immune anatomy/dealing with antigens - block c

Question 1

t cell stages

Answer 1

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

Question 2

peripheral lymphoid organs

Answer 2

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

Question 3

lymph nodes

Answer 3

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

Question 4

dendritic cells in lymph nodes

Answer 4

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

Question 5

spleen

Answer 5

red pulp - RBCs broken down/produced

white pulp - contains the region where b, t and apc interaction occurs

Question 6

peyers patch

Answer 6

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.

Question 7

leaving the lymph node

Answer 7

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

Question 8

lymphocyte recirculation

Answer 8

lymphocyte responds to antigen in the peripheral lymphoid organs

must then leave to reach the effector site

Question 9

dendritic cell role following infection

Answer 9

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

Question 10

the t cell receptor

Answer 10

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

Question 11

MHC antigen recognition

Answer 11

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

Question 12

adaptive immune response is initiated in peripheral lymphoid tissues

Answer 12

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

Question 13

when t cells recognise antigens

Answer 13

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

Question 14

what happens after activation

Answer 14

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

Question 15

b cell development

Answer 15

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

Question 16

antibody structure

Answer 16

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

Question 17

IgG antibody classes breakdown

Answer 17

IgG is broken down into 4 subclasses

Question 18

antibody effector functions steps

Answer 18

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

Question 19

IgA

Answer 19

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

Question 20

IgM

Answer 20

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

Question 21

IgG

Answer 21

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

Question 22

IgE

Answer 22

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

Question 23

IgD

Answer 23

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

Question 24

central tolerance

Answer 24

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

Question 25

positive selection

Answer 25

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

Question 26

negative selection

Answer 26

removes t cells that bind too strongly

ensures self reactive t cells are clonally deleted

Question 27

clonal deletion

Answer 27

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

Question 28

autoreactive t cells

Answer 28

high affinity for self antigens presented by mhc

Question 29

peripheral tolerance

Answer 29

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

Question 30

antibody dependent cellular cytotoxicity

Answer 30

antibodies bind antigens on surface of target cells

receptors recognize cell bound antigens

cross linking triggers degranulation

target cell dies due to apoptosis

Question 31

what does the t cell recognise?

Answer 31

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

Question 32

antibody vs tcr antigen recognition

Answer 32

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

Question 33

binding of peptide to mhc molecules

Answer 33

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

Question 34

how is the antigen recognised - intracellular

Answer 34

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

Question 35

how is the antigen rceognised - extracellular

Answer 35

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

Question 36

role of t cells

Answer 36

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

Question 37

dendritic cells antigen processing

Answer 37

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

Question 38

MHCII expression

Answer 38

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

Question 39

MHCI expression

Answer 39

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

Question 40

how is antigen recognised in MHC context

Answer 40

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

Question 41

MHC polymorphism

Answer 41

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 >

Question 42

3rd and 4th dimension of immune response

Answer 42

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

Question 43

timeline of response to infection

Answer 43

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

Question 44

phases of immune response

Answer 44

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

Question 45

cytokines effect on CD4+ t cell effector function

Answer 45

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

Question 46

cytokine effect on CD4+ effector function

Answer 46

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

Question 47

polarization of CD4+ t cell response

Answer 47

Th1 - secretes IFNy and activates macrophage functions

Th2 - secretes IL4 and helps antibody production

Question 48

CD4+ t cells subsets

Answer 48

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

Question 49

stages of differentiation by cytokines

Answer 49

activation via tcr antigen mhc

co-stimulation (CD28)

appropriate cytokines signal

Question 50

b cell generation

Answer 50

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

Question 51

b cell activation

Answer 51

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

Question 52

b cells are efficient apcs

Answer 52

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

Question 53

b cell help

Answer 53

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

Question 54

Recognition by T and B cells is protective

Answer 54

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

Question 55

antibody structure detailed

Answer 55

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

Question 56

functions of antibody

Answer 56

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

Question 57

neutralisation

Answer 57

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

Question 58

opsonisation

Answer 58

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

Question 59

complement activation

Answer 59

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

Question 60

neutralising toxin and blocking pathogen infectivity

Answer 60

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

Question 61

antigen-antibody complexes and complement

Answer 61

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

Question 62

what if tolerance fails

Answer 62

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

Question 63

autoimmunity and allergy

Answer 63

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.

Question 64

controlling immune response is critical

Answer 64

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

Question 65

immune response control failing

Answer 65

Immunodeficiencies - Primary (genetically acquired)

Secondary - Infections e.g., HIV, Metabolic dysregulation, Therapeutically-induced (e.g., chemotherapy)

Immune-evasion by pathogens

Question 66

trypanosomes

Answer 66

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