Immunology and Microbiology Flashcards
Barriers and non-immune antimicrobial defenses
Physical: Epithelial cells with tight junctions (skin) cilia, mucus saliva and tears, digestive tract, microbiota. Neutrophils.
Chemical: Fatty acids, pH, antimicrobial peptides/enzymes
- Production of antimicrobial proteins = defensins, cathelicidins, histatins. All are activated by proteolysis→ a pro-region is cleaved of for activation and the result is an amphiaphatic antimicrobial peptide
- Defensins - disrupts cell membranes of bacteria and fungi, and envelopes of some vira (epithelial and neutrophils) by forming a pore.
- Cathelicidins - cationic amphipathic plasmide that disrupts membranes and is toxic to microorganism (Neutrophils)
- Histatins - Cationic peptides that are active against fungi and promote rapid wound healing (oral cavity)
Microbial: microbiome
Pathogens:
Extracellular - interstitial spaces , blood, lymph (complement, phagocytosis, antibodies, autophagy) and epithelial surfaces (antimicrobial peptides and antibodies)
Intracellular - cytoplasmic (NK cells and cytotoxic T cells), vesicular (T cell and NK cell dependent macrophage activation)
Tissue damage Infection
- Direct damage: induce exotoxin production, endotoxin and direct cytopathic effect
- Indirect damage: Immune complexes, anti-host antibody and cell mediated immunity
escape the immune system and non immune system
-Anti-Crispr proteins
-MHC-1 cannot migrate to the surface and therefore cannot present viral peptides to CD8 t cells.
-Escape the phagosome into the cytosol.
-many others
Innate immune system
Macrophage, dendritic cells, Neutrophils, Eosinophils, Basophils, Mast cells, NK cells, Autophagy and Complement system
Pattern recognition receptors:
- Promote NF-κB signaling.
- Ubiquitination activates proteins upstream of kinase signaling.
- CARD-BCL10-MALT1 (CBM) Complexes mediate NF-kB activation.
Limited number of specificities
Non-self/damage
Limited memory
Macrophages
- Tissue residents
- Antigen presentation
- Secretion of cytokines
- Phagocytose and kill microorganisms
-Production of complement and macromolecules needed for tissue repair - M1 and M2 Activation- Cytokines
- PAMPS/MAMPs (TLR, NLR)
- Complement receptors (C5a and C3a)
- produce cytokines IL-1B, TNF-alpha, IL-6, CXCL8, IL-12, IL-23
Effector phase of cell-mediated immune response
ONLY reacts to INF-gamma and do not produce
Dendritic cells
-PAPC (presents both MHC class I and II)
- found in lymphoid organs, blood, tissues
-Macro and pinocytosis
- Capture antigen and bring it to the secondary lymphoid organs where an immune response is initiated
- Activation- By pamps and cytokines
- Activate T cells and the adaptive immune response
Cross-presenting abilities.
Initiates T cell response to protein antigen.
Types of dendritic cells
Conventional dendritic cells
- Circulates peripheral tissue
- Binds antigen and migrate to secondary lymphoid organs
- PAPC most potent stimulators of T-cell response
Plasmacytoid dendritic cells
- Can also act as antigen presenters
- Main function during inflammatory response is the production of antiviral interferons
Follicular dendritic cells
- present antigens to B-cells
- Reside in lymphoid follicles
- recognizes BAFF and APRIL, promote B-cell survival and proliferation
Cross presentation
After phagocytosis, exogenous antigens can be exported into the cytosol, where they are processed by the proteasome.
- The processed antigens can then be loaded on MHC class I molecules in the endoplasmic reticulum (ER) (the cytosolic pathway with ER loading)
- or re-imported into the phagosome to be loaded on MHC class I molecules (the cytosolic pathway with phagosomal loading).
The SNARE SEC22B, which localizes in the ER–Golgi intermediate compartment (ERGIC) and interacts with syntaxin 4 on phagosomes, mediates the recruitment of a subset of ER components, including transporter associated with antigen processing (TAP), to phagosomes.
- Alternatively, exogenous antigens can be degraded into peptides in the phagosome, where they are then loaded on MHC class I molecules (the vacuolar pathway).
Neutrophils
-Phagocytosis and killing of ingested microorganisms
- Contains primary/azurophilic granules, secondary/specific granules and tertiary granules.
-Phagosome fuses with granules to destroy internalized bacteria= oxygen dependent respiratory burst, which leads to apoptosis of neutrophil
-First to arrive at the crime scene
-NOT APC’s
Activated by cytokines for recruitment to the site of inflammation. Rolls over endothelial cells and via various ligands and receptors gets into the infected site. (vasodialation slows down the bloodflow, so the neutrophil has time to make proper contact)
Oxidative burst
Rapid release of reactive oxidative species
1. fMet activates Rac
2. RAC assembles NADPH oxidase complex
3. NADPH oxidase transfer free electrons to O2, generating superoxidase ions and other free oxygen radicals
4. Acidification leads to lysosomal protease activation and formatting of H2O2, killing all microbes.
Eosinophils
- Engage both in secretion of pre-formed granule-stored contents, including eosinophil specific toxic proteins, enzymes, cytokines, chemokines, and other bioactive mediators
- Masters of exocytosis
- Killing of antibody-coated parasites
Can be activated by cross-linking IgG and IgA Fc receptors by agarose beads with IgG, IgA or secretory IgA (being the most potent). Activation by cytokines.
Mast cells
- Release of granules containing histamine and active agents
- Found in tissues not blood
- Express IgE and complement receptors
Activated by IgE bound to mast cells
Basophils
-Promotion of allergic responses and augmentation of anti-parasitic immunity
-Induce inflammation
-Can function as APC in inducing Th2 response against helminth parasites allergens.
Activation activated by antigen crosslinking of FceRI receptor-bound IgE to undergo rapid degranulation and release their cellular contents and by inflammatory mediators (complement factors C5a and C3a)
NK-cells
-Releases lytic granules that kill some virus-infected cells and tumor cells
- NK cells are either activated by ITAM or inhibited by ITIM
- Activation:If they do not bind MHC-class 1, they release granules which kill the target cell (important in cancer regulation)
Binding to macrophage induce NK-proliferation and differentiation into natural effector cells, which secrete interferon gamma, inducing cytokines and phagocytosis
ILC
- promote host defense and contribute to tissue and metabolic homeostasis, wound healing and immune surveillance- effector cells which lack re-arranged antigen-specific receptors
Autophagy
Happens inside the cell, and is induced by starvation, pathogens (pamps) protein aggregates and ssRNA. Promoted by NOD1 and NOD2 sensors, p62, NDP52, Optn and TLR7.TLRs are dependent on the classical pathway NOD is not.- Mechanical stress Inhibit TOR, which inhibits ATG, this induce autophagy.- ATG6 and class III P13K complex activates ATG1. ATG16 conjugate system, ATG12,5,16 complex2. ATG8 conjugate system- ATG induces isolation membrane expansion, in creation of autophagy vacuoles- Fusion with lysosomes and the degradation of proteinLC3 is a marker for autophagyFunctions in the recycling of intracellular components, host defence and degradation of harmful proteins.
The Complement system
- Lectin pathway, is activated by cellectin (10 and 11), ficolin (1, 2 and 3) and MBL binding to MASPs stimulating C2/C4 complex facilitating C3 cleavage.
- Classical Pathway is activated when C1q recognizes a microbial surface directly, stimulating C2/C4 complex facilitating C3 cleavage or binds to antibodies
- Alternative pathway utilizes spontaneous activation of factor D, activates factor B and creates C3(H2O)BD complex, facilitating C3 cleveage and C3BBD complex formation, it is augmented by properdin and amplification loop for the two other pathways.
All pathways generate C3 convertase, which is cleaved to C3a and C3b. C3a is free and C3b is bound to the microbial surface.
- C3a and C5a recruits phagocytic cells to site of infection and induce inflamation
- Phagocytes with C3b receptors bind and undergo phagocytosis
- All pathogens generate a C5b convertase that leads to formation of C9 molecule membrane attack complex (MAC), which disrupts cell membranes.
C3b → cleavage of C5 to C5a.
leads to inflammatory response, opsoniazation, chemotaxis and direct killing
Inhibitors and regulation of complement
- Factor I → cleaves C3b to iC3bCR1
- DAF inhibits C3 convertase formation
- Factor H → binds to C3b and membrane, through membrane homologue sequence, and thereby inhibits further binding
- MCP -> cofactor for the factor I-mediated cleavage of C3b and C4b
- CR1 -> removal of immune complexes and pathogens coated with C3b and C4b.
Cytoplasmic acid sensors
Induce type 1 interferon INF-alpha, beta and wRIG-1- Detects viral dsRNA by sensing differences at 5´-capped end (triphosphate)
- Activates CARD to induce production of type 1 interferonMDA-5
- Detects longer viral dsRNA
- do not need 5´-capping to detectcGAS
- Binds directly to cytosolic DNA
- Activates STING through cGAMP binding, which stimulates interferon genes
Adaptive immune system
B- and T-cells
- Slow response 4-7 days
- T- and B-cell receptors
- Numerous highly selective specifities
- Pathogen-specific
- Strong memory
T cells
Regulates adaptive and innate immune responses
Recruits, activates, controls and maintains other immune cells
Orchestrates primary and memory immune responses
Ensures auto-tolerance
Kills virus infected cells and tumor cells
- Resting T-cells: Express CCR7 and reside in T-cell zones
- Activated T-cells: induce CXCR5- Some T-cells retain EB12 and remain
- CD4 function: T helper cells, amplifies and regulates responses to infection, helps B cells in affinity maturation, binds to MHC II.
- CD8 function: Cytotoxic T-cells. Kills cells in intracellular infections
T cell maturation
Neurogenic locus notch homolog protein 1 determines T cell fate from a CLP cell.
- T-cell development begins in the bone marrow and progresses to the thymus. Notch signaling triggers commitment to the T-cell lineage, initiating rearrangement. The process involves double-negative (DN) and double-positive stages.
- Double Negative (DN) Stage:
- DN1: Enters the thymus.
- DN2: Enters the cortex.
- DN3: Undergoes VDJ recombination.
- DN4: Tested for MHC affinity. - Pre-T Cell Stage:
- DN4: Tested for MHC affinity continues. - Double Positive (DP) Stage:
- VAlpha → JAlpha recombination.
- CD4 + CD8.
- TCR expression.
- Negative selection: High affinity to MHC leads to apoptosis.
- Positive selection: Low affinity to MHC receives survival signal.
- Alternative selection: Intermediate affinity becomes Treg. - Single Positive Stage:
- T-cells expressing TCR become CD4 or CD8.
- Determined by THPok or RunX3 and affinity to MHC II or MCH I.
- Interact with macrophages and epithelial cells.
- 1 and 10 happen in the medulla, 2-9 occur in the cortex in the thymus.
- Note: there are two time points of proliferation, because very few cells get to this point
- Note: RAG and TdT are active on certain time points. This is when the beta and alpha chains are produced, and the individual chains are made in a specific order
Fibroblast reticular cells (FRCs)
- Lymph node stromal cell found in T-cell zone of lymph node cortex- Creates collagen-rich reticular fibers that guide DCs, T lymphocytes and B lymphocytes
T cell activation
T cells are activated when encountering foreign antigen presented on MHC I or II with the co stimulatory signal from CD28 and B7, combined with an array of different cytokines.
- It can also happen in a non MHC activating pathway, this is when a t cell is activated by an array of cytokines and an activation by microbes for example TLR and NLR activation.
Dendritic cells present antigen and is ´hunted´down by T-cells, which can ´smell´the chemokines CCR7 and CXCR3.
Co-stimulation is a 2nd signal for activation of T cells and is only present when the innate immunity has sensed an infection and thus ensure activation of T cells only when there is an infection.
- Only dendritic cells, macrophages, and B cells will express co-stimulatory molecules only in the presence of infection so other cells don’t accidentally activate T cells
- This is a safety mechanism because selection in thymus is not 100% perfect. An autoimmune cell that sees its antigen in absence of infection will not be activated (in fact, it will be eliminated).
TCR
T-cell
T-cell receptor comlex is made up of a variable antigen-recognition proteins and an invariant signaling protein.
- TCR alpha:beta heterodimer, the beta-chain has to reassemble (recognizes MHC molecule)
- TCR gamma:delta, both has to reassemble to specifically each other or rearrengement stops (recognizes soluble agents at epithelial surface)
- CD3 and zeta chains that mediate signaling in the cells
Signaling from the T-cell receptor is initiated by ITAMs (10 ITAMs)
Instead of a light and heavy chain, it has an beat and alpha chain
- Always reside in the plasma membrane.
- 1 antigen binding site
Allelic exclusion
Expression of one of two alternative genes of a gene→ Restricted expression of antigen receptor genes => immunoglobulin and TCR of a single antigen specificity.
MHC I
- Expressed on all nucleated cells
- TCR recognizes MHC I, and CD8 binds to the side of the MHC I
- MHC class 1 binds to chaperone proteins, and binds to TAP via tapasin
- Cytosolic proteins are degraded to peptide fragments by the proteasome and is transported through the membrane by TAP
- TAP delivers peptides to the ER.
- This is further cut by ERAAP.
- A peptide binds to the MHC class 1 molecule and completes its folding
- MHC molecule is released from the TAP complex and exported to the cell membrane
MHC’s do NOT discriminate between self and non-self – T cells do
Detective Ribosomal products
- Peptides translated from introns in improperly spliced mRNA, translation of frameshift, improperly folded cytoplasmic proteins and membrane or secreted proteins that fail to enter ER- Tag with ubiquitin for degradation- Might help to generate peptide substrates from self-proteins and pathogen proteins for presenting by MHC I
MHCII
- Found on antigen presenting cells (B-lymphocytes, dendritic cells, macrophages)-
- CD4 binds to the side of the MHC
1. Extracellular peptides Invariant chain (Li) inhibits the binding of peptides and misfolded proteins, Li is cleaved in the acidified endosome.
2. CLIP is still bound, CLIP peptide blocks the binding of peptides and prevents the migration of MHC II.
3. HLA-DM binds to MHC II releasing CLIP, peptides can then bind to MHC II and MHC II migrates to the cell surface.
MHC’s do NOT discriminate between self and
non-self – T cells do
Non-conventional T cells
MAIT- Present in mucosal immune system- respond to bacterially folate derivates presented by non-classical MHC MR1INKT- Innate-like lymphocyte carries T-cell receptor invariant alpha and beta chain- Recognizes glycolipids presented by CD1 MHC class- Surface marker NK1 (same as NK cells)
T memory cells
IL-7 R is a true marker for memory T-cells that is only expressed on memory cells.Central memory T-cells(TCM): Arise from a primary T-cell response.- Express CD62 and CCR7- Recirculate in blood and secondary lymphoid organs.When antigen is recognized they get a recall response, and undergo rapid effector T-cell proliferation. Slower to acquire other effector functions,Effector memory T-cells (TEM): Arise from a primary T-cell response.- Lack CD62 and CCR7, but express high levels of beta1 and beta 2 integrins.- recirculate in blood and are rapidly recruited into inflammatory tissues where they initiate T-cell responses after restimulation.- express receptors for inflammatory chemokines and can rapidly mature into effector T cells, that secrete effector cytokines (IFN-gamma, IL4 or IL17)Tissue-resident memory T (TRM):Take up longterm residency in various barrier sites- Lack CCR7, but express other chemokine receptors (CXCR3 and CCR9) → allow migration into peripheral tissues- Express CD69, which reduces S1PR1, thereby promoting retention in tissues.- Can be both CD4 and CD8 T cells- Rapid response to TCR signaling or cytokines- surveillance and can initiate a particular immune module response locally
Type 1 response
TH1 cells play a crucial role in combating intracellular bacteria through the activation of macrophages, induction of apoptosis, and modulation of immune cell balance. Their cytokine production and effector functions contribute to both antimicrobial defense and autoimmune responses.
Activation: Triggered by IL-12, IL-15, and IL-18. in addition INF-gamma
Pathogens Targeted: Primarily fights against intracellular bacteria.
- IFN-gamma and CDL40 induce and activate M1 macrophages- FAS ligand and LT-beta, produced by Th1 cells, induce apoptosis
- Il-2 produced by Th1 cells acts on activated naive CD4 and CD8 → alters balance to favor Th1 cells from TFh and CD8 CTLs and memory.
- IL-3 and GM-CSF stimulate production of monocytes in bone marrow
- Produce TNF-alpha and LT-alpha acts on blood vessels and induce binding and exit of monocyte
Cytokines Produced: IFN-gamma, CD40 Ligand, IL-2, IL-3, TNF-alpha, and LT-alpha.
Proinflammatory Responses:
Responsible for killing intracellular parasites.
Contribute to autoimmune responses by inducing macrophages and monocytes.
can also differentiate to TFH cells, that again leads to B cell activation
Type 2 response
Activated by IL-25 and IL-33T
cells: Th2 cells
Pathogens: Helminth infections and parasites
Effects: IL-13 induce epithelial cell repair and mucus production → increased turnover and movement, which shreds parasitized epithelial cells. Mucus prevents adherence.
- IL-13 induce smooth muscle contraction → enhance infection expulsion
- M2 macrophages recruited via. IL-4 and IL-13 → enhance smooth muscle contractions and tissue repair.
- IL-5 recruits and activates eosinophils
- Mast cell recruitment via. IL-3 and IL-9 and specific IgE mast cell arms against helminths. → produce mediators as histamine, THF-alpha and MMCP → inflammatory response and remodel mucosa.
Cytokines: IL-13, IL-4, IL-5,IL-3, IL-9
Effector function: Increases epithelial turnover and mucus production, increase smooth muscle contraction, recruit and activate M2 macrophages → tissue remodeling and repair, recruitment and activation of eosinophils, enhance inflammatory response (mast cells)
can also differentiate to TFH cells, that again leads to B cell activation (different from Th1 response
Type 3 response
Activated by IL-23T-cells: Th17 cells
Pathogens: Infections agianst extracellular bacteria
Effects: IL-17 and IL-22 induce production of antimicrobial peptides → kills or inhibts growth of bacteria attached to epithelium
- IL-22 increase epithelial turnover
- IL-17 activates stromal cells and myeloid cells to produce G-CSF → stimulate neutrophil production
- IL-17 activates stromal cells and epithelial cells to neutrophil attracting chemokine production.
- CGL20 chemo-attractment of other Th17 cells
Cytokines: IL-17, IL-22, G-CSF and CGL20
Effector function:recruitment of neutrophils and the stimulation of epithelial antimicrobial defenses at infection sites
Treg
- Activation: Inhibited by IL-6, produced by DCs
- Function: Suppress immune responses, 1 and 2, and are able to inhibit T-cell proliferation and cytokine production, plays a critical role in preventing autoimmunity through binding with high-affinity IL-2 receptor and removing IL-2.
- Markers: CD25 and CD127, FowP3 intracellular.
- Produces: IL-10 and TGF-beta
TFH
antigen-experienced CD4+ T cells found in the periphery within B cell follicles of secondary lymphoid organs such as lymph nodes, spleen and Peyer’s patches, and are identified by their constitutive expression of the B cell follicle homing receptor CXCR5
Function: Upon cellular interaction and cross-signaling with their cognate follicular B cells, TFH cells trigger the formation and maintenance of germinal centers through the expression of CD40 ligand (CD40L) and the secretion of IL-21 and IL-4. TFH cells also migrate from T cell zones into these seeded germinal centers.
- Play a critical role in mediating the selection and survival of mature B cells or germinal center-dependent memory B.
B cells
- Resting B-cells: Express CxCR5 and reside in follicles
- Activated B-cells: induce CCR7 and EBI2
Antigen presentation to CD4+ helper T-cells in humoral immune responses.
B cell maturation
- Stem Cell Response: Responds to cytokines to coordinate VDJ recombination and B-cell development.
- Early Pro-B Cell:D-J rearranging of the heavy chain.
- Late Pro-B Cell: V-DJ rearranging of the heavy chain.
- Large Pre-B Cell: VDJ rearranged heavy chain transiently expressed on the surface.
- Small Pre-B Cell: V-J rearranging of the light chain.
- Immature B Cell: VJ rearranged light chain, expressing IgM on the surface.
- RAG Activity: High during the rearrangement of light and heavy chains.
- Testing for Autoreactivity (Central Tolerance) in Immature B Cell:
- Multivalent recognition of self-antigen leads to apoptosis or receptor editing.
- Weakly cross-linking self-antigen results in apoptosis due to unresponsiveness.
- Non-crosslinking antigen leads to immunological ignorance to the antigen.
Complete Maturation in Spleen: Tested for BAFF-R, BCR, affinity, and cross-linking. If low affinity and non-crosslinking, the B-cell matures.
In summary, B-cell development involves a series of stages from early pro-B cells to the testing of autoreactivity in immature B cells. The process includes rearrangements of heavy and light chains, expression of surface markers, and rigorous testing for self-reactivity to ensure central tolerance. The final maturation in the spleen involves further testing for B-cell receptor parameters, determining the maturity of the B-cell.
Secondary and primary diversification
- VDJ recombination → Primary diversificationRecombination occurs between gene segments on the same chromosome- RAG1/2 is essential for the recombination and is followed by the NHEJ and DSBR1.
- Binding of RAG1/2 to 23 RSS and 12RSS → leads to cleavage of DNA2. Ku70/Ku80 binds DNA endsa.
- Artemis:DNA-PK opens hairpin structure, the cut ends are modified which randomly add and remove nucleotides → then ligated by DNA ligase IVb.
- DNA ligase IV ligase DNA.
- CDR1 and CDR2 reside in the V region, CDR3 is formed by the VJ joining.
- AID → secondary diversificationEnzyme important in secondary diversification- Initiates somatic hypermutation and class switch recombination
- AID → MMRTLS → BER → APE1 → gene conversion → class switch recombination
- Happens at the immunoglobulin V-region
Somatic hyper mutation
Mutations in V-region DNA of rearranged immunoglobulin genes that produce variant immunoglobulins, for higher affinity to antigen.-Increases affinity and specificity towards the antigen
Class switch
- Somatic gene recombination in activated B-cells- Replace a heavy-chain constant region with a different isotype- Switching immunoglobulin isotype (IgI→IgA)
Allelic exclusion
Expression of one of two alternative genes of a gene→ Restricted expression of antigen receptor genes => immunoglobulin and TCR of a single antigen specificity.
B-cell activation
First signal required for B-cell activation is delivered through BCR migrates to germinal center of secondary lymphoid tissue- B-cells take up antigen through BCR phagocytosis and present antigen derived peptides on MHC class II- T cells express CXCR5 and B cells express CCR7- TFH cells recognize MHC II secrete cytokines, to deliver the second signal- CD40L binds to CD40- NF k beta is activated- NFk beta activates NIK, which stimulates pro-survival genes eg. Bcl-2- B cells migrate near the follicular and proliferate into B cell plasmoblasts and B cell memory cells
B cell types
B1: Secretes IgM (anti polysaccharide antibody) and binds IL-5 without help form T-cells. - Plasmacells: secrete antibodies- Plasmoblasts: Secrete antibodies, but retain surface Ig and MHC II molecules, migrate to bone marrowB2(follicular): B-2 cells are a subtype of B cell. They form part of the adaptive immune response and mediate humoral immunity. B 2 cells can produce high-affinity antibodies and generate immunological memory. B-2 cells are often used synonymously with classical B cells.B-memory cells:B memory cells arise from germinal center reaction during primary response. They express a class-switched surface and reside in the blood. They are poised to generate more rapid and robust antibody.
Primary lymphoid tissues
Bone marrow b cells develop in the bone marrow and is checked for central (self) tolerance before leaving.Thymust cells develop in the thymus, and are also checked for central tolerance before leaving. t cells upregulate S1PR1 to leave thymus
Secondary lymphoid tissues
Peyer´s patchesMucosal immune system, gut associated lymphoid lymphoid tissues(GALT) Peyer’s patchesPeyer’s patches = groupings of follicles in the mucus membrane and is covered by an epithelial layer containing M-cells which have ruffels, reside in the small intestineLymph nodeParacortical area (T-zone) → produces T-cell and DC attracting chemokines (CCL21 → CCR7)primary lymphoid follicle (B-zone) → produce a B-cell attracting chemokine (CXCL13 → CXCR5)Germinal center germinal centre (GC) of lymphoid organs is the main structure where antigen-activated B cells diversify their immunoglobulin genes by somatic hypermutation-Follicular B cells in lymph nodes transport antigen to FDC’sThe spleenMarginal zone: Dendritic cells, macrophages, and B-cellsB-cells in marginal zone transport antigens to FDC’sPals: T cells and dendritic cells - B and T-cells both migrate to follicular and interfollicular regions- B and T-cells aggregate at periphery of follicles (B-cells reduce CCR7)
Antibody
Structure and function
-2 heavy chains -2 light chains-Held together by disulfide bonds-Immunoglobulin fold= One β sandwich of two β sheets folded together and linked by a disulfide bond
-Variable regions(fab)= recognize antigen (proteins or haptens)
-Constant regions(fc)= dictate antibody class and isotype (effector function)
-Paratope= the region of the antibody that recognizes the epitope
-Idiotope= amino acid residues that do not have direct contact with antigen, but still contribute to antigen recognition
-Antibodies bind antigen via non-covalent interactions (e.g electrostatic forces)-CDR= hypervariable regions that interact with antigen (v-type) CDR3 region is the most critical in antigen recognition and specificity (CDR1 and CDR2 are also important)
-C-type=no variability-B-cell receptor can be in soluble or bound within TM domain
Functions:
- Bind to pathogens and toxins therby neutralize their infection and intoxication of host cell
- Promote phagocytosis (opsonization)
IgA
Major antibodies in extracellular fluid. Neutralization. Can be secreted as dimer because of J-chain.
IgD
Blood, not very abundant, effector function not well characterized
IgM
Blood stream, constant region provides strong activation of the complement system. First antibody to be expressed on naive B-cells. Can be secreted as pentamer because of J-chain.
IgE
mucosa. Often found in the skin. Associated with allergy. Defense against parasites by recruiting mast cells. Mast cells can secrete toxic compounds towards the parasite.
Inflammation IgE:
Sensitization- Der p 1 is taken up by DCs for antigen presentation and T-cell priming- TFH/TH2 cell induce B-cell switch to IgE production- IgE binds to FCepsilonRI on mast cell- Mast cell granule content cause allergic symptomsRe-exposure- Mast cell IgE bound to FCepsilonRI recognizes antigen- Mast cell secrete histamine, prostagladins and leukotrienes- Inflammatory cascade produced by mast cell activation is amplified by eosinophils, basophils, TH2 lymphocytes and B cells
IgG
most abundant isotype, in the blood. Several effector functions. Can be transferred to the fetus through the placenta. Activate complement (though not as strongly as igG).
Therapeutic antibodies:
Opzonization, neutralization and vaccines
Autoimmunity genetic
Allergy:- GeneticMain reason for developing an allergy= Susceptibility loci, these genes make it skewed towards TH2 responseIL4: IgE (promoter mutations high IgE) TIM genes: Th1 and Th2(p40) IL12 IL23: Th17
Autoimmunity enviromental
- EnvironmentalEarly exposure to ubiquitous microorganismsEary depletion of microorganisms by repeated use of antibioticsHelminth infectionHepatitis A virusComposition of gut commensal microbiota.Atopic individual: People who are allergic
NON IgE autoimmunity
Hypersensitivity reactions can be mediated by TH1 and T17 cells and CD8 cytotoxic T cells.
Chemokines
large family of small, secreted proteins that signal through cell surface G protein‐coupled heptahelical chemokine receptors. They are best known for their ability to stimulate the migration of cells, most notably white blood cells
- CXCL13 → produced in the follicle and the light zone of germinal centers that bind CXCR5 and attracts more B cells
- CXCL12 → produced by stromal cells in dark zone of germinal center binds CXCR4 expressed by centroblasts.
- CCL21 → produced by DCs and stromal cells in T cell zones in lymph nodes that binds CCR7, attract naive T cells
- ## CCL19 and CCL18 → produced by DCs attract T lymphocytes to developing lymph node
Cytokines
Mainly produced by dendritic cells, macrophages and some endothelial and epithelial cells.
Pro-inflammatory cytokines:
- IL-1 → macrophages and epithelial cells (permeable influence transport of immune components and sticky to leukocytes)
- TNF alpha → Macrophage, DCs, NK and T cells (epithel permeable influence transport of immune components and sticky to leukocytes)
- IL-6 → macrophages, T-cell and epithelial cells (promotes adaptive immune response)
- IL-12 → macrophages and DCs- IFN alpha → DCs and viral infected cells- IFN beta → viral infected cells
- IFN-gamma → see type responses above
- IL-2 → T cell growth factor
- IL-3 → monocyte and mast cell recruitment
- IL-4 → B-cell activation and M2 recruitment
- IL-7 → marker for memory B-cells
- IL-13 → Stimulates turnover and smooth muscle contraction
- IL-17 → induce activation of antimicrobial peptides and stimulate neutrophil production and attachment.
- IL-21 → germinal maintenance- IL-22 → production of antimicrobial peptides
- IL-25 → TH2 cytokine production, activates TH2 response and ILC-2
- IL-33 →TH2 cytokine production, activates TH2 response and ILC-2
- LT-beta → induces apoptosis
- TNF-alpha → promotes inflammation
- FAS and FAS ligand → cationic independent toxicity and apoptosis
- TRAIL → apoptosis of tumor cells and activated T cells
- APRIL → B cell proliferation
Autokrine
Cytokines affecting behavior of the cell that releases the cytokine
Parakrine
Cytokines affecting adjacent cells
Endokrine
Cytokines affecting distant cells, depends on their ability to enter circulation and half-time in blood.
Receptors, ligands and integrins
- CCR7 → Expressed by all naive T and B cells, binds CCL19 and CCL21 made by DCs and stromal cells in lymphoid tissue.- CCR9 → expressed by DCs, T cells, thymocytes and binds CCL25 and mediates recruitment of gut-homing cells- CXCR5 → Expressed by circulating B cells and activated T cells, bind CXCL13 and direct cell migration into follicle- CD40 and CD40L → CD40 on B-cells and CD40L on TH cells, co-stimulatory molecules required for the proliferation and class switching. Also expressed by DCs and CD40-CD40L interaction provide co-stimulatory signals to naive T cells- CXCL8 → produced by monocytes, macrophages (under inflammatory response) attract neutrophils and naive T cells.- P-selectin → Reside on activated endothelial cells- LFA 1 (integrins) → Reside on leukocytes binds to I-CAM 1- I-CAM 1 → reside on activated endothelial and leukocytes, binds to LFA 1- G-proteins → act as molecular switch in signal pathways (GPCR) to induce high affinity with LFA 1.- CD28 → activation receptor on T cells that binds to the B7 co-stimulatory molecules present on APCs.- BAFF → acronym for B-cell activating factor, binds to BAFF-R and TACI promote B cell survival.
CRISPR
Consists of cas genes, leader and repeat-spacer array- Class 1 is a multiprotein complex- Class 2 is a single proteinPAM adjacent protospacer motif and CRISPR protospacer is required for cas nuclease to recognize target and cut1. Short viral DNA is incorporated as a novel spacer into CRISPR array2. During expression CRISPR array is transcribed into pr-CRISPR RNA → mature crRNA with unique CRISPR spacer3. During interference, crRNA guide CAS effector nuclease → sequence-specific cleavage- Class 1, Cas 3 nicks DNA and Cas 10 cleaves- Class 2, Cas 9 nicks DNA and Cas 12 offset two nicksAltering CRISPR spacer or PAM → gain or loss of function→ Can be used in antimicrobial, anti-infective and genome editing systems
