a role in B-cells
What is the implication of this?
False; BTK is also a signalling molecule in other immune cells
BTK inhibition could also work via cell types other than B-cells
In the circulating B-cells of human auto-immune patients, BTK expression is [decreased/increased] when compared to controls.
This is the case for [all B-cells/antigen-specific B-cells].
What is the implication of this?
Increased, in all B-cells
Implication: if naïve B-cells also have increased BTK expression, it must be somehow induced by something other than BCR activation -> possibly an auto-immune micro-environment
In which auto-immune disease has BTK inhibition shown to be succesful in a clinical trial?
Multiple sclerosis (MS)
How can it be explained that BTK inhibition is not succesful in all auto-immune diseases? (2)
- BTK is nog a significant player in all auto-immune diseases
- Rewiring of BCR signalling, such that BTK is no longer a vital part of the cascade
Each pathogen is countered by a tailor made immune defence. Which cell type is responsible to orchestrate these responses?
Th-cells
How are Th-subset specific to the invading pathogen activated?
By cytokines & costimulatory signals from DCs
How are DCs steered to stimulate specific Th-responses?
The combination of activated pattern recognition receptors (PRRs) on DCs determines the type of response they will stimulate
What are important classes of PRRs? (4)
- Toll-like receptors (TLRs)
- Glycan-binding receptors (GLR)
- NOD-like receptors (NLR)
- Retinoic-acid inducible gene-I-like receptors = RIG-like receptors (RLR)
Where can PRRs be found? (3)
- On the cell membrane
- In the cytosol
- On the endosomal membrane
Which PRRs can be found on the cell membrane? (2)
- TLR
- GLR
Which PRRs can be found in the cytosol? (2)
- RLR
- NLR
Which PRRs can be found on the endosomal membrane?
TLR
How does an antigen-presenting cell know what kind of pathogen it is dealing with?
Specific activation patterns of PRRs
What kind of virus is Newcastle Disease Virus (NDV)?
Highly contagious avian airway virus
How do PRRs on different cell types induce a coordinated response to NDV? (5)
- Alveolar macrophage RLRs are activated by viral nucleic acids -> type I IFN response
- NDV suppresses macrophage type I IFN responses by suppressing downstream RLR signalling
- Plasmacytoid DCs are recruited by type I IFNs
- Plasmacytoid DC TLR7 in the endosmoal membrane detects presence of viral nucleic acids -> type I IFN response
- NDV is unable to block downstream TLR7 signalling -> increased IFN I response
What are plasmacytoid DCs?
pDCs are found in circulation and migrate to infected tissues upon cytokine signalling
What is the effect of type I IFN signalling on viruses?
Inhibits viral replication
What does TLR7 sense?
Single-stranded virus RNA
How do PRRs on different cell types induce a coordinated response to HCV? (5)
- Hepatocytes sense HCV RNAs through RLRs and TLR3
- HCV produces proteases that block downstream signalling of RLRs and TLR3
- pDCs are recruited and detect HCV RNA through TLR7
- HCV cannot block downstream signalling of TLR7 -> production of type I IFNs
Which downstream signalling molecules of RLRs and TLR3 are blocked by HCV proteases?
RLRs: IPS-1
TLR3: TRIF3
What is the downstream signalling molecule of TLR7?
MyD88
What is an example of coordinated action of PRRs being unfavourable to the host?
Disease exacerbation in influenza A infections
Which group is most at risk for influenza A mortality?
> 65 years = 90% of mortality
What happens upon influenza infection of the lungs?
- Monocyte recruitment -> differentiate into macrophages & DCs
- RLRs sense viral RNA & trigger IRF8
- IRF8 produces an IFN-response by macrophages that inhibits viral replication
What is the result of the impaired IFN response in individuals >65 in influenza infections?
High viral load due to lack of IFN response leads to strong RLR activation -> triggers MAVS -> leads to IL-1β secretion -> neutrophil recruitment & tissue damage
Why are individuals >65 unable to produce strong type I IFN responses in case of influenza infection?
- Higher proteasomal degradation of TRAF 3 (=downstream of RLRs)
- Impaired IRF8 function (needed to trigger IFN production)
Result: impaired type I IFN response
How can neutrophil recruitment & activation exacerbate the inflammatory response in influenza infections?
NETtosis by neutrophils can trigger additional TLRs, inducing more inflammation
How do IFN responses in healthy individuals regulate IL-1β secretion in case of influenza infection?
They inhibit the inflammasome -> less IL-1β secretion -> prevents severe damage by neutrophils
Why does the impaired type I IFN response in elderly create favourable conditions for bacterial superinfection?
The tissue damage caused by neutrophils that are recruited by the (excessive) IL-1β response forms a good niche for bacteria
What is a DAMP? (definition)
Damage-associated molecular pattern
Where are DAMPs derived from?
Dying/stressed cells
What happens when DAMPs trigger PRRs?
Strerile inflammation
What is sterile inflammation?
Inflammation in the absence of pathogen infection
From which parts of the cell can DAMPs be derived?
- Cytoplasm
- Mitochondria
- Endoplasmic reticulum
- Nucleus
What are cytoplasm-derived DAMPs? (2)
- ATP
- F-actin
What are mitochondria-derived DAMPs? (3)
- ATP
- mtDNA
- Formyl peptidases
What are endoplasmic reticulum-derived DAMPs? (2)
- ATP
- Calreticulin
What are nucleus-derived DAMPs? (3)
- HMGB1
- HMGN1
- Histones
What is the result of non-PRR DAMP-receptors?
Signalling tissue damage without causing inflammatory immune activation
What is the function of RAGE? What happens when it is activated? Which disease can follow from excessive activation?
Non-PRR DAMP-sensor, transports self-DNA/RNA into the endosome, causing TLR7/9 activation
Excessive activation can be caused by a defective clearance of self-nucleic acids -> leads to SLE
Which DAMP is known to be highly present in donor kidneys from DCD donors (when compared to living donors)? What causes this high DAMP presence?
HMGB1, caused by ischaemia
What is the result of high HMGB1 presence in donor kidneys from deceased donors? (3)
- Upregulation of TLR2 & TLR4
- Triggering of TLR2 & TLR4 by DAMPs
- Increase of pro-inflammatory cytokines
Which PRR especially contributes to kidney graft loss? Why?
TLR4 -> causes recruitment of inflammatory cells by triggering secretion of pro-inflammatory cytokines
What are the main goals of research into PRRs?
- Enhanced understanding of disease & development of treatments
- Development of vaccine adjuvants
Why can PRR research contribute to the development of vaccine adjuvants?
Adjuvants need to potently trigger the right TLRs to induce an immune response and direct it into the desiered type of response
What are the goals of PRR research for vaccine adjuvant development? (3)
- Develop less toxic, more targeted antigens
- Develop adjuvants more specific to the desired immune response
- Develop adjuvants that potently trigger memory formation
Which cell types & processes can be steered using vaccine adjuvants? (6)
- DC maturation
- Antigen processing by APCs
- Th1/Tfh induction
- CD8+ T-cell induction
- B-cell activatoin
- Memory formation
