32. Specific Immune Response Flashcards

Question

How many binding sites for antigens does each class of antibody have? [IMPORTANT]

Answer 1

* IgG = 5 * IgM = 10 * IgD = 14 * IgA = 12 * IgE = 12

Answer 2

It is the region that binds to the antigen.

Answer 3

* Complement activation * Binding to receptors on different cell types: * Macrophages and neutrophils -\> Triggers phagocytosis and activation * Mast cells -\> Triggers degranulation * Epithelial cells -\> This causes the immunoglobulin to be secreted into tears, saliva etc.

Answer 4

* High affinity-Ig * Often pre-bound to receptor (since the affinity is high) * Waits for antigen to come along * Low affinity-Ig * Fc receptor not normally occupied * The receptors are only occupied after antibody has become complexed to an antigen (useful in phagocytosis)

Answer 5

* Tears, Saliva, Colostrum, Gut -\> IgA * Across placenta -\> IgG

Answer 6

VDJ recombination (a.k.a. somatic gene rearrangement)

Answer 7

* They are variable regions on the Fab domain of the immunoglobulin that determine its specificity for antigens * The heavy chain contains a V, D and J region * The light chain contains a V and J region They regions are known as variable (V), diversity (D) and joining (J).

Answer 8

* Immunglobulins break the rule that each polypeptide is encoded by one gene. * They are made up of 2 copies of 2 different polypeptides, but 7 genes encode these. * Within each V, D and J gene, there are several different versions of that region that exist (segments) -\> One segment is randomly selected from each and they are recombined to give the final immunoglobulin structure * For the light chain (lambda version!), there are 30 versions of the V region, 4 versions of the J region and 1 version of the constant region (there is no D region) * For the heavy chain, there are 10²-10³ versions of the V region, 20-30 versions of the D region, 4 versions of the J region and 8 versions of the constant region

Answer 9

* VDJ recombinase consists of the RAG1 and RAG2 * It selects a random segment from each VDJ gene and then makes a loop out of the DNA between the segments, so that the segments are brought close together * It then catalyses a crossover event between the two, so that the two are now continuous in the DNA strand * The excised DNA is lost from the genome, so that B cells (and T cells?) can be distinguished by having less DNA

Answer 10

In the bone marrow and thymus

Answer 11

* Multiple copies of V, D, J and C gene segments may be randomly recombined * D region genes may be transcribed in multiple reading frames * Imprecise joining may occur during rearrangement of genes and excision of the intervening DNA * Nucleotides are randomly inserted or deleted from the regions flanking the sites where joining occurs * Any H chain may pair with any possible L chain to generate up to 10¹⁶antibodies with different specificity

Answer 12

* The idea that any lineage of lymphocytes only expresses one distinct type of immunoglobulin * This is the driving force behind clonal selection

Answer 13

* Clonal selection is the theory that specific immunoglobulins exist on lymphocytes and that an antigen causes the corresponding lymphocyte to be "selected". * After antigen presentation, selected lymphocytes undergo clonal expansion because they have the needed antigen receptor, multiplying rapidly.

Answer 14

* It is the process by which activated B cells produce antibodies with gradually increasing affinity for antigen during the course of an immune response. * With repeated exposures to the same antigen, a host will produce antibodies of successively greater affinities. * It is driven by somatic hypermutation.

Answer 15

* After activation, clonal expansion of B cells is associated with somatic hypermutation at hotspots within the immunoglobulin genes * These hotspots correlate with the CDRs (complementarity-determining regions), which means that mutations there alter the affinity of the immunoglobulin for its antigen * The mechanism: * Activation induced deaminase (AID) deaminates cytosine to uracil at the HV hotspots * Error prone DNA repair pathways create double strand breaks and introduce mutations * The beneficial mutations are selected for, and therefore the B cells produced have progressively higher affinity for the antigen

Answer 16

* Help T cells -\> CD4+ * Cytotoxic T cells -\> CD8+

Answer 17

The conditions under which APCs present antigens to T cells controls the terminal differentiation of the T cell. These then control B cells.

Answer 18

* Dendritic cells are professional APCs. * Macrophages and B cells are also APCs.

Answer 19

* Bone marrow derived leukocytes distributed throughout all interstitial and lymphoid tissues * Serve as ‘Professional’ Antigen Presenting Cells (APC) * Present components of foreign microorganisms to the lymphoid compartment

Answer 20

Langerhans cells

Answer 21

Lymphocytes which have not met a specific antigen and therefore did not have the opportunity to be activated by the antigen and subsequently be differentiated into memory and efficient cells. All lymphocytes that leave the central lymphoid organs are naïve.

Answer 22

T cells: * Activated by peptide forms of the original antigen * Peptide must be presented on an MHC complex B cells: * Activated by a wider range of antigens, including proteins, lipids, nucleic acids and polysaccharides * They are able to bind to entire antigens (not just peptide segments) because their function involves release of antibodies that are complementary to the antigens on an undigested pathogen. * Do not require an MHC to present the antigens but can instead bind to free antigens.

Answer 23

* The MHC is a large genetic locus spanning 3000kb * It encodes the MHC class I and class II molecules * It also contains many genes responsible for initiating and regulating the immune response including the complement genes

Answer 24

In humans it is called HLA (human leukocyte antigen), containing: * MHC class I encoded by A, B and C genes * MHC class II encoded by DP, DQ and DR genes * Complement genes

Answer 25

* They are proteins on the surface of cells, used to present the peptide forms of foreign antigens to T cells * They are also important because they are very highly polymorphic within the population, but each individual expresses only a limited subset of the many possible polymorphic forms -\> This means that they are important in transplants, etc.

Answer 26

* The human leukocyte antigen (HLA) complex is the main MHC in humans, and the HLA genes have a high degree of polymorphism. * This is relevant in transplants, where it is almost certain that an unrelated donor will trigger an immune response in the host (against the HLA of the donor). * However, since the HLA genes are linked (have very close loci on chromosome 6), they tend to be inherited together, so that an individual can be viewed as having a maternal and paternal haplotype. * Therefore, siblings have a ¼ chance of possessing the same haplotypes, while monozygotic twins have the same haplotypes, making them the best candidates for transplants.

Answer 27

* Composed of an alpha chain of 45kD folded into three distinct domains * Non-covalently associated with beta-2 microglobulin, a secreted globular protein of 12kD * The membrane distal portion is folded into a groove which may accommodate peptides of 7-9 amino acids in length

Answer 28

* The floor of the groove is composed of 8 strands of an antiparallel beta pleated sheet: the sides are composed of two alpha helices * Peptide binding is very degenerate: a single class I molecules may bind up to 13 million different peptides * However, all peptides capable of binding to a specific MHC molecule share a common ‘binding motif'

Answer 29

* Polymorphism in the MHC are primarily localised to the peptide binding groove * MHC molecules differ in the number, orientation and distribution of hydrophobic pockets within the peptide binding groove * These polymorphisms mean that each MHC molecule has a characteristic binding motif that determines what peptides it can present

Answer 30

* Composed of two integral membrane proteins: an alpha chain (33kD) and a beta chain (28kD) * Each chain is folded into 2 extracellular domains * alpha-1 and beta-1 domains fold to form a peptide binding groove similar to that of Class I

Answer 31

* In MHC class I, the alpha helices are supplied by alpha chains, while in MHC class II, the alpha helices are supplied by an alpha and a beta chain * MHC class I molecules are closed by disulfide bridges at each end, while MHC class II molecules are not -\> The peptide binding groove is open at each end so that longer peptides can bind to MHC class II. It also means that the anchor residues are distributed throughout the peptide, not at the ends, like in MHC class I peptides, since these ends hang out of the MHC molecule

Answer 32

No, it depends on their structure. They must have the correct anchoring residues at the right positions.

Answer 33

MHC class I peptides: * 7-9 residues long * Anchor residues are at the C and N termini * Derived from **intracellular** pathogens MHC class II peptides: * Up to 30 residues long * Anchor residues are throughout the molecule * Derived from **extracellular** pathogens

Answer 34

* MHC class I -\> All nucleated cells * MHC class II -\> Antigen-presenting cells only

Answer 35

* Endogenous pathway * Exogenous pathway

Answer 36

* The process involves sampling of the intracellular space for foreign proteins * Once found, the foreign proteins are tagged with ubiquitin for degradation by the same pathway as normal misfolded proteins (i.e. the proteasome, a multi-catalytic complex found in the cytoplasm of all nucleated cells) * Upon infection and inflammation, the cell upregulates certain components of the proteasome, making it the immunoproteasome * The immunoproteasome degrades the foreign proteins into peptides of 7-9 residue length (the right length for presentation by MHC class II) * The peptides are moved into the endoplasmic reticulum by the TAP transporter * Here they are attached to MHC class I molecules, which are then moved to the cell surface for presentation to CD8+ (Cytotoxic) T cells

Answer 37

* The process involved APCs (e.g. dendritic cells) taking up foreign proteins from the extracellular space * This can occur via phagocytosis or by endocytosis of just the antigens * The endosomes carrying the foreign proteins fuse with lysosomes, leading to the digestion and breakdown of the proteins into peptides * MHC class II molecules are translocated to the endosome, so that the peptides can be attached to them * Then the MHC class II molecules are presented on the cell surface to CD4+ (Helper) T cells

Answer 38

Endogenous pathway: * All nucleated somatic cells use this pathway * MHC Class I involved * Processes intracellular proteins * Activates CD8+ (cytotoxic T cells) Exogenous pathway: * Only APCs use this pathway (since only they can take up cells/antigens) * MHC Class II involved * Processes extracellular proteins * Activates CD4+ (helper T cells) This makes sense because the endogenous pathway is triggered by infection of a cell (since the pathogenic proteins are found intracellularly), meaning that activating cytotoxic T cells makes sense, so that the cell can be killed. On the other hand, the exogenous pathway enables helper T cells to fight extracellular pathogens by stimulating B cells.

Answer 39

* No, they can RECOGNISE the peptide on any cell, leading to its destruction. * However, they can only be ACTIVATED by peptides presented by APCs (dendritic cells).

Answer 40

* Most cells are able to present intracellular proteins as peptides on their surface following infection -\> This is done via the endogenous pathway * However, dendritic cells do not need to infected in order for this to happen * They use a process called cross-presentation of antigens * Usually, before a cell can present peptides on an MHC class I complex, a virus would have to infect a cell, insert its DNA and lead to expression of its proteins by the host cell, which can then be degraded and presented * However, dendritic cells bypass this by endocytosing/phagocytosing the pathogen/virus, and then using a transporter to pump the proteins from the endosome into the cytosol, where it can enter the normal endogenous pathway of antigen presentation -\> So it can present the peptide without necessraily being infected.

Answer 41

Using the T-cell receptor (TCR).

Answer 42

* The TCR is composed of 2 chains (alpha and beta), each of 40-50kD. * It is from the immunoglobulin supergene family, so it is similar in structure to the TCR.

Answer 43

The CD3 complex and zeta chains associated with the TLR are used to transduce the signal into the cell, activating it.

Answer 44

* It depends on the presence of the co-receptors CD8 (on cytotoxic T cells) and CD4 (on helper T cells) stabilize the interaction between the TCR and either MHC class I or class II. * CD4 recognises class II, while CD8 recognises class I.

Answer 45

VDJ recombination, similar to in B cells.

Answer 46

Note: It is basically the same as in B cells. * TCRs break the rule that each polypeptide is encoded by one gene. * They are made up of an alpha and beta chain, but 7 genes encode these. * Within each V, D and J gene, there are several different versions of that region that exist (segments) -\> One segment is randomly selected from each and they are recombined to give the final immunoglobulin structure

Answer 47

* Multiple copies of V, D, J and C gene segments may be randomly recombined * D region genes may be transcribed in multiple reading frames * Imprecise joining may occur during rearrangement of genes and excision of the intervening DNA * Nucleotides may be randomly inserted or deleted from the regions flanking the sites where joining occurs * Any alpha chain may pair with any possible beta chain to generate 10⁹ – 10¹⁶ TCRs with different specificity

Answer 48

A range of functionally independent lymphocytes is created during the process of maturation in the primary lymphoid organs (thymus and bone marrow).

Answer 49

Secondary lymphoid organs

Answer 50

* Signal 1 * Binding of the TCR to the MHC-peptide complex on dendritic cells * Signal 2 (co-stimulatory molecules) * Binding of CD28 receptor to B7 proteins (CD80 and CD86) on APCs * Cytokines (sometimes called signal 3)

Answer 51

Signal 1: * Binding of the BCR to an antigen Signal 2 (co-stimulatory molecules): * In T cell dependent activation: * Binding of C28 receptor to CD40 ligand on T cells * Signal 2 can also be elicited by binding of complement proteins to the CD21 receptor * Cytokines (sometimes called signal 3) * In T cell independent activation: * No co-stimulation

Answer 52

* Both types involve the same signal 1, elicited by binding antigens to the BCR. * Then, T cell-dependent activation involves the B cell acting as an APC, which includes internalisation of a free or pathogen-bound antigen, degradation into a peptide form, and presentation on the cell-surface, bound to MHC Class II. This complex is bound to by helper T cells, which lead to signal 2. * T cell-independent activation involves binding of antigens with repeating epitope units, such as polysaccharides in bacterial capsules, which can then bind to multiple BCRs, cross-linking them and activating the B cell. There is thus no need for signal 2. The diagram shows T-cell dependent activation.

Answer 53

Signal transduction from the receptor to inside B cells is enabled by the Igα/Igβ heterodimer associated with the BCR.

Answer 54

* In both T cells and B cells, co-stimulation strengthens the intracellular signalling elicited by signal 1. * Both signal 1 and 2 are required for fully activation, otherwise the lymphocyte is inactivated or undergoes apoptosis, which ensures that adaptive immune response is not triggered by self or by harmless molecules (Frauwirth, 2003). * The main costimulatory proteins that act on T cells are the B7 proteins (CD80 and CD86), which are induced on APCs by the presence of microbes in the innate immune response, as well as positive feedback from the effector T cells themselves -\> This means they are only activated during infection.

Answer 55

* Some viruses and tumours avoid immune surveillance by down-regulating or inhibiting MHC class I expression and becoming invisible to CTL * In order to avoid this scenario, natural killer (NK) cells are deployed which actively kill somatic cells devoid of MHC class I

Answer 56

* NK cells derive from the common lymphoid progenitor and are closely allied to T and B cells * However, they are considered components of the innate immune system, so they are frequently called ‘innate lymphoid cells', which seems like somewhat of an oxymoron

Answer 57

They are part of the innate immune system, but they are activated by the adaptive immune system.

Answer 58

* Natural killer cells lack either a TCR or surface Ig for antigen recognition * Killing of target cells does not require prior priming * The decision of whether to kill a target cell depends on the balance between activating and inhibitory receptor signaling * Killing occurs only if the activating signal is dominant: dominant inhibitory signals pacify the cell

Answer 59

Activating: * NK cells express CD16, which is a receptor for the Fc region of immunoglobulins. * Therefore, although NK cells are part of the innate immune response, they are stimulated by the adaptive immune response. Inhibitory [EXTRA]: * NK cells express KIRs (Killer Cell Immunoglobulin-like Receptors) * They bind specifically to MHC class I, regardless of the peptide presented * Stimulation of the KIRs inhibits the NK cell * Failure to do so results in NK cell activation and killing of the target cell -\> Thus this protects against certain virus infections or tumours that inhibit MHC class I expression

Answer 60

* Killing virally-infected/tumour cells, which involves the release of perforin and granzymes from cytotoxic granules at the synapse formed with the target cell * Stimulating the action of macrophages by secreting pro-inflammatory cytokines

Answer 61

* Bone marrow and thymus * It is where development of lymphocytes happens, as well as selection

Answer 62

* Lymph nodes, spleen, Peyer's patches and mucosal tissues * They are where initiation of the immune response first occurs by activation of lymphocytes * Secondary tissues sample antigens from different body compartments

Answer 63

* Immature lymphcytes differentiate into mature lymphocytes in the primary lymphoid organs * Naive lymphocytes are those which have not yet encountered their antigen and are therefore not yet activated

Answer 64

* Spleen is highly vascularised, so it samples the blood * Peyer’s patches sample the gut * Lymph nodes drain tissue fluid from interstitial tissues

Answer 65

It is made of two parts: * Red pulp -\> Contains a store of erythrocytes in case of haemorrhage, No immunological function * White pulp -\> Wraps around arterioles (periarterial lymphatic sheath) and contains: * Naive T cells freely arranged * Primary follicles containing naive B cells

Answer 66

Lymph nodes are swellings of the lymphatics at intervals along their length which harbour components of the adaptive immune system.

Answer 67

* Afferent lymphatics bring tissue fluid in * Tissue fluid accumulates in the marginal sinus (just inside the capsule), then percolates into the medulla, from which it exits via the efferent lymphatic * Cords in the medulla are made up of plasma cells that can secrete IgM antibodies (they are the source of the IgM that is produced early in the primary immune response) * The IgM exits at the efferent lymphatic and enters the blood at the subclavian vein * The paracortex contains naive T cells * The primary follicles contain naive B cells

Answer 68

These are all structures within secondary lymphoid organs (lymph nodes and spleen): * Primary follicles contain naive B lymphocytes * Secondary follicles are those that have developed a germinal centre * Germinal centres are the sites of actived B cell proliferation and somatic hypermutation In other words, B cells in primary follicles are activated during the immune response and then form germinal centres. The follicles are then known as secondary follicles.

Answer 69

* High endothelial venules (HEV) are found in the paracortex of the lymph nodes * HEV constitutively express the adhesion molecules GlyCAM-1, CD34 and ICAM-1 * Binding of L-selectin on naïve T cells to GlyCAM-1 and CD34 induces rolling along the luminal surface * Activation of LFA-1 results in tight binding to ICAM-1 and diapedesis * This means that lymphocytes can move in and out of the lymph node via this route

Answer 70

* To limit of the spread of infection by non-specific means * Transport of pathogens and their constituent antigens to the secondary lymphoid organ Acute inflammation: * Vasodilation of capillaries causing an increase in vascular supply and a rise in local temperature * Increased vascular permeability leading to the accumulation of serum proteins at the site of infection * Oedema caused by the build up of a protein rich exudate The products of the innate immune response, such as antigens, are drained into the lymphatic system, via which they are taken to the lymph nodes.

Answer 71

* They are taken there by dendritic cells * They are in the tissue fluid, which is drained into the lymphatics system and into lymph nodes

Answer 72

* Dendritic cells are a type of antigen-presenting cell (APC) that are resident under epithelia. * They have pattern recognition receptors (PRRs) that bind pathogens, leading to dendritic cell maturation. * This leads to upregulation of co-stimulatory molecules, cytokine secretion and migration (via the lymphatic system) to the T cell zone of secondary lymphoid organs.

Answer 73

In the paracortex, which is full of naive T cells. Note that they can also activate T cells in other secondary lymphoid organs.

Answer 74

* Activated cytotoxic T cells bind (using their TCR) to peptide-MHC class I complexes on infected/tumour cells * This triggers them to kill the cell by: * Binding to CD95 receptors using Fas ligand, which induces caspase activity * Degranulation of perforin and granzyme -\> Perforin produces pores on the surface, via which granzymes are released into the cell, triggering apoptosis

Answer 75

* Th1 * Th2 * Tfh * Th17 * Treg

Answer 76

T follicular helper (cell)

Answer 77

Creation: * Created when a naïve CD+ T cell recognises an antigen presented by a dendritic cell that secretes IL-6 * This stimulates the up-regulation of Bcl-6 and commits to the Tfh cell lineage Function: * Expression of CXCR5 means that Tfh cells can migrate from the paracortex to the primary follicles -\> Here, Tfh cells activate antigen-specific B cells through interaction of CD40L with the co-stimulatory molecule CD40 * Secretion of IL-21 sustains B cell proliferation and formation of germinal centres

Answer 78

B cells enter the lymph node from the HBV, then they start travelling towards the primary follicles: * If they encounter an antigen before they reach the follicle -\> They become short-term plasma cells, which migrate and form the medullary cords (that secrete IgM antibodies in the early immune response) * If they encounter an antigen in the follicle -\> They go through clonal expansion, forming the germinal centre (which is a region of rapid B cell expansion)

Answer 79

* Somatic hypermutation and affinity maturation * Immunoglobulin class switching * Development of memory B cells

Answer 80

* It is when an activated B cell changes its antibody production from IgM to usually IgG * It happens in the germinal centres * Different immunglobulins have different constant regions * The gene segments for each of these is flanked by switch (S) regions) * AID is used to excise segments out and then there is end joining, so that the VDJ region and constant region are juxtaposed

Answer 81

Once activated and having undergone clonal expansion, the naïve lymphocytes become either effector or memory cells: * Effector CD4+ helper T cells carry out the roles of activation of macrophages, stimulation of inflammation and activation of all lymphocytes. These effects are mediated by cytokines, such as in the autocrine/paracrine activation of T cells by IL-2 released by helper T cells themselves. * Effector CD8+ cytotoxic T cells carry out killing of infected cells. * Regulatory T cells suppress the immune response. * B cells differentiate into plasma cells, which secrete large numbers of immunoglobulins. This enables a response to extracellular pathogens, since the immunoglobulins are involved in opsonisation, neutralisation of pathogens and complement activation. * Activation of lymphocytes also generates memory cells, which are cells with a long lifespan. They provide a faster response in the event of exposure to the same antigen in the future.

Answer 82

* Short-lived plasma cells * Long-lived plasma cells * Memory B cells

Answer 83

Antibody-secreting cells (plasma cells) are present in secondary lymphoid organs, mucosae (IgA) and bone marrow.

Answer 84

* Memory cells have already undergone class switching and are, therefore, capable of producing an isotype appropriate for the pathogen * Memory cells show constitutive down-regulation of cell cycle inhibitors enabling them to rapidly undergo clonal expansion * Somatic mutation ensures that the affinity of antibodies is many orders of magnitude higher than that of naïve B cells

Answer 85

* Effector memory T cells (TEM): * Generated early in the immune response * Lack CD62L and CCR7 but express homing receptors for peripheral tissues enabling them to patrol lungs, liver, gut etc * Secrete IFN-g, IL-4 and IL-5 * Central memory T cells (TCM): * Generated late in the immune response * Express CD62L and CCR7 causing them to home to the secondary lymphoid organs * Secrete IL-2 only

Answer 86

Several years

Answer 87

Every 10 years

Answer 88

Over 10⁹ specificities.

Answer 89

There is a higher potential in the adaptive immune response.

Answer 90

* Innate -\> Recognises non-protein molecules to distinguish self from non-self * Adaptive -\> Recognises protein antigens to recognise foreign cells

Answer 91

* They are tethered to osteoblasts in the osteolastic niche * The osteoblast niche is found on the lining of the medullary cavity in bones

Answer 92

* The osteoblastic niche maintains quiescence among HSC to prevent their exhaustion * The endosteal surface offers physical protection from trauma and toxins: * Bone absorbs environmental radiation, preventing DNA damage * Significant distance from a blood supply ensures a low O2 tension, reducing exposure to oxidative stress

Answer 93

* While in the osteoblastic niche, the haematopoietic stem cells are kept inactive * As they begin to move away from this region, they become multipotent progenitors -\> They commit to either the lymphoid or myeloid lineage * Those which become committed to the T-cell lineage, they enter the sinusoidal vessels and go to the thymus * Those which become committed to the B-cell lineage, they remain in the bone marrow and are guided to differentiate by the stromal cells (i.e. VDJ recombination, etc.)

Answer 94

Tolerance is defined as the lack of response to a given antigen (that would usually be expected to elicit a reaction), following exposure of lymphocytes to that antigen.

Answer 95

* Central tolerance * Peripheral tolerance

Answer 96

Clonal deletion -\> The removal through apoptosis of B cells and T cells that have expressed receptors for self before developing into fully immunocompetent lymphocytes.

Answer 97

In the thymus and bone marrow.

Answer 98

* Stromal cells in the bone marrow express an Fc receptor that binds IgM immunoglobulins * These immunoglobulins have a low specificity and are bound to various different self-antigens that they are essentially presenting to the B cells * The B cell BCR attempts to bind to the self-antigens * If one of the B cells appears to have produced an immunoglobulin with self-reactivity, they are given a chance to rearrange their binding region (light chain editing) -\> This is not the case in T cells * If they are still self-reactive, they are deleted by clonal deletion -\> Caspases execute the apoptosis * If not, then they can leave the bone marrow

Answer 99

* There are lobules separated by septa, each with cortical and medullary regions * There are * Haematopoietic stromal cells (macrophages and dendritic cells) * Non-haematopoietic stromal cells (epithelial cells)

Answer 100

* T cells progenitors in the outer thymus begin as double-negative T cells that express neither CD4 or CD8 * During this time, VDJ recombination occurs * First the beta chain is rearranged (using VDJ recombinase). * While the beta chain is being rearranged, it is complexed with an invariant pT-alpha chain. Ligation of the pre-TCR terminates beta rearrangement and alpha rearrangement can occur. This occurs when the the pre-TCR undergoes auto-dimerisation (it is its own ligand), signalling that it is somewhat functional. * Then the alpha chain is rearranged (since the beta chain locus is inaccessible and the alpha chain locus is accessible to the VDJ recombinase). * This induces the T cell to then become double positive, expressing both CD4 and CD8 * The T cell proliferates ready for positive selection * Positive selection leads to only either CD4 or only CD8 being expressed

Answer 101

* Cortical thymic epithelial cells (cTECs) -\> Positive selection * Medullary thymic epithelial cells (mTECs) + Dendritic cells -\> Negative selection This means that cells travelling from the outer cortex to inner medulla first undergo postive selection and then negative selection.

Answer 102

Positive then negative

Answer 103

* Cortical thymic epithelial cells (cTECs) have a stellate morphology and form a 3-dimensional network with no basement membrane * This means there is interaction between developing T cells and the epithelial cells * The cTECs constitutively express both MHC class I and class II * If the TCR binds more to the MHC class I than class II, then the CD8 receptor is stabilised and the CD4 receptor is lost * If the TCR binds more to the MHC class II than class I, then the CD4 receptor is stabilised and the CD8 receptor is lost * If there is insufficient affinity, then the cell dies by apoptosis

Answer 104

* Rescues the T cells from apoptosis * Imposes MHC-restricted antigen recognition on the emerging T cell repertoire * Lineage commitment to either the CD4+ helper T cell lineage or to the lineage of CD8+ CTL

Answer 105

It prevents self-reactive T cells from surviving and leaving the thymus.

Answer 106

* Capillaries draining the cortex are impermeable to plasma proteins or the passage of cells * Vessels in the cortex are composed of non-fenestrated endothelium and a thick basal lamina * A reticular sheath surrounds the vessels composed of reticular cells and macrophages

Answer 107

* Occurs in the medulla of the thymus * Self-antigens are processed and presented by thymic antigen-presenting cells (APCs), which use either MHC to present the antigen in a peptide form. * The APCs include: * Dendritic cells, which collect self-antigens from around the body and travel to the medulla of the thymus via the blood * Medullary thymic epithelial cells (mTEC) * Autoimmune regulatory protein (AIRE) is a transcription factor expressed within mTEC cells that allows promiscuous expression, which involves the expression of various antigens that are typically found in peripheral tissues, allowing a wider range of self-antigens to be presented in the thymus. * mTEC cells can also transfer the antigens to dendritic cells for presentation. * Negative selection occurs via binding of the complementary T cell receptor (TCR) to the MHC complex presenting the self-antigen, meaning that non-tolerant T cells are deleted from the population. * Caspases lead to the final apoptosis of the T cell.

Answer 108

Autoimmune regulatory protein (AIRE) is a transcription factor expressed within mTEC cells that allows promiscuous expression, which involves the expression of various antigens that are typically found in peripheral tissues, allowing a wider range of self-antigens to be presented in the thymus.

Answer 109

Autoimmune Polyendocrinopathy Candidiasis-Ectodermal Dystrophy (APECED), also known as APS-1: * AIRE mutations can lead to autoimmune polyendocrine syndrome type I (APS-1). * The symptoms include autoimmune adrenal insufficiency and hypoparathyroidism, which can be experimentally demonstrated by AIRE knockout mice. * This is because there is a failure of negative selection of T cells that are self reactive against glands.

Answer 110

Exosomes containing the protein components are sent from mTEC cells to dendritic cells using exosomes.

Answer 111

* The result of the positive and negative selection process is dependent on the avidity of the TCR-MHC complex binding, known as the ‘affinity model’ (Starr, 2003). * Only T cells with a moderate avidity for the antigen undergo maturation, while those with little/no avidity undergo apoptotic ‘death by neglect’ (during positive selection) and those with very high avidity undergo deletion (during negative selection). * How the TCR differentiates between a low and high avidity interaction is not known for certain, but it has been suggested that high-avidity interactions may involve a zipper mechanism that joins the CD8 and α-chain of the TCR, leading to a signalling cascade (Palmer, 2009). * Caspases cause the final apoptosis of the cell.

Answer 112

* Not all peripheral antigens are presented in the thymus and bone marrow, so that there is not complete negative selection. * Ectopic re-expression of developmental antigens in later life may activate self-reactive T cells that were never subject to negative selection * Molecular mimicry among T cell epitopes may stimulate self-reactive T cells * In B cells, somatic hypermutation partially negates some of the effect of negative selection. However, the effect of somatic hypermutation on tolerance is limited by the fact that B cells required a corresponding T cell to fully activated them and T cells do not undergo hypermutation.

Answer 113

BCR rearrangment cated in certain B cell lymphomas, where mistargeting of the mutation to oncogenes can lead to cancer (Odegard, 2006).

Answer 114

Tolerance can be damaging in cases of molecular mimicry, where a pathogen presents antigens that are highly similar to self-antigens, such that an infection by that pathogen can also lead to an autoimmune response or alternatively there is no response to the pathogen due to tolerance.

Answer 115

* T and B cell anergy * Regulatory T cells * Immune privileged tissues * T and B cell apoptosis

Answer 116

Atolerance mechanism in which the lymphocyte is intrinsically functionally inactivated following an antigen encounter, but remains alive for an extended period of time in a hyporesponsive state.

Answer 117

T cells: * In T cells, full activation requires both binding of the antigen (signal 1), as well as co-stimulatory signals (signal 2), such as those through B7 molecules on APCs. * If no co-stimulatory signals are provided or inhibitory receptors on the T cell are stimulated instead, then the T cells may enter an anergic state (Schwartz, 2003). * This is because no co-stimulation leads to a lack of transcription factors, such as AP-1, which would usually complex with NFAT to stimulate transcription of genes associated with activation. Instead, the NFAT homodimerises, and acts as a transcription factor for genes that lead to anergy. * APCs in the periphery present self-antigens (such as bone marrow-derived APCs that express AIRE) that typically do not present co-stimulatory molecules also, thus inducing anergy. B cells: * Can also enter an anergic state upon encountering a self-antigen if signal 2 is not provided by a helper T cell, or if inhibitory receptors on their surface are activated.

Answer 118

* Anergy is the functional inactivation of lymphocytes that are not co-stimulated, which means that if the conditions are not like those in the immune response or if the antigen encountered is not being presented to the lymphocyte, then the lymphocyte does not attack it. * Anergy also limits the strength of the immune response because the anergic T cell can still compete for co-stimulatory molecules from APCs, thus impeding activated (effector) T cells.

Answer 119

* Transgenic mice expressing hen egg lysozyme are bred with transgenic mice expressing anti-lysozyme IgM and having B-cell receptors capable of recognising lysozyme (i.e. one parent expresses a protein and the other expresses B cells and IgM against it) * The resulting mice produce lysozyme, but despite having lysozyme-recognising B-cells, they do not produce anti-lysozyme antibody after immunization with lysozyme * This demonstrates that the simultaneous presence of lysozyme and lysozyme-reactive B-cells leads to B-cell anergy * B-cells from the hybrid strain transferred into irradiated wild-type mice were indeed able to make anti-lysozyme antibodies * This proves that anergy was related to continued stimulation by lysozyme, but could be reversed when B-cells were in a host without the tolerising effects of lysozyme

Answer 120

* Immune privilege is the capacity of some tissues to protect themselves from the impact of an immune response * Immune privilege may be either ‘innate’ or ‘acquired'

Answer 121

* The central nervous system * The anterior chamber of the eye * The testis

Answer 122

* Physical barriers to sequester tissue-specific antigens from the immune system * Lack of lymphatic drainage (isolating the tissue from the adaptive immune system) * Expression of inhibitory receptors such as FasL that induce apoptosis * Induction of a local anti-inflammatory environment due to secretion of TGF-b * Depletion of essential amino acids to deprive T cells of the nutrients they require

Answer 123

* Secretion of anti-inflammatory cytokines such as IL-10 and TGF-b may counteract the local inflammatory response * Down-regulation of MHC class I renders tumour cells invisible to CTL * Recruitment of plasmacytoid dendritic cells and M2 macrophages may help reinforce a tolerant state * Secretion of chemokines such as CCL22 confers on tumours a form of ‘acquired immune privilege’ through recruitment of regulatory T cells

Answer 124

Immune-privileged tissues are relevant because infection or other tissue damage at these sites is likely to result in long-term inflammation, such as in the case of orchitis (testicular inflammation) after trauma.

Answer 125

It required recruitment of regulatory T cells (Tregs).

Answer 126

Regulatory T cells are CD4+ T cells that have a role in suppressing the activity of self-reactive helper T cells, which enables wider control because helper T cells are coordinators of the immune response.

Answer 127

* Foxp3 * It commits the cell to the regulatory lineage * It leads to the expression of anti-inflammatory cytokines,m including IL-10, IL-35 and TGFβ

Answer 128

* Naturally-occurring mutations in FoxP3 cause Immunodysregulation Polyendocrinopathy Enteropathy X-linked Syndrome (IPEX) -\> IPEX is associated with early onset autoimmune disease * Treatment is primarily done using corticosteroids, and bone marrow transplants have been suggested to show remission, but data is lacking and long-term outcomes are not certain (Wildin, 2003). * FoxP3 deficient mice (Scurfy mice) experience a premature wasting disease which is autoimmune in nature and T cell mediated

Answer 129

* Natural Treg cells (nTreg) -\> Formed during selection in the thymus, with a threshold for positive selection that is higher than for helper/cytotoxic T cells, meaning that they have a relatively high affinity for self-antigens. * Induced Treg cells (iTreg) -\> Formed outside of the thymus from CD4+ T cells under specific conditions, namely during inflammation and when the cell is sub-optimally activated.

Answer 130

* iTreg modulate responses to harmless foreign antigens * nTreg inhibit responses to self antigens

Answer 131

* Expression of anti-inflammatory cytokines, including IL-10, IL-35 and TGFβ * Expression of CTLA-4, which reacts with B7 on APCs and thus inhibits T cell activation (via CD28). This leads to direct inhibition (via cytokines) of effector T cell activation and also induces a tolerogenic state in dendritic cells. These dendritic cells in turn cannot fully activate new T cells, so these also become regulatory T cells (thus, the regulatory T cells are 'infectious').

Answer 132

* If the avidity of a T cell to MHC complexes presenting self-antigens is too low, then it undergoes death by neglect * If the avidity of a T cell to MHC complexes presenting self-antigens is too high, then it undergoes clonal deletion * If the avidity of a T cell to MHC complexes presenting self-antigens on the upper end of the range in between these, then it becomes a regulatory T cell (Treg)

Answer 133

* Lymphocytes that encounter self-antigens may also undergo apoptosis (as opposed to conversion to Tregs). * Mature T cells are believed to undergo apoptosis by either Bim upregulation, which affects the mitochondrial function, or activation of the Fas receptor.

Answer 134

* Physical barriers to the maternal immune system * Pacification of NK cells * Nutrient starvation of infiltrating effector T cells (in particular tryptophan) * Induction of Treg cells In effect, the foetus becomes an immune-privileged site.

Answer 135

* Trophoblast cells lack expression of HLA-A and B, that contribute to allograft rejection * Expression of HLA-E and HLA-G protects from NK cell lysis * HLA-G and E are invariant between individuals

Answer 136

* Trophoblast cells separate maternal and fetal blood supplies * Trophoblasts express high levels of indoleamine 2,3 dioxygenase (IDO) which catabolises tryptophan to kynurenine * T cells have a cell cycle check point that is tryptophan sensitive * Depletion of local tryptophan paralyses infiltrating T cells, preventing their clonal expansion

Answer 137

Activated CD4+ T cells ("Helper Cells") secrete cytokines that promote the growth and differentiation of other lymphocytes and that activate macrophages: e.g. IL-2, IL-4, IFN-γ. (From spec)

Answer 138

* IPEX syndrome caused by FoxP3 mutation -\> This is where T cells cannot be committed to the regulatory lineage * APECED resulting from failure of the AIRE gene -\> This is where a full range of self-antigens cannot be presented to T cells in order to induce tolerance

Answer 139

\>3% (in the US population)

Answer 140

Autoimmunity can present in childhood (type I diabetes), midlife (MS and myasthenia gravis) or old age (rheumatoid arthritis).

Answer 141

* Gender * Environmental factors * Geographical location: MS is prevalent in temperate zones * History of previous infection * Physical trauma * Genotype * Concordance between identical twins supports a genetic element * Numerous susceptibility loci have been identified by GWAS * Expression of specific MHC alleles confers greatest susceptibility

Answer 142

HLA-B27 is the only allele that encodes MHC class I which explains why it has such a huge effect on the risk of developing ankylosing spondylitis.

Answer 143

* Molecular mimicry between epitopes from infectious microorganisms and autoantigens * Impaired presentation of self antigen during self-tolerance * Ectopic expression of developmental antigens later in life * Failure of immune privileged sites to sequester self antigen e.g. breaches of the blood-brain barrier

Answer 144

* An infectious microorganism with similar epitopes to a self-antigen may infect the human * Peptides from this microorganism are presented with many immunogenic and inflammatory stimuli, so they lead to activation of T cells * Once activated, these T cells no longer need co-activation so they can mount a response against self-antigens

Answer 145

* Diabetic patients display molecular mimicry between Glutamic Acid Decarboxylase 65 (GAD65) and an epitope from the P2-C protein of Group B Coxsackievirus * CTL from patients with Autoimmune Hepatitis Type 2 recognise an epitope from the HCV core antigen (178-187: LLALLSCLTV) which cross-reacts with cytochrome P450 (8-17: LVALLVCLTV)

Answer 146

It can affect both.

Answer 147

Rheumatic heart disease: * Initiated following infection by Group A beta-hemolytic streptococci (S. pyogenes) * Molecular mimicry leads to the production of antibodies that also bind to proteins that are expressed by cells of the mitral value * HLA-DR7 haplotype confers genetic susceptibility * If left untreated, RHD causes heart failure in 46.9% of patients, pulmonary arterial hypertension (32.7%) or atrial fibrillation (13.9%)

Answer 148

Myasthenia gravis

Answer 149

* The disease shows an incidence of between 50-125 cases per million (0.01% of the general population) * Associated with progressive weakness of the extra-occular and respiratory muscles * Prior to the 1960s, the disease had a 30% mortality rate

Answer 150

α subunit of the nAChR

Answer 151

* Activation of complement, which leads to simplify the end-plate * Internalisation and degradation of the AChR * Steric hindrance of ACh binding

Answer 152

* Molecular mimicry -\> The nAChR contains a seven amino acid sequence in the α-subunit that cross-reacts with a shared immunodominant domain of gpD of the herpes simplex virus (HSV) * Ectopic re-expression of the fetal nAChR -\> The fetal nAChR has a γ chain, but this is changed usually before tolerance can develop. If the γ chain is ectopically re-expressed, an immune response can be launched.

Answer 153

* Prevalence of MS is 0.1% of the general population * Disease results in progressive demyelination of motor neurons * Follows a relapsing-remitting course

Answer 154

* It is an autoimmune reaction against the myeling sheaths of motor neurons * Various self-antigens have been associated with MS, but the most studied is MBP (myelin basic protein) * This protein is expressed by thymic epithelial cells under the control of AIRE, but tolerance is not established as would be expected * This is thought to be because the MBP does not properly bind to MHC class II * You would also therefore think that the MBP would not lead to T cell activation in the periphery, but low affinity can be compensated for by high avidity * The T cells can be exposed to many antigens by: * Molecular mimicry -\> Involves a high concentration of cross-reactive peptides that is renewable and alongside acute inflammation * Physical trauma -\> This can release large amounts of MBP into the blood

Answer 155

* Functional reconstitution (i.e. replacing the function of the destroy tissue, such as delivery of insulin for Type I diabetes) * Anti-inflammatory drugs * Immune suppression (e.g. calcineurin inhibitors) * Biologicals, such as cytokines and antibodies (e.g. IFN-b for MS and anti-TNFa antibodies (Infliximab) for Rheumatoid Arthritis) * Haematopoietic stem cell transplantation (e.g. for MS) * Re-establishment of self-tolerance

Answer 156

* There may have already been very extensive damage to the tissue, such that tolerance alone won't be enough to fix the symptoms * Frequency of autoreactive T cells is much higher in a primed immune system than one that is naïve -\> Due to clonal expansion * Inducing tolerance in memory T cells is much more difficult than in naïve cells * Autoimmunity is characterised by epitope spreading, which conceals the identity of the autoantigen involved

Answer 157

* The diversification of specificity towards epitopes * In other words, the autoimmunity first affects one epitope on a self-antigen and then it spreads to more epitopes * These epitopes can be on other epitopes on the same self-protein (intramolecular spreading) or other proteins (intermolecular spreading)

Answer 158

Many autoimmune conditions feature periods of relapse and remission. The remissions correspond to a new epitope being attacked each time.

Answer 159

Epitope spreading leads to diversification of the autoimmune repertoire, greatly complicating treatment options

Answer 160

* Infection leads to an immune response against the bacterial epitopes * This leads to T cell activation and macrophage activation * The macrophages lead to tissue damage that releases self-proteins * These self-proteins may be taken up by APC and presented to T cells, leading to an autoimmune response against the self-proteins * This is a positive feedback loop, where each round of self-protein release leads to triggering of an autoimmune response against the protein and therefore epitope spreading, so that there is more damage and more self-protein release

Answer 161

* Granulocytes (a.k.a. polymorphonuclear leukocytes) -\> Neutrophils, eosinophils and basophils * Mononuclear leukocytes -\> Monocytes, lymphocytes and natural killer cells The lymphoid differentiation pathway leads to the production of just the lymphocytes, while the myeloid pathway leads to the production of all the others. Dendritic cells come from both pathways.

Answer 162

Flow cytometry involves using specific fluorescent antibodies to detect cell-surface antigens that are markers of different leukocyte cell types. The flow cytometer then uses these antibodies to determine the numbers of different leukocytes in a sample.

Answer 163

* CD3 is a marker of all T cells * CD4 is a marker of helper T cells * CD8 is a marker of cytotoxic T cells * CD19 or CD20 is a marker of all B cells

Answer 164

* Cells are labelled using antibodies and then fed one by one into the path of a laser * Forward scatter detector -\> The larger the cell, the more forward scatter there will be * Side scatter detector -\> The more granulated, the higher the scatter * Fluorescent detectors -\> Detect fluorescence from antibodies that are used to label the cells

Answer 165

They contain cells that are CD3 positive, CD20 low and HLA-DR low.

Answer 166

Hybridoma -\> This is a fusion of a B cell and a plasma tumour cell, leading to the mass production of monoclonal antibodies.

Answer 167

A mechanism of cell-mediated immune defense where an effector cell of the immune system actively lyses a target cell, whose membrane-surface antigens have been bound by specific antibodies.

Answer 168

Pros: * Unlimited supply (when using a hybridoma) * Purity Cons: * Cost * Immunogenicity (especially if rat/mouse-derived) * Variable potency, although can be engineered to have high specificity

Answer 169

* First, mouse antibodies were used * Then, chimeric antibodies were used, which were a mix of mouse and human antibodies, becoming increasingly human * Finally, pure human antibodies were achieved The advantage of using more human antibodies is that they tend to be less immunogenic than mouse antibodies.

Answer 170

* ...omab = Mouse-derived * ...ximab = Chimeric * ...zumab = Humanized * ...mab = Human

Answer 171

Alemtuzumab

Answer 172

* Alemtuzumab is an anti-CD52 monoclonal antibodym that recognises an antigen present on nearly all lymphocytes * This means that it leads to the destruction and apoptosis of T and B lymphocytes, which are responsible for the demyelination in multiple sclerosis (it is an autoimmune condition) * This clearance of lymphocytes allows repopulation, in the hope that the new lymphocytes will feature more regulatory T cells and fewer self-reactive effector cell * (Cohen, 2012): * Compared Alemtuzumab with interferon beta 1a in reducing relapses in patients with relapsing-remitting multiple sclerosis * Alemtuzumab produced superior results in terms of reducing relapse

Answer 173

* Monoclonal antibodies are used to target the cytokines that are used to recruit immune cells (i.e. the 'master' cytokines) * These include: * Anti-TNF antibodies (e.g. infliximab, etanercept, adalimumab) -\> Combined with methotrexate * IL-6 receptor antibodies (e.g. Tocilizumab) * Can also target immune cells directly: * B cells (e.g. Rituximab targets CD20+ B cells) * T cells (e.g. Abatacept blocks T cell co-stimulation)

Answer 174

IL-6 is a “cardinal” pro-inflammatory cytokine: * Involved in antibody production * Activates T cells, macrophages and osteoclasts * Triggers acute phase response and systemic inflammation

Answer 175

It is a monoclonal antibodies that deplete B cells by: * Increasing B cell apoptosis * Complement-mediated lysis of B cells * Antibody-dependent cytotoxicity ADCC

Answer 176

Anti-PCSK9 antibodies: * PCSK9 is a protein secreted from cells * It binds to LDL receptors on the cell surface, leading to their internalisation * Anti-PCSK9 antibodies stop this from happening and thus increase the number of LDL receptors on the cell surface * In turn, this leads to increased uptake of LDL into the cell, so that plasma levels are reduced and there is a decreased risk of CVD events (Robinson, 2014): * Found that alirocumab in addition to maximal statin therapy reduced plasma LDL by 62% compared to maximal statin use alone * The fall in LDL was rapid

Answer 177

* It is a monoclonal antibody against HER2 receptors, which are upregulated in some breast cancers * Thus it is used as a treatment for some breast cancers * It is sold under the brand name Herceptin

Answer 178

* T cells -\> CD3 * B cells -\> CD20

Answer 179

* PD1 -\> Suppresses T cell inflammatory activity by promoting apoptosis (programmed cell death) of antigen-specific T-cells in lymph nodes and it reduces apoptosis in regulatory T cells. * CTLA-4 -\> Suppresses T cell inflammatory activity. When CTLA-4 is bound to another protein called B7, it helps keep T cells from killing other cells, including cancer cells. * Fas and Fas ligand -\> Involved in apoptosis

Answer 180

* Immunogenicity -\> Refers to the ability of a substance to induce cellular and humoral immune response * Antigenicity -\> The ability to be specifically recognized by the antibodies generated as a result of the immune response to the given substance.

Answer 181

A small molecule which, when combined with a larger carrier such as a protein, can elicit the production of antibodies which bind specifically to it.

Answer 182

* Strong antigens are a.k.a. T-cell dependent antigens * Weak antigens are a.k.a. T-cell independent antigens For example, the response to polysaccharides (e.g. to bacterial capsules) doesn't involve T-cells and is consequently weak and short-lived; relevance to vaccination.

Answer 183

* Tfh (T follicular helper cells) * These are the ones that go to primary follicles and activate B cells * Tfh are created when they are activated in the presence of IL-6, which causes upregulation of Bcl-6 * Th1 -\> Defence against intracellular pathogens through activation of cytotoxic T cells -\> Secrete IL-12 and IFN-γ * Th2 -\> Defence against large extracellular organisms -\> Secrete IL-4, IL-5 and IL-13, which drive eosinophils and mast cells. * Th17 -\> Recently discovered and linked to inflammatory conditions. Primarily triggered in response to fungal or extracellular pathogen infection. * Tregs -\> Suppress the activity of helper T cells: * Natural Treg cells (nTreg) -\> Formed during selection in the thymus, with a threshold for positive selection that is higher than for helper/cytotoxic T cells, meaning that they have a relatively high affinity for self-antigens. Modulate responses to harmless foreign antigens. * Induced Treg cells (iTreg) -\> Formed outside of the thymus from CD4+ T cells under specific conditions, namely during inflammation and when the cell is sub-optimally activated. Modulate response to self-antigens. * Tregs express Foxp3, which commits the cell to the regulatory lineage * It leads to the expression of anti-inflammatory cytokines, including IL-10, IL-35 and TGFβ.

Answer 184

* Follicular dendritic cells have important functions in the selection of memory B lymphocytes during germinal center reactions (GCR). * They present native antigens to potential memory cells, of which only B cells with high affinity B cell receptors (BCR) can bind. * Retention of antigen-antibody complexes is required for B cell memory.

Answer 185

Cell mediated: * Type 1 diabetes * Rheumatoid arthritis Antibody mediated: * Myasthenia Gravis * Grave’s disease * Rheumatic fever (Inappropriate inflammation in the heart, skin, joints or brain following the production of antibodies to connective tissue proteins such as myosin and collagen. This typically follows antibody mutations during the response to an infection with *Streptococcus pyogenes*)

Answer 186

The first line of defence in the resistance against infection, via inhibiting bacterial and viral adhesion to epithelial cells and by neutralisation of bacterial toxins and virus, both extra- and intracellularly.