2. Pathogen detection by the immune system Flashcards
What are the innate immunity and adaptive immunity cells?
Innate imm cells/molecules:
- Macrophages
- Dendritic cells
- Mast cells
- NK cells
- Complement proteins
- Granulocytes: basophils, eosinophils, neutrophils
Adaptive imm cells:
- T cells
- B cells
How is pathogen detection different in innate and adaptive immunity?
Innate: recognises generic ‘danger’ signals (PAMPs / DAMPs) -> limited receptor diversity
Adaptive: recognises very specific microbial / non-microbial molecules - antigens -> very large receptor diversity
What is the Complement System in pathogen recognition? What are the pathways of working?
The Complement System - biochemical cascade that functions to recognise pathogens and destroy them - early warning system
Has 3 pathways of working:
- Alternative (innate immunity)
- Lectin (innate immunity)
- Classical (adaptive immunity)
What functions can be performed using the Complement System to destroy pathogens?
The Complement system does to destroy pathogens:
- Recruit immune cells
- Label microorganisms for phagocytosis by other cells
- Lyse pathogens
How each Complement system pathway is activated?
- Direct pathogen recognition => alternative + lectin pathway
- Via adpative immunity + antibodies => classical pathway
Explain the alternative pathway of the Complement System
Alternative pathway acts as innate immunity sensor:
- C3 protein - (C3 convertase) -> C3a + C3b
- C3b attacks amino + hydroxy groups on pathogen surface
- Complement system cascade ativated to neutralise the pathogen
Problem: host cells also have amino + hydroxy groups on the surface - must de-activate C3b
Explain lectin pathway of the Complement System
Lectin pathway acts as innate immunity sensor:
- lectin receptors bind to mannose on pathogen surface
- binding activates C3 convertase -> C3b produced -> bind to pathogen amino and hydroxy groups
- Complement System cascade ativated to neutralise the pathogen
What does the innate immunity use to recognise pathogens?
Innate immunity uses evolutionary conserved molecules in many classes of microbes that are not present in host cells - PAMPs
What are PAMPs?
Pathogen Associated Molecular Patterns (PAMPs) - evolutionary conserved molecules shared by various classes of microbes, ex: mannose
PAMPs - on pathogens
PRRs - on imm cells
What are the receptors used to detect PAMPs?
Pattern Recognition receptors (PRRs) - proteins / receptors on the surface of innate immunity cells used to recognise PAMPs, ex.: mannose binding lectin
PAMPs - on pathogens
PRRs - on imm cells
Explain the mechanism of phagocytosis
- Chemotaxis: attract phagocytes to the site
- Attachment: phagocyte attaches to surface of foreign particle
- Engulfment: ingested
- Phagosome maturation: fusion with lysosomes with digestive enzymes -> phagolysosome
- Degradation: in phagolysosome particle digested
- Exocytosis: waste eliminated form phagocyte
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What are sentinel cells?
Sentinel cells - general term for any immune cell at the first line of defence - always alert, ex.: macrophages, dendritic cells
What are the roles of sentinel cells to sense infection and induce response?
- Use phagocytosis to sample environment
- If detected APC - communicate to T cells
- Activate T cells
What are APCs?
Antigen Presenting Cells (ACPs) - immune cell that detects, engulfs, and informs the adaptive immune response about an infection
Compare macrophages and dendritic cells (DC) as sentinel cells
Explain macrophages as sentinels
Macrophages as sentinels - found** in all barrier tissues** - skin, intestine, lungs
Resting state - help regulate metabolism:
- clear apoptotic cells
- remove debris
- sample env for antigens via PRRs-PAMPs
Activated state:
- detected DAMPs (1st danger signal) - warning but not necessarily infection - activate Complement System pathway - ready for phagocystosis
- detected PAMPs (2nd danger signal) by PRRs - infection alert - increase in size, increase phagocytosis, release toxic molecules + cytokines
- in the end - macrophages revert to resting state / apoptose
What are DAMPs?
Damage-Associated Molecular Patterns (DAMPs) - molecules released from damaged / necrotic cells
- potential break in barrier
- pathogen is causing damage while invading
Do innate immunity cells express only one PRR? Where are they found?
No, innate immunity cells can express multiple PRRs - can recognise and respond to wide range of pathogens with different PAMPs
PRRs are both on the surface and inside the cell - intracellular / extracellular
What are the examples of PAMPs?
Possible PAMP molecules:
- mannose
- lipopolysaccharides (LPS) - Gram-
- lipoteichoic acid (LPA) - Gram+
- teichoic acid (TA) - Gram+
- peptidoglycan
- flagellin
- dsRNA
- ssRNA
- unmethylated CpG DNA
Recognised by PRRs - majority by Toll-like receptors (TLRs)
How can pathogens try to avoid recognition by the immune system?
Pathogen adaptations:
- Modification of PAMPs
- Inhibition of PRRs signalling pathways
Summary of macrophage activation as a sentinel cell
Explain how inflammation is induced
- By both innate / adaptive immunity
- Release of pro-inflammatory cytokines (ex: interleukin-1 (IL-1), tumor necrosis factor-alpha (TNF-α))
- Recruit immune cells to infection site
- Activate immune cells and stimulate to produce more cytokines
- Production of APPs
=> tissue redness, swelling, fever
What are APPs? What are the types?
Acute Phase Proteins (APPs) - group of plasma proteins - the conc varies - produced in response to inflamm / infection - function is to regulate imm response
- Positive APPs: increase in conc upon inflamm / infection, ex: CRP - binds to pathogens and enhances recognition + activates Complement system (practical 1: diagnostic for severity of inflamm), fibrinogen
- Negative APPs: decrease in conc upon inflamm / infection, ex: albumin
What are the functions performed by neutrophils?
Neutrophils:
- recruited from blood to the infection site
- phagocytosis of pathogens
- release of destructive chemicals (cytokines, chemokines, ROS, enzymes, defensins)
- short-lived - apoptose
What are the immune cells involved in killing pathogens during inflammation?
Killers in inflammation:
- Neutrophils
- NK cells
- Macrophages
What are the functions performed by NK cells?
Natural killer (NK) cells:
- recruited from blood to infection site in response to cytokines / chemokines
- produce cytokines / chemokines
- kill pathogens / infected + abnormal cells without activation - detect downregulation of MHCI
- kills by releasing cytotoxic granules with perforin + granzyme -> induces apoptosis
- apoptose / revert to resting state
What are the main immune cells involved in inflammation?
- Macrophages: phagocytic, produce cytokines/chemokines
- Neutrophils: phagocytic, produce cytokines/chemokines
- NK cells: recognise + kill infected / cancerous cells, release cytotoxic granules, produce cytokines
Can PAMPs be toxins?
Yes, ex.: PAMP - LPS toxin - induce too strong cytokine production => sepsis:
- inhibits heart contractions
- fluid leaks into tissues
- increased blood clotting
- cachexia (muscle wasting)
=> reduced blood presure
=> septic shock
What is sepsis?
Sepsis - body’s extreme response to an infection - life-threatening medical emergency - happens when an infection you already have triggers a chain reaction throughout your body
What are the advantages of innate immunity sensing?
Adv:
- PAMPs allow distinguish foreign microbes + indicate what kind of microbe - PAMPs evolutionary conserved - well detected - small number of PRRs needed
- PRRs germline encoded - don’t need modifications - can be used for quick response
- multiple cell types can express same PRRs - many cells can respond to same infection
- one cell can express many PRRs - can detect many PAMPs - many different microbes
What are the disadvantages of innate immunity sensing?
Disadv:
- not very specific - rough idea of microbe type
- not adaptable (only through evolution)
- doesn’t develop into immune memory
What are the advantages of adaptive immunity sensing?
Adv:
- very adaptable - somatic rearrangement of gene segments allows creation of receptors for any antigen
- very specific for the antigen
- having a receptor gives immune memory - can identify particular microbes for the rest of organism’s life
What are the disadvantages of adaptive sensing?
- slow - takes time for clonal expansion
- highly specific - easy for microbe to evade by slightly changing antigens
- receptors can’t tell what they are recognising - can’t distinguish pathogen from self / innocuous molecules (ex.: pollen)
What are innocuous molecules?
Innocuous molecules - harmless molecules, ex.: pollen, other allergens
Define what is an antigen
Antigen - a molecule recognised by adaptive immune cells as non-self
Bound by B or T cell receptors:
- T cells only bind Ag on APC presented on MHC
- B cells recognise Ag on their own
Define what is an epitope
Epitope - the precise part of the antigen recognised by antibody / T cell receptor
An antigen can have multiple epitopes
Define what is a paratope
Paratope - the part of the antibody / T cell receptor that binds the epitope
Where do antibodies come from?
Antibodies - secreted B cell receptors
What are the adaptive immunity cells?
- B lymphocytes
- Helper T cells (Th)
- Regulatory T lymphocyte (Treg)
- Cytotoxic T lymphocytes (CTL)
What is the difference how B and T cells recognise antigens?
B and T cells have different receptors:
- B cells: recognise Ag on their own - membrane bound receptors - B cell receptors (BCR) = surface immunoglobulins (sIg) same thing - when secreted Ab = immunoglobulins Ig same thing - secreted form has effector function
- T cells: recognise Ag presented by APC (ex: macrophages / DC) - T cell receptors only membrane bound - T cell receptors (TCR)
How do the antigens recognised by B and T cells differ?
B cell recognised Ag:
- pretty much any organic molecule
- bind on their own without APC
- conformational - structure important in binding
- epitope can cross loops - discontinuous
- native molecule - also recognises native molecules + unprocessed native molecules
T cell recognised Ag:
- recognises only proteins
- Linear
- 8-25 am a long
- must be presented by APC
- protein has to be broken down into peptides
How do B and T cell receptors differ?
- T cell receptors have one Ag binding site
- B cell receptors have two Ag binding sites
What are the types of antibody epitopes?
Antibody - antigen binding:
- Linear
- Discontinuous
What is the structure of an antibody?
Antibody (Ab) = immunoglobulin (Ig) - secreted B cell receptor structure:
- Light chain
- Heavy chain
- Fc region
- Fab region
What is the in depth structure of a T cell receptor?
- α and β chains
- sulphide bonds
- transmembrane region
How is almost an infinite range of antigen receptors created?
- Some are encoded in germline - not enough
- Somatic recombination - antibodies are modular - different VDJ combinations can be created
- Junctional diversity (part of somatic recombination) - addition / deletion of bases - new DNA sequences at borders between VDJ modules
Explain what is somatic recombination
Somatic recombination - genetic info in non-reproductive cells rearranged for new gene combinations
- occurs during B / T cell development - V(D)J gene recombination - antigen binding domains are modular - segments can be re-arranged using recombinases - higher diversity of BCRs and TCRs for Ag recognition
- somatic recombination can also generate self-reactive BCRs and TCRs - autoimmune disorders
What is an antigen binding domain characteristic which allows somatic recombination?
Antigen binding domains are modular - VDJ domains can be miss-matched for specific antigen complementarity - highly variable sites created - VDJ recombinase used
Explain what is junctional diversity
Junctional diversity - variability that arises at junctions between VDJ segments during somatic V(D)J recombination
- addition of a base
- deletion of a base
=> changes amino sequence -> more unique Ag
What kind of rearrangements can be produced by somatic recombination (+junctional diversity)?
New rearrangements can be:
- Productive: results in functional receptor - those B cell survive
- Non-productive: results in non-functional receptor - B cell that produces non-productive arrangement for a receptor (-> Ab) die - apoptosis
- MAJORITY of rearrangements non-productive - not sustainable mechanism
Where are VDJ genes located for VDJ modules of antigen receptors?
VDJ genes are located on both chromosomes 14 (from each parent) - two chances to make productive VDJ arrangements for each cell because:
- each B cell is specific for one Ag
- only one Ab (BCR) is allowed per one B cell
=> successfully rearranged chain will block gene rearrangement on the other chromosome - already has a functional receptor in the B cell
What is clonal expansion?
Clonal expansion:
- T/B cell sees Ag - becomes activated
- T/B cells divide -> all daughters have identical Ag specificity
- time required to activate + proliferate to an effective number makes adaptive immunity slow - 5-7 days
What is the timeline of an adaptive immune response to a specific pathogen?
How can pathogens evade adaptive immune recognition?
Pathogens can mutate their Ags - immunity can’t recognise them - adaptive immunity especially - even single change can cause the receptor to be non-complement for Ag - because highly specific
What is the central tolerance?
Central tolerance - a mechanism by which T and B cells that are capable of recognising self Ag are deleted before they are released to fight self
- Self-reactive B cells removed in bone marrow
- Self-reactive T cells removed in thymus
[However, doesn’t remove T cells which have receptors to recognise innocuous antigens (food) - ?? B cells can also recognise]
What is the main problem with B and T cell antigen detection?
B and T cells can’t distinguish what they recognise - pathogen / toxin / innocous antigen / self
How does innate immune system communicate with T cells?
Correct T cells are activated by professional APCs which are innate immunity cells - mostly dendritic cells (DC)
What is a naive T cell?
T cell - circulating in the body - haven’t been exposed to an Ag
- professional APCs introduce to Ag -> activation / differentiation => activated functional T cell
What is MHC?
Major Histocompatibility Complex (MHC) - class I + class II proteins - present Ag on APC surface for T cell recognition - can bind several peptides - not highly specific as receptors
What is the structure of MHC I and II?
MHC I: α chain transmembrane - intra-cellular Ag
MHC II: α + β chains trnsmembrane - extra-cellular Ag
S-S - disulphide bonds
What is the difference between MHC I and II?
MHC I:
- binding peptide 7-11 am. a.
- α chain embedded in membrane
- binds intra-cellular Ag - endogenous pathway
- present on all nucleated cells
- binds CD8+ CTL cells -> infected cells killed
MHC II:
- binding peptide 12-15 am. a.
- α + β chains embedded in membrane
- binds extra-cellular Ag - exogenous pathway
- present only on professional APCs
- binds CD4+ Th cells -> cytokines produced to regulate imm response
What is MHC haplotype?
MHC haplotype - set of MHC alleles present on each chromosome - MHC genes are codominantely expressed - alleles from both parents expressed equally
Each organism expresses a diverse set of MHC molecules - encoded by MHC class I /II genes (HLA-X)
What is the difference between intracellular and extracellular Ag?
Intracellular Ag: processed within the cytoplasm - tumor / bacterial / viral proteins / cellular proteins - processed within the cytosolic pathway (MHC I)
Extracellular Ag: internalised by phagocytosis / endocytosis - processed within the endocytic pathway (MHC II)
What are CD4 and CD8?
CD4 / CD8 - proteins which form a bridge between TCR and:
- MHC II - CD4+ Th cells
- MHC I - CD8+ CTL cells
=> CD4 and CD8 termed co-receptors and considered an integral part of this multimolecular complex
Why is MHC haplotype important in organ transplant?
MHC haplotypes of donor - recipient must be matched - tissue typing - foreign MHC molecules on graft activate T cells - kill the graft as an infection
=> hard to find donor matches - everyone has different mixes of MHC - MHC genes mots polymorphic genes in mammals
How are pheromones involved in MHC haplotype?
T shirt experiment: the opposite sex smells best when the MHC alleles match the least - ensures that children have varied MHC alleles - best for Ag recognition if different MHC present
What is the sequence of events in endogenous and exogenous pathways?
Extra reading for MHC I, MHC II, Ag processing and presentation
https://microbenotes.com/mhc-antigen-processing-presentation/
What is the role of DC cells in immune response?
Dendritic cells (DC) - innate immunity cells:
- present in all barrier tissues - scan for infection via PRRs by sampling environmental Ag
- when Ag found - take to lymph nodes (LN) - talk with T cells - present self-Ag, harmless Ag and pathogenic Ag to T cells
- don’t kill like macrophages
What are the three phases of DC cells?
- Sampler: samples the env for Ag - expressed PRRs to detect DAMPS and PAMPs - bad at presenting Ag
- Traveller with cargo: has taken in env Ag - both dangerous and innocolous Ag - carries to LN to present for T cells
- Presenter: presents Ag to T cells in LN - upregulates MHC II + molecules for pathogen signalling (B7 or CD80/CD86) to T cells
How does DC communicate danger to T cells in LN?
DC need to release signals to activate T cells:
1. Communicate Ag specificity: MHC-Ag interacts with TCR
2. Co-stimulation: danger signals - PAMPs - upregulate B7 (CD80/CD86) on APC - signals to T cell via CD28
=> T cell activates -> clonal expansion + effector functions
What is the difference between B7 and CD80/CD86?
B7 - type of integral membrane protein - on activated APCs - when paired with CD28 / CD152 surface protein on T cell
-> costimulatory / coinhibitory signal to enhance / decrease activity of a MHC-TCR signal between the APC and the T cell
No difference, same thing: B7 I = CD80, B7 II = CD86
What does it mean if no signal 2 is released by APC for T cell?
If no signal 2 - B7-CD28 binding - no danger - self / food Ag => T cell not activated
Why do B and T cells don’t have more than one receptor?
If B and T cells had several receptors - chance that the same cell could have receptors for pathogen + self - if activated for pathogen - would also act on self => self destruction - autoimmune disease
What are cytotoxic T lymphocytes and what is their function?
Cytotoxic cells (CTL) - type of T cell:
- CD8+
- recognises Ag presented by MHC I on APCs - intracellular Ag
- identifies
- kill infected cells
What is the role of macrophage as APC?
Macrophages act as APCs by initiating iflammatory cascades:
- senses DAMPs, LAMPs - signals to Th cells -> go kill / the infection has been cleared - no more adaptive imm needed
What is the role of B cells as APC?
B cells require permision from T cells to have fulll effector functions to fight the infection
?? read more
Explain the process from DC cells acting as APCs to activating Th cells to Th cell communication with macrophages
What is the difference between macrohpages and neutrophils in inflammation?
Macrophages vs neutrophils in inflammation:
- timing: neutrophils first -> then macrophages
- phagocytosis: macrophages more effective
- cytokines: macrophages produce more
- tissue damage/repair: macrophages play critical role in repair - produce growth factors + ECM proteins; neutrophils damage - produce enzymes + ROS
Explain humoral vs cell-mediated immunity
Humoral immunity: mediated by B lymphocytes
Cell-mediated immunity: mediated by T lymphocytes
