immune anatomy/dealing with antigens - block c Flashcards
t cell stages
naïve precursor –> trafficked to the thymus –> undergoes rearrangement of the T cell receptor genes to produce a unique TCR that recognises unique antigen in MHC context
In the thymus, an APC (DC) presents the immature T cells with MHC
those which interact moderately are positively selected, receiving signals for survival
those which recognise the MHC too strongly are sent signals for apoptosis, and so negatively selected
migrate into peripheral lymphoid organs
peripheral lymphoid organs
t cells produced in the bone marrow
selected in the thymus
exit through lymphatics
lymphatics drain the periphary towards lymph nodes
lymph nodes are aggregates of T cells, B cells, and APCs and act as the headquarters that decide when and where immune responses need to occur.
other nodes spread throughout
lymph nodes
various entry and exit points
artery and vein provide blood supply, and also entry for some lymphocytes via HEVs
main point of entry is the afferent lymphatic, inflow form lymphatics
germinal center houses B cells
paracortical area mostly contains T cells
parafollicular area forms interface at which T and B cells talk to each other
medullary cords house antibody producing plasma cells and macrophages
dendritic cells in lymph nodes
circulating body through blood and lymphatics
enters lymph node via afferent lymphatics, and brings antigen to the lymph node
the interactions between b cell/t cells and our antigen laden dendritic cell can occur at the follicular region
b cells can present to t cells, dcs can present to b and t cells - this is where the activation of t cells that can provide help to b cells occur
once help has been provided, the t and b cells can leave via different lymphatics to the rest of the body
spleen
red pulp - RBCs broken down/produced
white pulp - contains the region where b, t and apc interaction occurs
peyers patch
organised surface structures in the gut
dendritic cells present here can extend their pseudopods through and into the gut to sample antigen
they can interact with t cells, potentially activating b cells and Ab production
m-cells – specialised apc (modified epithelial cell) can present directly or indirectly (via dcs) to t cells.
leaving the lymph node
dendritic cells enter via different lymphatics
t cells enter via hevs
those that recognise antigen leave via efferent lymphatics
not all recognise antigen, those that do not leave the lymph node via the cortical sinuses
lymphocyte recirculation
lymphocyte responds to antigen in the peripheral lymphoid organs
must then leave to reach the effector site
dendritic cell role following infection
dcs carrying antigen go via lymphatics to lymph node
encounter naive t cells from the thymus here which react to test specificity
activated t cells then return to the blood and proliferate
they can either become memory cells or return to periphery and exert protection
the t cell receptor
antigen is recognized by the T cell when antigen is presented by an MHC molecule
for CD4+ T cells MHCII, for CD8+ T cells MHCI
the TCR comprises 2 paired protein chains; normally α + β (sometimes γ + δ)
like the Ab receptors it has a variable region that recognizes the diversity in antigens
also has a transmembrane domain and cytoplasmic tail which interacts with signalling molecules
MHC antigen recognition
MHC-I intracellular + killer –> CD8+ T cells
MHC-II for extracellular + helper –> CD4+ T cells
CD4+ T cells will help other cells and coordinate immune response
CD8+ T cells will kill virally infected cells
The cognate interaction between CD molecules and MHC molecules is critical to T cell activation and thus mounting of an effective immune response
adaptive immune response is initiated in peripheral lymphoid tissues
immature dcs are present in all tissues( (sometimes with different names)
once they have taken up some antigen in the periphery, they travel through the lymphatics to lymph nodes
once it has entered that lymph node it will attempt to interact with the T cells here
most will not respond to the antigen, but some will - and if they do, they will be activated upon being presented the antigen
when t cells recognise antigens
naive antigen-specific t cells recirculate looking for phagocytes presenting their cognate antigen
upon recognition, t cell and antigen-presenting cell form interaction
tcr transmits signals and t cell becomes activated
what happens after activation
firstly, the activated t cells start to proliferate
secondly, they lose the ability to leave the lymph node - this ensures they are then activated
finally the differentiate into their effector functions and then they can exit the lymph node and return to the periphery to carry out their effector functions
b cell development
immature b cells migrate to the spleen
completion of b cell development is in the spleen
b cells express different classes of membrane Ig molecules at particular stages of their development
immature b cells only express membrane bound IgM
mature but unstimulated b cells express membrane bound IgM and IgD
expression of the other classes of antibody (IgA, IgG, IgE) requires an additional and irreversible DNA recombination step
Ig expression relies on the cytokines released from t cells and apcs in the proximity of the activated b cell
antibody structure
antibodies consist of four poly chains (same as bcr)
two identical light and two identical heavy chains - detrmines the isotope class of the antibody
antigen binding region made up of both light and hevay chains - two antigen sites per antibody
fc portion (heavy chain constant regions) bind to a cell surface receptor
IgG antibody classes breakdown
IgG is broken down into 4 subclasses
antibody effector functions steps
neutralise (masks pathogen binding site to host cells)
aggulinate (clump together – Ab and pathogen)
opsonisation (from Greek – means make tasty)
activate complement cascade
antibody-dependent cell-mediated cytotoxicity (ADCC)
trigger degranulation of granulocytes
IgA
found in the circulation, but are the major isotype found in secretions (mucus in the gut, breast milk, tears and saliva
neutralize both toxins and pathogens
cannot fix complement (no inflammation)
advantageous as they are continuously interacting with self antigens and ‘good’ bacteria that form our mucosal surfaces
can mediate adcc by binding to fcrs on NK cells/granulocytes
trigger degranulation of granulocytes
long half life, fc portion not degrade by proteases present
monomer/dimer
IgM
first class of antibody to be produced during a primary immune response
low affinity of antibodies
pentavalent (five binding sites (fab portions) - making them highly efficient at binding antigen
circulating in the body
excellent at fixing complement (induce membrane attach complex to perforate pathogen)
induce lysis of pathogens they are bound to
form antibody antigen complexes that can be engulfed by macrophages
pentamer
IgG
most common antibody isotype (> 75% circulation)
Most diverse (further 4 sub-types)
all bind to Fc receptors (FcR)
can enhance phagocytosis by macrophages (through opsonisation)
good at fixing complement (especially IgG1 and IgG3)
IgG1 very good at mediating ADCC by NK cells
IgG1 antibodies are most commonly used in tumour therapy (can fix complement and ADCC mediation)
monomer
IgE
best known for its role in allergy & asthma
protect agaisnt parasitic helminths (worms)
made in very small quantities
very potent effects
basophils & mast cells express a high affinity IgE specific receptor
degranulation of eosinophils and basophils
release histamine and many vasoactive mediators
monomer
IgD
accounts for less than 0.25% of serum antibodies
found in both membrane and secreted forms
it has specific antigen binding activity
signals activation of b cells from bone marrow maturation
short half life
secreted IgD protective against mucosal pathogens
enhance mucosal homeostasis and immune surveillance
arms basophils and mast cells with IgD antibodies reactive against mucosal antigens including commensal and pathogenic microbes
not a lot known around its function
monomer
central tolerance
adaptive immune system generates a diverse range of antigen-specific cells, all recognising different antigens
education in the thymus removes self-reactive cells by clonal deletion
after being generated in bone marrow, lymphocytes travel to the thymus to be educated – and tested
positive selection
t cells don’t have enough affinity don’t receive ‘survive signal’ - death by neglect
selects for t cells with tcr of moderate/high for mhc
ensures mature t cells can recognise mhc and antigen in periphery
negative selection
removes t cells that bind too strongly
ensures self reactive t cells are clonally deleted
clonal deletion
t cells with too low an affinity for self-MHC undergo death by neglect
t cells with too high an affinity for self-MHC are deleted by signals for programmed cell death – or “apoptosis
Positive selection leaves cells that interact with antigen, but not too strongly
autoreactive t cells
high affinity for self antigens presented by mhc
peripheral tolerance
different mechanisms exist to ensure that mature t cells dont activate inappropriately
remember how t cells are activated - multiple signals needed - recognition of antigen via tcr - mhc complex and presence of cd4, co-stimulatory molecules, and eventually cytokines
this is where the innate system plays a role - the early innate danger signals upregulate apc co-stimulatory molecules eg. cd40 for b cell, cd28 for a dc, lack of costim –> anergy
antibody dependent cellular cytotoxicity
antibodies bind antigens on surface of target cells
receptors recognize cell bound antigens
cross linking triggers degranulation
target cell dies due to apoptosis
what does the t cell recognise?
antigen is taken up by phagocytes in the process of phagocytosis
it is taken from extracellular space and stored in intracellular vesicles (endosomes)
endosomes are inactive - until macrophage is activated - ph is decreased (acidified)
activates proteases which degrade antigens into peptide fragments
vesicles containing peptide fragments fuse with vesicles containing MHCII
antibody vs tcr antigen recognition
antibodies and t cell receptors recognise through very diff mechanisms
epitopes recognised by t cells can be any portion of the protein and can be buried within
by contrast antibodies recognise things i their 3d conformations and must be on the surface
t cells can because the antigen has been chewed into smaller pieces and presented to it
binding of peptide to mhc molecules
the sequences of amino acids determines shape of peptide
MHCI and MHCII interact with molecules on the MHC binding cleft and form covalent bonds
there are other differences between the two, but this principles is the same
how is the antigen recognised - intracellular
In this case, the endogenous antigen comes from a virus – e.g. Covid
The virus binds to the surface of the cell and infiltrates it, translocating to the nucleus where it can start its replication
During this replication, it will produce and release proteins into the cytoplasm e.g. spike proteins
These are then degraded into small peptides (8-9 amino acids long) by a proteasome which are loaded into peptide transporters (TAP-1 & TAP-2)
MHC produced in the RER associates with molecular chaperones including β2M and binds peptide
The complex is then transported via the golgi to the cell surface for presentation to a CD8+ T cell
how is the antigen rceognised - extracellular
Now lets look at exogenous antigen – e.g. allergen, or a protein from a pathogen
Taken up and degraded by phagocytosis in endosomes
MHCII is assembled in the ER, packaged in endosomes and trafficked via golgi
When it encounters peptide containing endosomes they fuse, and antigen can be loaded onto MHCII
This is then transported to the surface in a similar manner to MHCI
Antigen is now being presented to CD4+ T cells in the context of MHCII
role of t cells
the majority of t cells are helper cells - aim to direct, help or orchestrate the cell mediated immune response
also regulate the b cell response to antigen
eg. virus infects the cell and produces proteins in the cytosol
these are then shipped through the golgi, bind to MHCII and are presented on the cell surface
dendritic cells antigen processing
Able to process a wide array of pathogens not just viruses
Receptor mediated phagocytosis – could be e.g. a TLR, or when the antigen is bound by antibodies or complement.
Macropinocytosis – direct uptake of soluble antigens or virus particles in the milieu
Cross presentation – where receptor mediated phagocytosis has occurred, but antigen has been released into the cytosol
Transfer – where an incoming DC transfers to a resident DC
MHCII expression
MHCII is often said to be expressed by “professional” antigen presenting cells
Discussed later – but these “professional” APCs not only express MHC, they also express co-stimulatory molecules
Antigen presentation via MHC is often not enough to stimulate CD4+ or CD8+ T cells – co-stimulation is also required
Professional APCs include B cells, macrophages, DCs and epithelial cells
MHCI expression
Remember, these deal with intracellular pathogen e.g. viruses
Viruses can infect every cell of the body – nerve cells, liver cells, kidney cells etc can all be infected by viruses
The body needs to be able to recognize which cells have been infected with a virus and then be able to respond
Essentially every cell in the body (with the notable exception of red blood cells – no nucleus) can express
MHCI and present antigen to T cells
Some cell types are better at this process than others
how is antigen recognised in MHC context
High diversity in the MHC haplotypes (everybody’s MHC has different genetics) within the population
The progeny within a species have further increased diversity >
Increases the range of peptides presented to the immune system within species
Reduces the chance of pathogen evading the immune system
If everyone had the same MHC haplotype, the species as a whole would be susceptible
MHC polymorphism
MHC polymorphism affects how antigens can be recognised by T cells.
MHC binding the antigen is not the only determinant of “fit”
There are also contacts between the TCR and MHC, and between the peptide antigen and the TCR
All 3 of these must match for the fit to be correct, and for recognition to occur >
3rd and 4th dimension of immune response
Adaptive immune system takes time to respond
Immune responses occur in different locations
Requires cells to move, interact and produce cytokines to influence effector function
Although it takes time, this is needed as we need different immune responses in different locations at different times
timeline of response to infection
It starts with the entry of the pathogen near the origin
It might be dealt with quickly by innate response, and so we might need to induce adaptive immune response
However, if the microorganism is not dealt with quickly by the innate immune system it will start to establish an infection
Once we reach the inductive phase, DAMPs are produced and PAMPs will further enhance response – the body resident APCs now know to fetch T cells
The effector phase is reached once activated T cells are brought back from lymph and this begins to clear the infection
Finally – memory may be induced and shorten this
phases of immune response
The immune system is activated by inflammatory inducers that indicate the presence of pathogens or tissue damage
Innate immunity is normally initiated within minutes, and the initial response can be seen within hours
The adaptive immune response takes over later, with a variable timeline that could span days-weeks, even to years if it can’t clear the infection
Finally, we have the critical induction of memory including the production and maintenance of memory T cells
cytokines effect on CD4+ t cell effector function
once t cells have recognized the antigen, the apc will send signals - starting proliferation
signals sent through upregulation of IL-2 receptors and production of its own IL-2 receptors
the IL-2 cytokine binds to its receptors on the T cell - this is the signal for proliferation
other signals - such as IFNy (interferon gamma) instruct the cell to differentiate and kill
cytokine effect on CD4+ effector function
one effector function of helper t cells is to assist b cells in making antibodies
in addition to specialized apcs, b cells can also present antigen and activate t cells
the signals induce production of IL4, IL5, and IL6 which tell b cells to proliferate
these can then differentiate to resting memory cells or antibody secreting plasma cells
polarization of CD4+ t cell response
Th1 - secretes IFNy and activates macrophage functions
Th2 - secretes IL4 and helps antibody production
CD4+ t cells subsets
Th17 cells are important in response to extracellular bacteria and production of neutrophils
Tfh are found in the germinal centers and help b cells produce antibodies
treg cells downregulate immune response and prevent harmful immune responses
stages of differentiation by cytokines
activation via tcr antigen mhc
co-stimulation (CD28)
appropriate cytokines signal
b cell generation
bcr structure is a surface bound version of ig
when b cell is activated, secretes antibody of same specificity
once b cell expresses functional bcr, matures from primary bone marrow and enters periphery
migrates via lymph nodes
b cell activation
recognition of antigen by bcr leads to activation
once internalized, antigen is broken down to peptides
peptides are loading into mhc-II within the b cell and presented to antigen-specific CD4+ T cells
if t cell also recognizes antigen, provides help to b cell (costim)
allows b cell to fully activate and secrete antibodies
b cells are efficient apcs
b cells can only produce one antibody
on recognition the bcr will undergo endocytosis and be degraded along with the antigen
it will the load the epitope onto MHCII and express antigen on the cell surface at high density
here it can interact with a t cell that also recognizes the antigen
b cell help
CD4 helper cells provide help to b cells via CD40
t cells can influence antibody production through secretion of cytokines
induces proliferation of b cell and differentiation
Recognition by T and B cells is protective
Linked recognition by T and B cells is important in ensuring a robust and appropriate antibody response – but DCs can also play a part
Here, the DC uptakes antigen, breaks it down and
presents it via MHCII to a CD4+ T cell
If a B cell recognises the surface epitope of that antigen as well it can also process it, but it can also present other epitopes – linked recognition
Downstream, TFH cells can provide help after recognising a linked epitope
antibody structure detailed
Variable region binds to specific antigen
Different antibodies recognise/bind to different antigens or different parts of antigens
Binding site of antibody is known as the epitope
- Can be linear sequence or based on antigen-folding
functions of antibody
Neutralisation
Opsonisation
Complement
All depend on antigen-specific binding of the variable region
Different functions are associated with the constant region
Depends on the isotype of antibody secreted by the B cell
Binds to Fc receptors on effector cells
neutralisation
Involves the antibody binding bacterial (or other) toxins
Prevents the interaction of the toxin with its target protein and thus prevents damage
The antibody complexes can then be ingested by a macrophage and destroyed
opsonisation
A response to bacteria in the extracellular space e.g., in serum or tissue fluid
Antibodies bind to the surface of bacteria, coating them
The constant region of the Ab is free to interact with Fc receptors on the surface of macrophages
This triggers the ingestion and destruction of the bacteria
complement activation
A response to bacteria present in plasma
Complement is a cascade of enzymes which punch holes in cell membranes by assembling an MAC (membrane attack complex)
As before, Abs coat the pathogen – but this time they recruit complement proteins which puncture and kill the pathogen
The remains can then be taken up by a macrophage
neutralising toxin and blocking pathogen infectivity
High affinity IgG and IgA antibodies can neutralize toxins and block the infectivity of viruses and bacteria
Viruses can bind receptors on the cell surface, and become endocytosed
Once inside the cell, the virus can release its own DNA into the cell, and attempt to take over the host cells cellular machinery for replication
Antibodies can prevent all of this by binding to the receptor and preventing entry
You can see where vaccines and mAb therapies exploit these mechanisms
antigen-antibody complexes and complement
In the classical complement activation pathway, antigen-antibody complexes bind to complement component C1q, which initiates the complement cascade
Here, we see how tertiary Ab structure contributes to this activation. IgM is most stable (and most common) as a pentamer – it can bind many antigens at the same time and a single structure is required for C1q binding.
In the case of IgG, it exists as a monomer, and multiple IgGs are required to bind C1q
what if tolerance fails
If a T cell escapes clonal deletion in thymus and isn’t tolerised in periphery, it can become activated…
To non-harmful antigens > allergy
An example of this is celiac disease, where antibodies are produced against the harmless gluten in wheat following erroneous T cell “help”
The resultant inflammatory response in the gut causes damage in the gut – “enteropathy”
Villi (responsible for nutrient absorption) are lost, the epithelium becomes leaky, and there is an increased number of goblet cells (produce mucus)
can also respond to inhalants or self antigens
autoimmunity and allergy
Genetic factors are known to predispose people to both allergy and autoimmune disease
However, about 40% of us carry the gene that predisposes us to allergy, and few develop these
Likely that environmental factors and infection also play a role
A good example is ankylosing spondylitis, an autoimmune condition against MHC
If a person harbours the gene that predisposes them to ankylosing spondylitis and they are infected with the bacterium shigella, it is likely they will develop the autoimmune condition
This is likely due to a degree of cross-reactivity, but also because of innate activation > danger signals > increased co-stim. expression.
controlling immune response is critical
central tolerance - selects cells based on affinity, - approx. 95% of cells deleted, failing positive selection or negative selection
prevents immune responses to other antigens, E.g. food antigens, ‘good’ bacteria, autoantigen, Peripheral tolerance usually works because danger signals are lacking – no PAMPs or DAMPs, so no upregulation of costimulatory molecules, normally > anergic T cells
it is only in rare situations where you might have a danger signal being encountered at the same time as these antigens that you will go on and make an immune response
immune response control failing
Immunodeficiencies - Primary (genetically acquired)
Secondary - Infections e.g., HIV, Metabolic dysregulation, Therapeutically-induced (e.g., chemotherapy)
Immune-evasion by pathogens
trypanosomes
the parasite that causes sleeping sickness
These trypanosomes have an antigen coat on them, called the VSG (the variant surface glycoprotein)
Much like the immune system, they are encoded by many genes which can recombine to produce lots of different forms of these VSG
In this way, as the immune system begins to mount a response towards the VSG antigen, they start to recombine their VSGs
Once these are selected out, a new type of VSG will have become predominant – and so on and so forth
The parasite changes its antigenic markers to stay a step ahead of the immune response and evade it
