Checkpoint Questions Compiled
Lecture 1: Basic Concepts in Immunology
Why were Edward Jenner’s observations critical to our understanding of immunology?
Jenner is credited with developing the first live vaccine. By inoculating a boy with pus from a cowpox virus he became immune to the more severe smallpox virus. This continues to be the basis of vaccines today, where a small portion of the disease is given to the host in order to train the immune system on how to deal with a full blown attack of this disease.
What key observations led to the discovery of soluble mediators that protect us from infection?
Antibodies are the soluble mediators of our bodies that protect us from infections. The guinea pig experiment with serum from an infected pig contains serum proteins (antibodies) and protects the 2nd pig from gaining the infection. Antibodies are involved in passive immunity and are part of the innate immune system.
Vaccines have proven highly effective in reducing the incidence of many infectious diseases. Some diseases, such as diphtheria, have been virtually eliminated in the United States due to successful vaccination campaigns. Looking at the graph below, when was the diphtheria vaccine widely distributed in the United States?
Based on the graph, the diphtheria vaccine was widely distributed around 1955 bc this is when the reported cases level off. The vaccine was developed in 1940 and cases were falling from 1940 to 1955 but they were still forming a triangle and thus vaccines were likely not easily placed in the population.
Lecture 2: Principles of Innate Immunity
What are the two lines of defense against pathogens?
Adaptive and innate immunity
What are the two major cell types that function in the adaptive immune system? In which arm of the adaptive immune system does each cell type function?
Major cells in the adaptive immune system are the B cells and the T cells. B cells are active in the humoral branch of the adaptive immune system, and are present when secreted from plasma cells. And T cells are active in the cell-mediated branch of the immune system, they secrete cytokines or they bind to APC cells and attack the infected cell.
How do symbiotic microorganisms protect us from pathogen infection?
Symbiotic microorganisms like the microbiome of our gut help protect us from infection by taking up space and outcompeting pathogens within our gut from establishing a site there.
What are the different categories of pathogens?
Viruses, bacteria, parasites, and fungi.
Some examples of physical and chemical barriers.
Physical barriers: Eyelids, Stomach lining, intestine lining, skin etc.
Chemical barriers: Tears, Saliva, C3, complement proteins, etc.
How does the enzyme lysozyme act as a chemical barrier?
Lysozyme works to chop of the peptidoglycan on gram positive bacteria’s thus leaving them vulnerable to other enzymes that can destroy the pathogen or punch holes in its inner membrane. The lysozyme only is functional in gram positive pathogens because gram negatives have two layers of membranes and the peptidoglycan is sandwiched in between and inaccessible by the lysozyme enzyme on the outside.
What is the mode of action of beta-defensins?
Beta defensins are positively charged molecules, that are attracted to and embedded within the pathogen membrane and cause the membrane to pull apart in the membrane and form holes in the pathogen membrane causing the pathogen to die.
What are the two lineages derived from HSCs?
HSC (Hematopoietic stem cells) form the lymphocyte and the myeloid lineages. Most of the innate immune system cells are derived from the myeloid lineages including: dendritic cells, mast cells, macrophages, eosinophils, basophils, monocytes (become DC or macrophages). Most of the adaptive immune system cells are derived from the lymphocyte lineage including: B cells, T cells, ILC (Innate lymphoid cell) along with an innate immune system cell natural killer cells.
What are the different types of granulocytes in the immune system?
The granulocytes in the immune system are the mast cells, eosinophils, macrophages, basophils, neutrophils.
What are the different types of agranulocytes in the immune system?
The agranulocytes (cells without contained granules within them) are dendritic cells, B cells, T cells, monocytes, ILC and natural killer cells.
What are the different steps in inflammation?
1. Bacteria recognized and phagocytosed by the macrophage trigger the macrophage to release cytokines and chemokines. The cytokines and chemokines travel into the blood stream.
2. Vasodilation (blood vessel expansion) results in increased vesicle permeability of and innate immune cells (neutrophils and monocytes) from the blood stream can squeeze outwards into the tissue, causing redness, heat and swelling.
3. Inflammatory cells migrate into the tissue (T cells – blue in textbook diagrams), releasing inflammatory mediators that cause pain.
Cytokines increase the permeability of blood vessels, allowing for fluid and proteins to pass into the tissues.
Chemokines detect the migration of neutrophils to the site of infection.
What are the cardinal signs of inflammation?
1. Pain
2. Swelling
3. Redness
4. Heat.
Lecture 3: Cellular mechanisms of the innate immune system
What are the major classes of PRRs? What types of PAMPs can PRRs bind?
PRRs are pattern recognition receptors are found on the sensor cells (macrophages, DC). Families of PRRs:
1. Toll-like receptors (TLRs):
2. Lectin (mannose receptor): Aka CD206, binds to carbohydrates, sulfated sugars and polysaccharides, prompts phagocytosis.
3. Scavenger receptor: Bind to negatively charged ligands, sulfated polysaccharides and LTA (gram positive bacteria) and LPS (gram negative bacteria), prompts phagocytosis
4. Cytosolic innate receptor: Binds intracellular (inside the cell) PAMPs. Cytosolic nucleic acids (DNA and dsRNA), cytosolic bacterial signalling molecules (cyclic dinucleotides). Inhibits pathogen growth, Prompts WBC to kill infected cells.
5. Opsonin receptor: Bind to pathogens or foreign molecules tagged with opsonin’s. Prompts phagocytosis. Complement receptors CR3 and CR4.
What are the major cytokines secreted during an innate immune response?
IL-1, IL-6, IL-12, TNF-a and IL-8.
What structural features are shared within the TLR family of proteins?
? looking shapes, top curl is the leucine rich domain, then transmembrane domain then dot is Toll-IL-1 receptor within the cytosol. Often dimerize to initiate signalling.
TLR 1 : TLR 2 form a dimer and face extracellular space can recognize mycobacteria, bacteria and fungi.
TLR 2 : TLR 6 form a dimer and face the extracellular space recognize mycobacteria, bacteria and fungi.
TLR 5 faces the extracellular space and can recognize flagellin on fungus
TLR 4 faces the extracellular space and can recognize LPS on G- bacteria
TLR 3 faces the endosome and recognizes the dsRNA
TLR 7 faces the endosome and recognizes the ssRNA
TLR 8 faces the endosome and recognizes the ssRNA
TLR 9 faces the endosome and recognizes the CpG DNA.
What key signaling molecules responsible for aiding the innate immune response are secreted by macrophages?
IL-1b : activates vascular endothelium, activates lymphocytes increases access of effector cells. Fever production of IL-6
TNF-a: Activates vascular endothelium and increases vascular permeability which leads to increased entry of IgG complement and cells to tissues and increased fluid drainage to lymph nodes. Fever, mobilization of metabolites, shock.
IL-6: increased antibody production. Fever, induces acute-phase protein production.
CXCL8 : recruits neutrophils , basophils and T cells to the sites of infection.
IL-12: Activates NK cells.
What are the four stages of neutrophil migration?
1. Rolling adhesion: selectins on blood vessel wall bind to the neutrophil carbohydrates
2. Tight binding: chemokines in vessel bind receptors on the neutrophil. Now tightly bound to inside wall of vessel.
3. Diapedesis: Integrins on neutrophil become active when bound to vessel integrins neutrophil stops rolling.
4. Migration: Integrins and chemokines allow the neutrophil to squeeze out through blood vessel walls.
Describe how NK cells can detect an intracellular pathogen.
NK cells can detect an intracellular pathogen by binding of NKG2D binding the infected cells MIC and 2B4 binding the CD48. Activation of cytotoxic machinery in the NK cell is released. It expels perforins which punch holes in the infected cells membrane and granzymes cause the cell to undergo apoptosis.
Why is the release of TNF in the bloodstream problematic?
Causes vasodilation in the bloodstream so increase rate of cytokine released into the tissues is increased. When this occurs when its not supposed to it induces inflammation for the tissues when not needed.
Lecture 12: Development of T lymphocytes
What three major cell types found in the thymus play a role in T-cell development? Explain the function of each type in T-cell development.
cTECs (cortex Thymic Epithelial Cells) = express MHC I or MHC II s have a role in positive selection.
mTECs (medullary Thymic Epithelial Cells) = present peripheral antigens and have a role in negative selection.
CD4 and CD8 T cells: become mature and are derived in the thymus depending on their location.
Why are individuals who lack the IL-7 receptor unable to produce functioning T cells?
This is because the IL-7 receptor is needed to interact with the IL-7 cytokine which when bound to its receptor promotes the cell survival through the upregulation of anti-apoptotic proteins such as Bcl-2 and Bak.
Explain the role of Notch1 in T-cell development and its importance in lymphoid progenitor cell commitment to thymocyte development.
Notch1 signalling is essential for T lineage commitment and is further required during the early phases of thymocyte differentiation up to the DN3 (double negative 3) phase. Signalling with Notch turns off only when the large pre-T cell (DNA) stage because once the cell is committed to its T cell lineage it isn’t needed anymore (during beta chain selection).
What checkpoints can occur as part of the T-cell development process? Why don’t all three checkpoints need to be passed by a developing T cell?
1. Beta chain testing: The beta chain once formed is paired with a surrogate light chain in order to test if the TCR is functioning and that allelic exclusion is occurring. Allelic exclusion prevents more than 1 beta chain from recombining on the same T cell.
2. Alpha chain testing: Both CD4 and CD8 are expressed, and alpha chain begins to recombine. many chances for recombination of the alpha chain exists because there are many Valpha and Jalpha segments that are possibilities for recombination. Continues trying to recombine until its runs out of molecular machinery (v and J segments).
3. Negative selection: The whole TCR is tested against being self reactive to self antigens. If it is, its destroyed though apoptosis, ensuring the only T cells that survive are those that will NOT react with the hosts own antigens (preventing auto-immunity).
Why do developing thymocytes need to use the pre-Tα chain to progress through the β-chain checkpoint?
The pre-Ta chain is needed so the TCR receptor beta chain can be tested earlier. This provides a test TCR that can be tried for self-tolerance and destroyed if already reactive. That way the body doesn’t spend energy rearranging an alpha chain for a beta chain that’s already defective. Autoreactive T cells with self reactive beta chain are destroyed now via apoptosis.
What are the three possible fates of double-positive thymocytes continuing their development in the thymus?
1. Death by neglect. When the T cell has no binding affinity to cTEC (MHC I or II), the cell is destroyed. The cell is not reactive when it should be.
2. Positive selection/maturation to single positives: Low to moderate affinity of T cell binding to cTEC. (Perfectly right, goldilocks principle)
3. Negative selection/apoptosis: high binding affinity from cTEC to APC to T cell. This is too strong an interaction, to a potentially self antigen so cell is destroyed via apoptosis.
Lecture 13: Development of B lymphocytes
Which signal in differentiating progenitor cells is required to commit differentiation to B-cell development?
Differentiating progenitor cells need to receive E2A and PAX5 and IL-7 (survival signal) signal to commit to B-cell development. IL-7 signal provided via mesenchymal cells in the bone marrow tell the B cell to continue surviving by up-regulating the expression of anti-apoptotic molecules like Bcl-2 and Bak. E2A and PAX5 are additional signals the early pro-B cell receives which are transcription factors for B cell specific promoters and enhancers.
What are the critical checkpoints of B-cell development?
1. Pre BCR testing: At this point the heavy chain for the antibody (IgM) has recombined and we need to test that this chain is functioning and will pair with a light chain. A surrogate light chain is created and used for testing purposes. The surrogate light chain is made of λ5 or VpreB. If the B cell passes this check point the cell proliferates and light chain rearrangement can begin. Tests with allelic exclusion meaning that if one heavy chain rearranges properly another on the same cell will not be rearranged. This stage is antigen independent as it hasn’t met its antigen yet.
2. Negative selection 1: The immature B cell is still in the bone marrow and the light chain has recombined, testing if it binds to the heavy chain and produces a feasible BCR that isn’t self-reactive to self-antigens in the bone marrow. Light chain has to be allelic exclusion (if one chromosome combines, another will not) and isotypic exclusion (if the λ light chain has rearranged, then the κ light chain cannot rearrange and vise versa). Antigen dependent, as the BCR is tested with self antigens on the stromal cells and soluble antigens in the bone marrow. Central tolerance because testing against any immature B cells that are reactive to antigens in the central lymphocytes (bone marrow). Receptors can undergo receptor editing.
3. Negative selection 2: transitional B cells are tested for self-reaction against antigens expressed in the periphery. Antigen dependent, as the BCR is tested for reaction for antigens expressed in the splenocytes (spleen cells) or soluble molecules in the spleen or circulating in the blood. and if reactive destroyed. Peripheral tolerance. And NO receptor editing can occur.
What is the composition of the surrogate light chain, and how does it resemble the immunoglobulin light chain?
The surrogate light chain is composed of l5 and VpreB regions that are versions of the constant and variable regions on the light chain respectively. These allow the BCR to be tested with heavy chain binding to light chain binding and those that aren’t binding properly to be destroyed without wasting extra energy on their growth.
Why is allelic exclusion of an immunoglobulin heavy chain that has not recombined necessary to normal B-cell function?
This is essential to prevent multiple heavy chains from rearranging and being present on the same B cell. Allelic exclusion stops another chain from rearranging when one has already rearranged on the large pre-B cells.
Compare and contrast the three possible fates of negative selection of self-reactive immature B cells.
1. Apoptosis: When a cell fails tests, its will be killed in a regulated way to keep things organized and allow for reuse for some aspects of the cell.
2. Heavy chain rearrangement: The heavy chain gets 2 chances for rearrangement. Provided the D-J rearrangement has been successful on both chromosomes, the V-DJ rearrangement needs to be attempted. The V-DJ rearrangement is tried on the first chromosome and if it fails its tried on the second chromosome, if this also fails, the cell dies via apoptosis.
3. Light chain rearrangement: The light chain gets 4 attempts to rescue itself, because both chromosomes are tested but there are 2 different isotypes that could form. So rearrangement of k on the first chromosome is tested, if failed then the rearrangement of k on the second chromosome is tested, if failed then the rearrangement of l on the first chromosome is tested, if failed then the rearrangement of l on the second chromosome is tested, if failed then the cell dies via apoptosis. The light chain could form either a l or a k isotype and be functional.
Define the process of peripheral tolerance that occurs in B-cell development in the spleen.
Peripheral tolerance is a process of testing immature B cells for self-tolerance (making sure the B cell doesn’t react to antigens from the hosts body). Peripheral tolerance occurs in the peripheral lymphoid organs like the spleen where there are self-antigens presented on splenocytes or in the soluble molecules of the spleen and circulating blood. If the cell is found to react to any of these self antigens its destroyed as it would cause an autoimmune response if left to proliferate in the body.
Lecture 4: The complement system
Which complement protein is most important in directly targeting the pathogens for destruction?
C3 is needed for all three pathways of innate immunity the classical, lectin, alternative pathways all require C3 before they continue.
What are the cleavage products of that (from above) protein, and what does each cleavage product do to facilitate pathogen elimination?
C3a and C3b. C3 is cleaved via C3 convertase. C3a is a smaller fragment and also an anaphylatoxin which induce inflammation. The C3b component is the larger fragment and is used to opsonize the pathogen surface and flag it for elimination.
What are the three pathways of complement activation?
Classical complement pathway: via antigen-antibody complexes (adaptive immune system).
Lectin pathway: via MBL (mannose binding lectin) and MASP (MBL associated serine pathways) complexes that bind to specific carbohydrates.
Alternative pathway: Initiated by spontaneous hydrolysis and activation of C3, bind directly to microbial surfaces.
During the alternative pathway of complement activation, two C3 convertases are formed. Which proteins make up these convertases?
C3 convertases are made up of C3bBb and C3bBbP. C3bBb is made up of C3b and one factor B molecule that cleaves to activate the enzyme. C3bBbP made up of the same but also includes properdin which stabilizes the C3bBb and enhances its activity.
Which complement protein is responsible for forming pores in pathogen membrane within the MAC?
The C5b component first binds to the pathogen surface and recruits the C6, C7, C8 and C9 proteins all combine to the form the MAC (membrane attack complex).
Which acute-phase proteins are the two initiating opsonins of the lectin and classical pathways?
C4b and later C3b binds.
Which complement cleavage products constitute the classical C3 convertase?
In the classical pathway it forms C3 convertase by combining C2a + C4b to make C2aC4b
What are some common complications associated with a deficiency in the complement system?
Deficiencies in the complement system leads to abnormal clearance of bacteria and fungi. Hypersensitivity response and autoimmune disorders improper clearance of soluble immune complexes. Increased infection rate due to malfunctioning MAC.
Lecture 5: Principles of Adaptive Immunity
What are the differences between primary and secondary lymphoid tissue?
Primary lymphoid tissue is where naïve B and T cells reside. SO in the bone marrow or the thymus respectively. The secondary lymphoid tissue is where the cells travel to
meet their antigens and become activated. So the lymph nodes, the spleen, etc.
Explain the role of secondary lymphoid tissue in the adaptive immune response
Secondary lymphoid tissue provides a location and link for the naïve B and T cells to come in contact with their antigens. Antigens from infected tissues are taken up and travel via the lymph, to the lymph nodes where they can interact with their B and T cells.
At what locations within lymph nodes are T and B cells activated?
T cells are the T cells are activated in the paracortical areas. B cells are activated in the primary lymphoid follicles.
How are antigens delivered to MALT?
The MALT is the mucosal associated lymphoid tissue. Antigens from the gut enter into the lumen, through M cells on Peyer’s patches and are then able to be taken into the MALT.
Lecture 6: Antigen Recognition by Lymphocytes
Describe the structure and composition of an antibody and the functions associated with its primary components.
Antibodies are composed of variable and constant regions. The variable regions are the sites where the antigen will bind to the antibody, and allow their corresponding antibody to bind two identical antigens. The constant region is the regions that do not bind antigens, and distinguishes between the different antibody isotypes (IgG, IgA, IgM, IgE, IgD). Contains heavy and light chain regions.
Define the Fab and Fc regions of an antibody?
The Fab is the fragment antigen binding. This is the top two parts of the variable (heavy and light chains) of the antibody. To the variable regions of the Fab the antigen will bind. The Fc is the constant fragment of the antibody and this part doesn’t interact with the antigen but instead has all other biological activity of the H chain isotypes.
What is the importance of an MHC molecule in the adaptive immune system?
Allows a small peptide from the pathogen to be presented on the surface of the antigen presenting cell (APC). This allows a T cell to recognize the antigen via its TCR (T cell receptor) and trigger a response to the antigen. Comes in two classes (I and II).
What are the five major functions of soluble Igs?
1. Neutralization: antibodies bind pathogens and prevent them from entering or harming host cells.
2. Opsonization: the antibodies coat the pathogens in opsonins to make them targeted for phagocytosis by macrophages and DC.
3. Complement activation: Antibody-antigen interactions trigger the classical pathway. Help clear pathogens and end in the lysis (cutting open) of the pthaogen or inflammatory responses
4. Antibody dependent cellular cytotoxicity (ADCC): Some antibodies can recruit or activate immune cells (like NK cells) to destroy infected or cancerous cells.
What types of antigens do MHC class I and II typically present?
MHC I molecules recognize intracellular antigens and present them on the surface of their cells
MHC II molecules recognize extracellular antigens and present them on the surface of their cells.
What subunits are required for a properly functioning TCR complex?
- The TCR itself, and its binding partner MHC presenting antigen on the APC.
- Co receptors are also needed (CD4 or CD8)
- CD3 (ε, ζ, δ, γ)on the T cells surface is needed for signaling molecules).
Draw similarities and differences between TCRs and BCRs/Igs
Both TCR and BCR bind antigens to show the body what needs to be destroyed. TCR can bind only one antigen at a time but the BCR can bind 2 identical antigens at the same time. TCRs are bound to the membrane of the T cell whereas, B cells can secrete their BCRs in the form of antibodies. Both TCRs and BCRs have a constant and soluble region that functions the same way.
Why is the CD3 complex required in a functional TCR complex?
CD3 brings the TCR to the surface of the T cell when ready to recognize MHCs. Without the CD3 co-factor, the T cell wouldn’t be able to be expressed. CD3 recruits signalling molecules necessary for T cell activation.
Compare and contrast the structures of MHC I and II.
MHC I: has 1 chain bound in the membrane. Three subunits of the alpha chain, and soluble b microglobin adds structural support, binds to small peptides made within the cell (intracellular)
MHC II: has both chains bound to the membrane, 2 alpha and 2 beta subunits. Binds larger peptides made outside the cell. Peptide binding groove b1 and a1. Peptide derived from outside the cell (extracellular).
Lecture 7: Generation of lymphocyte antigen receptors
What are the similarities and differences between somatic recombination in T cells and somatic recombination in B cells?
Genes of B and T cells contain regions that must be spliced together to code for their BCR or TCR regions, these regions include variable (V) regions, diversity (D) regions and junction (J) regions.
What key component of an immunoglobulin is removed by alternative splicing to produce soluble, secreted immunoglobulins?
In T cells the soluble components of the TCR are removed and only the components for membrane binding are produced. In the B cells the section for coding membrane binding regions is removed and only the soluble region remains. Heavy chains require all three types of segments VDJ and light chains require only the VJ regions.
Deficiencies in RAG-1 or RAG-2 cause a form of SCID in which patients lack B cells and T cells. Why is this the case?
RAG1 and RAG2 form a complex responsible for VDJ recombinase activity. If someone is immunodeficient in RAG1/2 complex wouldn’t form and there would be no expression of antibodies at all as these genes would not splice mRNA together properly. The RSSs (recombination signal sequences) wouldn’t get removed and coding joints wouldn’t be made.
How is the V domain of the heavy chain and light chain genes broken up?
The heavy chain is created with the V, D and J segments. The light chain is created with the V and J segments only.
Describe the process of making heavy chains.
1. RAG1:RAG2 bring the D and the J regions close together and holds them in a hairpin. The VDJ recombinase removes the RSSs at coding regions. Ku70 and Ku80 bind to coding regions and stabilze ends. Artemis and DNA-PK open up the hairpins at the ends of the coding regions. TdT adds nucleotides to the opened hairpins to extend the line. DNA ligase and XRCC4 repair the hairpin in the DNA
2. Now the D and the J regions are fused together.
3. The whole process repeats (step 1) is repeated to join D to J.
Describe the process of making light chains.
1. Light chains have only V and J segments. They are created in the same way as step one of the heavy chain rearrangement but with V and J directly attaching to each other (no D segments needed).
What are the mechanisms by which B cells generate receptor diversity?
Through VDJ recombination, there are many possible rearrangements of the components for V D and J segments. Diversity in receptors is important to allow antibodies to gain their specificity for individual antibodies.
Lecture 8: Antigen presentation to T lymphocytes
Explain the process of antigen presentation by MHC class I and II pathways.
MHC I is loaded with peptides from inside the cell (intracellularly) cytosol that’s moved to the ER to meet the MHC’s. There the protein/peptide is chopped up in the cytosol via the proteosome (molecular trash can) and moves on the ER to meet the MHC I which travels to the surface of the cell and presents the antigen to the DC.
MHC II is loaded with peptides that originate from outside the cell (extracellularly). The peptides are brought inside via endosomes, which have inactive proteases and a proton pump within them. The pump shoots H+ into the endosome and makes it acidic. The acidic endosome chops up the protein. There is a vacuole with an MHC II molecule embedded in its membrane. The MHC II is bound to an invariant chain. The endosome with the peptide fuses with the one holding MHC II and the acidity in the endosome causes the invariant chain to chop up leaving only a CLIP. The endosome with the antigen loads onto the MHC II. Loaded MHC II moves to the cell surface and presents the antigen on the MHC II.
What is the role of cross-presentation in DCs?
Cross-presentation is the ability of dendritic cells to take up antigens and present them outside the cell and process and present them to MHC I and CD8 T cells. This is the action of a MCH II molecule but being done by an MHC I molecule. When extracellular proteins are taken up they are removed from their necrotic cells via a phagolysosome. Then the antigen is presented on the MHC I as if it was always an internal antigen.
Define promiscuous binding site as it relates to MHC molecules and the role if anchor residues in peptide binding to MHC molecules.
MHC molecules can bind to a wide range of variety of peptide antigens. Single MHC can present many different antigens and a diverse immune response can result.
Give an example of non-peptide antigen presentation
Specialized MHC I molecules can act as ligands for the activation and inhibition of NK cells and unconventional T cell subsets. Presented by structurally similar proteins, encoded outside MHC locus, CD1 family of molecules.
Lecture 9: Investigating the role of MRGPRX2/b2 in S. aureus induced atopic dermatitis.
Why might a patient be given mupirocin, ahead of surgery?
Mupirocin is an antibiotic, before surgery sometimes patients are prescribed antibiotics to clear ut the S. aureous because its so virulent before their surgery. S. aureous is a pathobiont meaning 20% of the adult population is colonized by this bacteria without depicting any negative symptoms.
What distinguishes a superantigen and what does it lead to the production of?
A super antigen is a class of antigens that can activate a large number of T cells non-specifically leading to a massive immune response. Excessive activation of lymphocytes causes lots of cytokines to be secreted. Increased production of IL2 leads to fever, nausea, toxic shock syndrome and autoimmunity immune system is attacking the bodies own cells.
Describe two examples of how S. aureus may evade the host immune system.
1. S. aureus interferes with the activation of the complement system by preventing C1q (classical pathway) from binding the SAK antibodies, the spa and spi protein from S.aureus bind to the constant regions of antibodies and halt their function
2. Complement inhibitor, stabilizes inactive C3 convertase. Stopping the progression of each of the complement pathways (classical, lectin, and alternative)
3. Creation of a fibrin shield on tLhe surface of the s. aureus pathogen CIFA proteins that allow them to bind to each other forming a clump. Can shield themselves with fibrin (host bacteria protein) to block their detection.
Lecture 10: Lymphocyte receptor signaling
What costimulatory interaction is required between T cells and APCs?
Co-stimulatory molecules regulate the interactions between T cells and antigen presenting cells. On the T cell CD4 stabilizes the TCR : MHC interaction, the T cell also has the CD3 co-factors, and on the T cell the CD28 molecule binds to the B7 on the APC cell.
What is the importance of activating protein-tyrosine kinases at the initiation of the formation of an immunological synapse between T cells and APCs?
The cytoplasmic tails of the CD3 and the TCR domains have ITAMS (immunoreceptor tyrosine activation motifs) which are the docking sites for Lck kinase. The Lck kinase phosphorylates the tyrosine residues which allow the ZAP-70 kinase to bind. ZAP-70 induces another phosphorylation and induces 3 transduction pathways.
Clonal expansion of T cells requires the activation of transcription factors to promote gene activation. What three transcription factors are activated during T-cell activation?
1. NFAT initiates the first transduction pathway.
2. NFkB initiates the second transduction pathway.
3. AP-1 initiates the third transduction pathway.
Is binding of a single cell-surface Ig to an antigen sufficient for B-cell activation? Why or why not?
Generally no! The Ig likely needs to be bound to several mechanisms for B-cell activation to occur. The co-stimulatory signals (CD28, and CD4) also need to be present, and cytokine signalling also needs to occur.
How is B-cell activation through BCR complex similar to T-cell activation through the TCR complex?
B cells are activated with signal transduction via Ig alpha and Ig beta membrane bound proteins. T cells are activated with signal transduction via CD3.
How is the transcriptional activation in B cells during their activation similar to that within T cells?
Both B cells and T cells need co-stimulatory signalling to be activated, (CD28 on T cells and CD40 on B cells). Both require TFs like NFAT, NFkB to promote transcription of genes needed for survival proliferation and differentiation. Both need cytokine responses, T cells need IL-2 and B cells need IL-4 and IL-6. Activation of B cells and T cells leads to clonal expansion.
Lecture 12: Development of T lymphocytes
What three major cell types found in the thymus play a role in T-cell development? Explain the function of each type in T-cell development.
Thymic epithelial cells (TEC) needed for positive selection of T cells, these are the cells that express MHC I and MHC II thymocytes with TCRs able to weakly bind to the MHCs are positively selected for and survive. Others that bind too tightly or not at all are negatively selected for and die.
Thymocytes Developing T cells originate in the hematopoietic stem cells of the bone marrow and migrate to the thymus where they learn to become self-tolerant.
Dendritic Cells specialized antigen presenting cells needed for negative selection of T cells. DC capture and process self antigens to present on their surface and test thymocytes for their reactivity.
Why are individuals who lack the IL-7 receptor unable to produce functioning T cells?
IL-7 is a cytokine needed for the development proliferation and survival of T cells in the thymus. IL-7R (receptor) on the T cells is essential for them to signal with the cytokine that this thymocyte needs to progress into a T cell.
Explain the role of Notch1 in T-cell development and its importance in lymphoid progenitor cell commitment to thymocyte development.
Notch1 signalling causes the early thymic progeninator to commit to become a T cell lineage rather than a B cell lineage. Notch signalling causes T cell specific surface expression (GATA3 and TCF1). Induces expression of IL-7 receptor alph chain. Progress through each stage of T cell development. Notch1 signalling is only turned off when beta-selection happens in DN4 stage.
What checkpoints can occur as part of the T-cell development process? Why don’t all three checkpoints need to be passed by a developing T cell?
1. TCR-beta rearrangement: the beta chain of the TCR starts to form in the pro B cell phase (via recombinations of D and J then V and DJ). Beta chain binding to alpha chain is tested via a surrogate alpha chain (pTa). If not functioning the cell is destroyed (prevent extra energy being used to develop a unusable T cell). Beta chain stops recombining though allelic exclusion (prevents more than one beta chain from being produced on the same cell).
2. TCR-alpha rearrangement: Large DP have stopped proliferating and become small DP cells the alpha chain begins to rearrange, and has many attempts at rearranging. Selection processes down-regulates one of the receptors forming either CD4 or CD8 T single positives.
3. Negative selection: Removes any T cells that strongly recognize self MHCs. This leaves only T cells that are self-tolerant making sure they wont initiate an immune response from the hosts own cells (prevents auto-immunity).
Why do developing thymocytes need to use the pre-Tα chain to progress through the β-chain checkpoint?
To make sure that the beta chain is functional and will bind to an alpha chain. Don’t want to waste energy creating a full on alpha chain only to find out that the beta chain is faulty.
What are the three possible fates of double-positive thymocytes continuing their development in the thymus?
1. Death by apoptosis: If the T cell doesn’t bind the MHC with any affinity
2. Positive selection and maturation to the single positive thymocyte: will later release from thymus. These T cells bind their MHCs with moderate affinity (Goldilocks, not too high, or too low).
3. Negative selection/apoptosis: Theses cells vind their MHC too strongly and could lead to autoimmunity, these cells must die so they aren’t released into the body.
Lecture 13: Development of B lymphocytes
Which signal in differentiating progenitor cells is required to commit differentiation to B-cell development?
The IL-7 survival signal produced in BM stromal cells. Majority of the CLP (common lymphoid progenitor) cells are biased to B cell lineage meaning if they don’t receive Notch1 signalling they will default to B cell development.
What are the critical checkpoints of B-cell development?
1. Pre BCR testing: Heavy chain antibody has already recombined we want to test if this was made properly before committing to making the light chain of this antibody. Surrogate light chain is used to form a pre BCR with the recombined heavy chain. Proper signallinf stops the rearrangement of the heavy chain, tests if the VDJ recombination of the 1 H chain per chromosome causing allelic exclusion, expression of only one of the two alternative alleles. Antigen independent. No antigen is present yet, still in the bone marrow.
2. Negative selection 1: Light chain has formed. Checks If a functional BCR is formed it should not recognize self antigens. Central tolerance is tested by exposing the BCR to the a self antigen originating in the bone marrow. Allelic exclusion is found on the first chromosome if the second chromosome rearranges properly. Nothing else can recombine and isotypic exclusion is seen if the k chain is rearranged then the l chain cannot and vise versa. Antigen dependent because central tolerance is tested. Receptor editing can occur.
3. Negative selection 2: pre B cell moves to the peripheral organ through the lymph and to the spleen (for example). Testing begins here to see if the BCR is self reactive to any periphery self-antigens. Antigen dependent, No receptor editing can occur here.
What is the composition of the surrogate light chain, and how does it resemble the immunoglobulin light chain?
The surrogate light chain is composed of the VpreB1 and the l5. The VpreB1 acts as the variable region of the light chain and the l5 acts as the constant region of the light chain.
Why is allelic exclusion of an immunoglobulin heavy chain that has not recombined necessary to normal B-cell function?
Allelic exclusion allows only 1 type of immunoglobulin heavy chain to be expressed on the B cell surface if more than one type was expressed, self-tolerance tests done on one wouldn’t be reflective of the other and it could still cause autoimmunity.
Compare and contrast the three possible fates of negative selection of self-reactive immature B cells.
1. Apoptosis: cells that are self tolerant are recognized as disruptive and marked for distruction via programmed cell death. This pathway is triggered when self antigens are bound with high affinity.
2. Receptor editing: The light chain of the BCR can keep trying to rearrange and give the immature B cells a chance to replace their autoreactive BCR. This will keep occurring until the cell runs out of molecular machinery (light chain so V and J segments) to use. This only occurs during the 2nd checkpoint Negative selection1.
Define the process of peripheral tolerance that occurs in B-cell development in the spleen.
Peripheral tolerance in the spleen occurs when the APCs in the spleen present self antigen on their surface in order to determine the B cell response to them. If the B cell binds with high affinity its failed its peripheral self tolerance test and is killed. If the B cell binds with low affinity or not at all, its passed the peripheral tolerance test and will survive as that cell is unlikely to initiate an immune response against the bodies own cells (autoimmunity).
Lecture 14: T Cell Cell-Mediated Immunity
What is the role of T-cell priming in an adaptive immune response?
T cell priming is the first contact that antigen-specific naïve T cells have with an antigen. After the naïve T cell has been primed, it can undergo clonal expansion and differentiate into CD4 or CD8 effector T cells or memory T cells. Memory T cells are essential in immune response as they allow the body to keep a record of the antigens it has encountered and build a stronger and faster immune response if those antigens were to infect the body again (principle of vaccines).
Both macrophages and DCs are capable of phagocytosis and processing antigens. Why are macrophages not a major contributor to T-cell activation?
Macrophages aren’t a major contributor to T-cell activation because they aren’t located in the right spot the lymph tissue to meet naïve T cells, however dendritic cells to populate the lymph and so can uptake antigens and present them to naïve T cells readily.
Explain the process of T cell migration into secondary lymphoid tissue.
1. T cells formed in the thymus begin circulating in the blood stream T cells must move to peripheral lymph tissues to contact their antigents
2. Circulating naïve T cells in the blood/lymph enters a HEV (high endothelial venule) in the lymph node.
3. Binding of L-selectin (on the T cell) to GlyCAM-1 (on the endothelial cell) and CD34 (endothelial) allows rolling interaction.
4. LFA-1 (T cells) is activated by CCR7 (T cell) signalling in response to CCL21 or CCL19 bound to endothelial surfaces
5. Activated LFA-1 binds tightly to ICAM-1 (endothelial surface)
6. Lymphocyte crosses the endothelium and enters lymph nodes via diapedesis (squeezing between vesicles).
What costimulatory interaction is required between T cells and APCs?
Describe the overall roles of the effector T cells TH1, TH2, Tregs and CTLs.
Th1 cells: releases IFN g attacks intracellular bacteria on macrophages. Targets microbes that resist macrophage killing.
Th2 cells: Release IL-4, IL-5 which targets bone marrow and IL-13 which targets goblet cells to release mucus for eosinophils, mast cells, and basophils. Targets parasites like helminthes worms.
Th17 cells: Releases IL-17 for stromal cells and IL-22 for epithelial cells on neutrophils targets extracellular bacteria.
Tfh cells: Release IL-21 and enhance the B cells and plasma cells and targets nearly all microbes.
Treg cells: Release TGF b and IL-10 to inhibit activation of other T cells. And targets self and microbiome derived antigens.
Summarize two mechanisms of apoptosis induction that CTLs use on target cells.
Explain the role of Tregs in peripheral tolerance.
T reg cells induce peripheral tolerance by inhibiting the activation of other T cells. This is essential for when a T cell has recognized a self-antigen and initiating a full immune response against it would cause autoimmunity. T reg cells stop another T cell from activating others this stopping autoimmune responses from occurring.
Extrinsic Apoptotic Pathway
1. The FasL (ligand) from one cell binds to and attaches to the Fas receptor from another cell causing the Fas receptor to form a trimer.
2. The trimer of the Fas receptor brings the cytosolic death domains in their tails within contact of eachother. The close contact of the death domains recruits FADD to its death domain.
3. The clustered death effector domains (DD + DED + DISC) of FADD recruit and activate pro caspase 8 via similar DEDs in the pro-caspase
4. Activated pro caspase 8 cleaves pro caspase 3 which then cleaves I-CAD, releasing CAD to enter the nucleus and begin chopping up the cells DNA thus killing it.
Intrinsic Apoptotic Pathway
1. In a normal cell cytochrome C is present only in mitochondria allowing the cell to survive!
2. When programmed cell death is induced, the mitochondria release cytochrome c which binds to and induces a conformational change in Apaf-1 (apoptotic protease activating factor 1).
3. Apaf-1 binds to cytochrome c and froms a self complex which assembles into an apoptosome (large protein structure formed in the process of apoptosis) which recruite and activated many copies of pro caspase 9, which in turn activates pro caspase 3.
4. Caspase 3 cleaves I-CAD releasing CAD which enters the nucleus to cleave DNA and destroy the cell.
Lecture 15: B cell Humoral Immunity
Explain the interactions that must occur on the surface of a B cell that recognizes a TD(thymus dependent) antigen for activation to take place.
The B cell must have an MCH molecule presenting an antigen, a CD40 receptor bound to its ligand, an IL-2 cytokine bound to its receptor and a co-factor CD4 molecule to stabilize the interactions on its surface to recognize a thymus dependent antigen in order for the B cell to become active.
Contrast the activation of B cells that recognize TI-1 and TI-2 antigens.
Thymus independent 1 antigens are recognized via antibodies on B cells. The antigens recognize the carbohydrates on the pathogens surface. These pathogens can also be detected by B cells via TLRs that come together and dimerize on the surface.
Thymus independent 2 antigens are recognized via antibodies binding many antigens on the surface of the pathogen and a co-stimulatory interaction between C3d on the pathogens surface and CR2 on the B cells surface.
What signals are provided by TH cells to activate B cells recognizing TD antigens?
T cells are required for recognizing TD antigens because they are an thymus dependent system. They require signaling from the CD40 and CD40L survival signal and proliferation. And also from the IL-21 proliferation and differentiation signal from the cytokines.
Compare primary vs. secondary foci in B-cell differentiation.
First phase of primary immune response: If the B cell doesn’t interact with Tfh cells outside of the follicle (it stays in the red pulp of the secondary lymphoid organ) if forms plasma cells and plasmablasts/primary focus.
Second phase of the primary humoral response: The proliferated B cell can interact with Tfh cells and remain in the follicle where it creates a germinal center (secondary lymphoid follicle) and eventually becomes a plasma cell.
Why is it important that centrocytes undergo a second round of selection within germinal centers?
Centrocytes in the light zone of the foci. Second round of selection in the germinal center is essential for the optimization of the immune response by ensuring high-affinity antibody production, proper isotype switching, and the elimination of potentially harmful self-reactive B cells.
How does the activity of TH cells drive isotype/class switching?
The cytokines secreted by Th cells facilitate class switching. Occurs after contact with germinal centers after antigen content. Class switching from the constant heavy chain regions genes initiated by AID (activation induced cytokine deaminase).
What are the properties and functions of different antibody isotypes?
IgM (): Default C region used for mature and naïve B cells antibodies. Rapid first response phase of B cell to primary infection. Low affinity. Large primarily in blood.
IgD (): Co-expressed with IgM during maturation. No known functions.
IgG (): Class switching (GC B cells). 4 subclasses, always monomeric, smaller and can diffuse into tissues, blood and extracellular fluid, predominant antibody call, transported across placenta, high affinity, most abundant in serum.
IgE (): Class switching (GC B cells). Always monomeric, smaller and can diffuse into epithelial cells but less abundant, sensitization of type 2 immune cells (mast cells) high affinity, allergy sensing.
IgA (): Class switching (GC B cells), can exist as monomers or dimers, smaller and can diffuse into secretions at mucosal epithelial surfaces. Transferred through breastmilk, high affinity.
Lecture 16: Immunological Memory
What are the different properties of ILC subsets in terms of their immune function?
Some examples of ILCs are dendritic cells, macrophages, epithelial cells / tuft cells. Some properties of ILC (innate lymphoid cells) subsets are cytotoxic events, effector kinases that amplify the innate immune response. Cytotoxic ILC and group 1 ILCs release IL-12 and IL-18 to trigger the release of IFN-g. IFN-g intensifies inflammatory responses. Group 1 ILCs are activated when macrophages release IL-12 and IL-18 which also releases IFN-g. Group 2 ILCs are activated when TSLP and IL-25 and IL-33 released by epithelial cells and triggers the ILC2 to release IL-13 and IL-5. Group 3 ILCs are activated when IL-23 and IL-1b are released by macrophages and dendritic cells. ILC3 then releases IL-17 and IL-22.
How does immunological memory work to prevent and fight disease?
Immunological memory is the ability of certain cells to recognize pathogens that have been previously encountered and respond more effectively upon re-exposure. When a pathogen is first encountered memory T or B cells could be created after the cells respond to the antigen presentation and should that same pathogen, then it will already know well how to fight off this pathogen.
Name the various memory T cells and explain their migration pattern and functions.
T(CM): T central memory cells circulate between the blood and T cell zones of the SLO and the lymph.
T(EM): T effector memory cells recirculate between the nonlymphoid tissues, lymph, lymph nodes and blood. Some remain in blood circulation and only migrate through the spleen.
T(RM): T resident memory cells do not recirculate but rather are confined to a single tissue (are residents of that tissue).
Differentiate between primary and secondary immune response.
Primary immune response occurs upon first encounter with the antigen and includes B cell and T cell activation, proliferation and differentiation.
Secondary immune response involves antibody responses from memory B cells rather than activated B cells and thus occurs upon second or higher encounter with an antigen.
What is the purpose of negative signaling in naïve B cell through activation of FcγRIIB1?
The purpose of the negative selection through activation of FcgRIIB1 is to inhibit naïve B cell production during the secondary response. This will allow the memory B cells to step in and fight the infection off more rapidly and more effectively.
What are the properties and functions of different antibody isotypes?
IgA: Class switching (GC B cells), can exist as monomers or dimers, smaller and can diffuse into secretions at mucosal epithelial surfaces. Transferred through breastmilk and high affinity binding.
IgM: Default C region used for mature and naïve B cells antibiodies. Rapid first response to primary infection. Low affinity binding to antigen, large primarily in blood.
IgG: Class switching (GC B cells) 4 subclasses, Always monomeric, smaller and can diffuse through tissues, blood and extracellular fluid. Predominant antibody class, transported across placenta, high affinity, most abundant in serum.
IgD: Co-expressed with IgM during maturation, no known function
IgE: Class switching (GC B cells), always monomeric, smaller and can diffuse into epithelial cells but less abundant, sensitization of type 2 immune cells (mast cells) high affinity allergy sensing.
Lecture 18: Immunity at Mucosal Surfaces
Why are mucins effective as a defense against infection at mucosal surfaces?
Mucins are highly glycosylated cell surface proteins. They are effective as a defense against infection at mucosal surfaces because they act as a physical barrier between the epithelial cells and their external environment. They promote immune responses, neutralize harmful pathogens, and facilitate pathogen clearance to prevent infection at mucosal surfaces.
Compare and contrast the delivery of antigens to secondary lymphoid tissue when captured at an open wound and at a mucosal surface.
Open wound: Pathogen enters the tissue directly, where its identified by innate immune cells like DC, and macrophages which present the pathogens antigen via MHC. The APC travels via the lymph to secondary organs where it meets naïve T cells. T cells can then recognize MHC antigen and bind though signalling can kill neutralize, opsonize or kill pathogen via MAC).
Mucosal Surface: Antigen moves to follicle associated epithelium(FAE) where it comes in contact with a microfold cell (M cell) and can enter via this cell into the subepithelial dome. Their it contacts DCs which can intake the pathogen and present an antigen on their MHC molecules. T cells in the T cell zone of the sub epithelial dome can interact with the APC and trigger an immune response. B cells from the germinal centers of the dome can create antibodies to fight off the pathogen.
Explain the process of antigen delivery to mucosa-associated lymphoid tissue driven by M cells.
see above Mucosal surface presentation.
Would you predict that an organism that is deficient in the production of NOD2 would be more or less susceptible to infection in mucosal tissue? Why?
NOD2 is a protein that recognizes microbial peptidoglycan of pathogens, within the cells cytoplasm. No NOD2 and the organism would become more susceptible to infections because impariered immune detections (less efficient at recognizing and responding to mucosal tissues infections).
How do dendritic cells provide oral tolerance for an organism?
DC provide oral tolerance via the activation of T reg cells. Oral tolerance is the suppression of specific immune response to an antigen by the prior administrations of the same antigen via the oral enteric route. T reg cells are cells that are capable of inhibiting naïve T cell expansion and allow the memory T cells to respond to the known antigen instead.
Name the innate immune cells that play a role in mucosal immunity and describe their functions.
Dendritic cells reside in the Peyer’s patches and recognize antigens that have travelled through the M cells and presents their antigens on their surface to T cells.
Macrophages: can stretch through the tight junctions of the epithelial cells to grab an antigen utside and give it to the APC on the inside.
Goblet cells transport antigen through the epithelium and allow internal DC to present the antigen on their surface.
Explain the role of antibodies in mucosal immunity.
Antibody A is secreted by plasma cells in the lumen and dimerizes. Can now move from the lumen to the outside (apical layer) via transcytosis where it can interact with an antigen. The dimerized IgA could neutralize the pathogen, neutralize an endocytosed pathogen, export an internalized pathogen, or bind to Dectin 1 on the surface of the M cell and move towards the inside to bind with the DC-sign receptor on the DC.
Lecture 19: Failures of Host Defence Mechanisms
What is immunodeficiency?
A state in which the immune system in compromised or absent, causing the individual to be very susceptible to infection and disease. Primary ID: Is inherited, and not as rare as once believed as we’re getting better at testing and recognizing it. Secondary ID: is acquired (non-inherited) from the environmental fators such as malnutrition, age, infection, radiation, chemotherapy exposure to toxins. Combined ID: are impairments in both T cell and B cell functions dues to inherited mutations. Because inherited mutations falls under the primary ID umbrella.
How does inherited immunodeficiency differ from acquired immunodeficiency?
Inherited immunodeficiency is passed down from parent to child and unavoidable, wherease acquired immunodeficiency is created during the individuals lifetime based on their environmental factors like malnutrition, radiation, chemotherapy and exposure to toxins.
How does a deficiency in the innate immune system lead to disease?
Innate immune system deficiency can lead to disease by upsetting the first line of defence your body has against pathogens. The person may not be able to initiate inflammatory responses, and antigen presentation would be affected.
How does a combined deficiency in lymphocyte development or action lead to disease?
Combined deficiency results from impairments to both B and T cells and lymphocytes wouldn’t properly develop into either B or T cells. If there was a mistake in B and T cell formation, then the adaptive immune response would be greatly affected. Body may not be able to learn what antigens its seen before (not memory cells). And no self-tolerance could be developed. Very dangerous to the individual. Very immunocompromised.
How does a deficiency in T-cell action lead to disease?
No CD4 T cells wont be able to activate other immune cells like B cells. No CD8 killer T cells wont be able to recognize/kill infected cells. Autoimmune disease could occur, T reg cells wou;t be able to supress immune responses and maintain self-tolerance. Th17 cells won tdefend against intracellular pathogens. And an impaired vaccine response as memory T cells aren’t functioning meaning vaccines would be ineffective for this individual.
How does a deficiency in B-cell action lead to disease?
Certain epitopes aren’t accessible because no soluble antibodies. Impaired/lack of memory B cells renders vaccines ineffective, and all infections would trigger a primary response. Persistent infections because no secreted antibodies immune evasion by cancerous cells. Low levels of all isotypes of antibodies, No class switching, or affinity binding, Co-factors not targeting to aid in MHC : TCR response.
How does HIV cause AIDS?
HIV virus binds to CD4 and co-receptor of host cell and fuses with viral genome to enter hosts cell. Reverse transcriptase whichn the genome causes the copies of viral RNA to immediately be made (Don’t have to use host cells machinery here because it came with its own) RNA into DNA. Viral DNA enters nucleus and inserts itself in the host DNA. T cell activation causes small amounts of provirus to be transcribes. TNA transcripts make proteins, needed to make the viral coat. Initial infection causes spike of CD4 T cells to combat the virus, virus becomes latent (hides) and concentration of CD4 T cells goes down. CD4 T cells concentration continues to decrease and the hosts immune system is very impaired, eventually another pathogen gets to infect the host and with its weakened immune system the host is killed very quickly, because no CD4 T cell defense.
What are the primary ways that pathogens evade immune system defenses?
1. Antigenic variation: changes in surface proteins of pathogen hiding it from the immune system.
2. Immune system inhibition/suppression: Deplete CD4 helper T cells, inhibit interferons, block antigen presentation process.
3. Masking/mimicry of host: camouflage themselves as a host cell to their antigens aren’t recognized.
4. Inhibit phagocytosis: capsules prevent pathogens from being destroyed in lysosomes survive within endosomes
5. Resistance to complement system: bind complement regulators and prevent activation. Bind antibodies prevent activation or neutralization.
How does genetic variation allow pathogens to evade the immune system?
The pathogen that the body had recognized previously has changed its outer antigens to such a degree that the host cells can no longer recognize it as the same pathogen as previously detected. The primary immune response must occur again.
How do pathogens hide from the immune system?
see how do pathogens evade immune defenses.
Lecture 20: Allergies and Hypersensitivities
What are the different types of hypersensitivity reactions?
Type I hypersensitivity: IgE dependent reaction that occurs when the immune system creates an allergic reaction in response to an allergen (antigen that is harmless to host but detected as harmful) like pollen, dust, certain foods etc.
Type II hypersensitivity: A non-IgE dependent response. Occurs when IgG recognize the cell surface of molecules and bind to them, leading to their destruction of the cell. Antibodies are directed against the cellular or extracellular matrix antigens, resulting in cellular destruction, functional loss and damage to tissues.
Type III hypersensitivity A non-IgE dependent response. Deposition of immune complexes into tissues causes a lcal inflammatory response known as the Arthus reaction. Inflammation and tissue damage could occur. Eg. Serum sickness.
Type IV (delayed type) hypersensitivity: A non-IgE dependent response. Occurs hours to days after initial exposure. Cell-mediated immune response primarily driven by T cells, and leads to delayed inflammation and tissue damage.
How does Type I hypersensitivity reaction occurs?
1. Sensitization phase: Initial exposure to the allergen is taken up by DC and presented to a T helper 2 cell which releases cytokines and stimulates B cells to produce IgE antibodies.
2. Production of IgE antibodies: B cells begin class switching from IgM to IgE. IgE binds to the surface of the mast cells and basophils. Primed to respond to the antigen again
3. Subsequent exposure to antigen: re-exposure to the antigen causes it to bind to mast cells or basophils that are primed with IgE and triggers their activation.
4. Degranulation of mast cells and basophils: release mediators stored in their granules (histones, cytokines and proteases).
5. Inflammatory response: Release of inflammatory mediators causes acute inflammatory response. Anaphylatoxins could occur leading to shock, airway constriction, cardiovascular collapse.
What factors are responsible for Type II hypersensitivity reactions?
B cells which are class-switched from IgM to produce IgG. Natural killer cells which kill the target cell coated with the IgG antibody resulting in tissue damage. Activates the classical pathway of complement system.
How does Type III hypersensitivity reaction occurs?
1. Antigen in immune individual with IgG antibody.
2. Local immune-complex forms and activates complement C5a to and sensitizes the mast cell to respond to immune complexes
3. Activation of FcgRIII on mast cells induces their degranulation
4. Local inflammation, increased fluid and protein release, phagocytosis, and blood vessel occulusion.
What is delayed-type hypersensitivity reaction?
A reaction that takes a few days to respond. Directed by chemokine and cytokines released by antigen-stimulated Th1 cells. Macrophages squeeze out of blood vessels in causes inflammation to occur.
Lecture 21: Autoimmunity and transplantation
What is the relationship between self-tolerance and autoimmunity?
Autoimmunity occurs when self-tolerance is not activating properly. A person has autoimmunity when their immune system responds against their own self cells or antigens and starts to destroy itself. If a person is tolerant of their own antigens and cells, then their immune system will not attack these cells bc they will recognized as non-harmful.
How do genetic and environmental factors affect the progression of autoimmune diseases?
They can alter negative selection (the removal of self-reactive cells). Autoreactive T cells cause the activation of B cells and those B cells will create autoantibodies. Genetic factors can cause MHC mutations, along with environmental factors such as infections, chemical exposure and physical trauma. Environmental factors could break self tolerance.
Explain why many autoimmune diseases are caused by the production and action of autoantibodies?
Many autoimmune disease are caused by the production and action of of autoantibodies because these antibodies are primed and ready to attack the bodies own cells. When the body is filled with autoantibodies its very dangerous as they start to destroy cells needed by the host and they could kill entire tissues.
When is a normal adaptive immune response to a pathogen capable of inducing an autoimmune response?
When the body accidentally targets its own cells as pathogenic. The body will create a defense and start to put into place pathways to destroy these seemingly dangerous antigens/cells. This is seen in the Grave’s disease, Myasthenia Gravis, Systematic Lupus Erythematosus, Type 1 diabetes mellitus, Multiple sclerosis, and rheumatoid arthritis.
What are some strategies to treat autoimmune diseases?
Corticosteroids are often prescribed to treat immune diseases. They work by switching off genes that encode for inflammatory mediators like cytokines, adhesion molecules preventing the diapedesis of molecules from blood vessels into tissues. Non-steroidal inflammatory drugs also work by inhibiting COX1/2 which otherwise enables the production of the pro-inflammatory factor prostaglandin E2. Anti TNF-a inhibits the bind of ligands to TNF receptors thus stopping the activation of NFkB and its movement to the nucleus where it would transcribe genes coding pro-inflammatory proteins.
Compare and contrast the direct and indirect pathways of allorecognition.
Allorecognition is the ability of an organism to distinguish between its own tissues and those from another.
Direct allorecognition: occurs when a donor cell present the antigen to the recipents T cells. Acute rejection of a kidney graft. The DC form the donor kidney move to the recipients lymph node where they recipients T cells recognize the antigen on the donor kidney and mature into effector T cells which attack the donor kidney.
Indirect allorecognition: Occurs when a recipients DC presents the antigen to the recipients T cells. A dead/apoptotic cell has MHC on its durfface that are phagocytosed by recipient DC and eventually the recipients DC are presenting the antigen on their own MHCs which are recognized by the recipients T cells and attacked.
Explain how cyclosporin A functions to block T-cell activation.
Cyclosporine A and tacrolimus prevent signally with Ca2+, calcineurin signalling. So no NFkB activation and no IL-2 transcription and no binding to IL-2 receptor and no cyclin/CDK production thus halting the cell cycle and preventing the T cell from clonally expanding.
Lecture 22: Fighting Infectious Diseases with Vaccination
How do vaccines prevent disease?
Vaccines prevent disease based on the principle of the memory T and B cells. By inoculating a person with a live, dead or weakened version of a pathogen the person’s immune system gets a taste of what the pathogen looks like and can learn what antibodies bind to its antigens and create memory T cells to recognize it invading again and prevent a large scale disease in an additional encounter with the SAME pathogen.
What are the different types of viral and bacterial vaccines?
1. Live attenuated (weakened) vaccines: Vaccines containing a weakened or inactive form of the pathogehn so that it wont replicate within host cells but still initiate an immune response from the host so CD8 T cell responses and potent because they activate CD8 T cells and CD4 T cells to make an antibody response.
2. Killed pathogen vaccines: contain killed pathogens. The body gets to see them but no immune response is triggered because they are no longer a threat they’re killed.
3. Inactivated toxoid vaccines: toxoids that cause sickness from the disease are inactivated and they can no longer cause infection and then are injected into the host to initate B cell antibody production.
4. Subunit/conjugate vaccines: take advantage of linked recognition to boost B cell responses against polysaccharide antigens and T cell activation by presenting a peptide of the polysaccharide via B cell MHC to the T cell.
What are the strategies to make attenuated vaccines?
1. Selecting for growth in non human cells. Viruses are removed from a human sample and placed in another organism (eg. Monkey) where the virus acquires many new mutations to allow it to grow very well in the monkey host cells. The mutated virus is removed from the monkey and placed in a human host, now the virus is not well adapted to life in the human host and buys the human immune system time to recognize and destroy this virus.
2. Recombinant DNA technology: Pathogenic virus is isolated and the virulence region of its gene is identified. The virulence region is mutated to such a point that it will no longer be dangerous to the host, or the virulence region is fully removed. The virus is still live and will trigger a full blown immune response (good for virus identification and memory cell production) but there is no risk that the host will become infected as the virulence portion of the virus is non-functional/removed.
What are the criteria for a safe and effective vaccine?
1. Safe (not cause infection or illness itself)
2. Protective (against illness resulting from exposure to the live pathogen)
3. Gives sustained protection (protection must last for several years)
4. Induces neutralizing antibody
5. Induces protective T cells (intracellular viruses will not be attacked by B cells)
6. Practical considerations (how cost effective is its production, is it feasible to distribute).
7. Perceived as safe (have to educate public on its use and misuse, public must be willing to have it administered, easier said then done people are dumb).
What is the role of an adjuvant in a vaccine?
Adjuvants are any substance that enhances the immune response to an antigen with which they are mixed. Few are approved for human use. Adjuvants help activate components of the innate immune system like TLRs , inflammasomes and release of cytokines. Ensures that they body produces sufficient amounts of antibodies, activates appropriate T cell responses and retains memory of a pathogen long-term.