Integrity: Immunology Flashcards
Give brief definitions of each of these molecules and cells of the immune system:
Molecules
* Complement
* Cytokines
* Chemokines
* Antibodies
Cells
* Leukocytes
* Innate cells
* Adaptive cells
Molecules:
- Complement - system of soluble serum proteins that interacts with pathogens to mark them for destruction by phagocytes
- Cytokines - immune messenger hormones
* Chemokines (cytokines which specialise in making cells move) - Antibodies - secreted molecules which bind pathogens
Cells
- Leukocytes = all immune cells (innate and adaptive) Literally “white
blood cell” - Innate cells (Macrophages, dendritic cells, neutrophils, eosinophils,
basophils and mast cells) - Adaptive cells (T cells, B cells) (lymphocytes)
How are the following tissues involved in the immune system?
- Lymphatics
- lymph nodes
- spleen
- thymus
- bone marrow.
- Lymphatics - drainage system for peripheries therefore a good place to scan for problems
- Lymph nodes - collections of immune cells at lymphatic junctions
- Spleen - filters blood so immune cells present
- Thymus - involved in the creation of immune cells
- Bone marrow - where all blood cells originate hence all immune cells
How does the skin provide a barrier to pathogens?
The epidermis consists of dead cells and viruses need alive cells to infect
What is the anti-viral state?
When a cell is infected by a virus it releases IFN-alpha and IFN-beta.
These cause the surrounding cells to enter an antiviral state
- Upregulate antiviral proteins (including more IFNs), and antigen
presentation - Downregulate everything else by degrading mRNA and
inhibiting protein translation factors (suppress viral
proliferation)
What are the interferons involved in inducing an anti-viral state?
IFNα and IFNβ
What are IFNα and IFNβ
They are interferons released when a cell detects that it is infected by a virus and they induce an anti-viral state in surrounding cells
What are the two things you need in order to get an adaptive immune response?
Danger and non-self
Two types of danger molecules?
PAMPs = Pathogen Associated Molecular Patterns
- types of molecules only produced by infectious agents
and not host tissue - critical for survival/virulence - Example = bacterial cell wall constituents
(lipopolysaccharide - LPS)
DAMPs = Damage Associated Molecular Patterns
- Molecules released from injured cells
- Examples = DNA, RNA, ATP, breakdown products of
extracellular matrix
What are PAMPs and why do pathogen make them?
PAMPs = Pathogen Associated Molecular Patterns
- types of molecules only produced by infectious agents
and not host tissue - critical for survival/virulence - Example = bacterial cell wall constituents
(lipopolysaccharide - LPS)
They are usually critical for pathogen survival otherwise the pathogens would evolve not to make them and therefore not get recognised
What are DAMPs
DAMPs = Damage Associated Molecular Patterns
- Molecules released from injured cells
- Examples = DNA, RNA, ATP, breakdown products of
extracellular matrix
What is a pattern recognition receptor (PRR)
These are the things that recognise PAMPs and DAMPs
Toll like receptors are an example of PRRs.
What do each of the toll like receptors recognise?
- TLR3
- TLR4
- TLR5
- TLR3 binds double-stranded RNA (viruses)
- TLR4 binds LPS (bacterial cell wall)
- TLR5 binds flagellin (flagellated bacteria)
Three pathways of complement activation
- Classical pathway
- Mannose-binding
lectin pathway - Alternative pathway
Describe the classical pathway of complement activation
- This occurs in the presence of antibodies specific to foreign antigens
- The antibodies bind to compliment C1q
- C1q then activates the rest
Which complement is first activated in the classical pathway?
C1q
Describe the mannose-binding lectin pathway of complement activation
Mannose is present on the surface of bacteria and not on any host cells.
Mannose binding lectin then bind to mannose triggering complement activation
Describe the alternative pathway of complement activation
Complement componant C3 spontaineously binds to surrounding cells
Host cells contain control proteins which prevent further complement activation
Bacteria do not
Complement involved in the alternative complement activation pathway?
C3
Describe the process of complement membrane lysis
- Membrane Attack Complex (MAC) forms in membrane of bacteria, this is a barrel-like structure formed from multiple late complement components (C5b,C6-C9)
- Water rushes in, ions rush out, bacteria swells and
bursts - Can also happen to host/foreign cells marked for killing
What is the barrel like structure in complement membrane lysis called?
Membrane attack complex
MAC
Which complement componants are involved in forming the membrane attack complex?
C5b,C6-C9
What are anaphylatoxins?
They are complement componants that cause vessels to become leaky
This allows the flodding of immune cells in the blood to the site of infection
What complement are anaphylatoxins?
C3a,C5a
What is opsonisation
This is where compliment C3b and C4b bind to pathogens and mark them for phagocytosis
Complement factors involved in oponisation?
C3b and C4b
Describe the complement cascade using all the complement componants
C1
C2 a/b
C3 convertase
C4 a/b
C3 a/b
C5 a/b
C6-C9
We need to get to the formation of C3 convertase which will cleave C3 into C3a and C3b
Classical: C1 cleaves C2 and C4. C3 convertase is then formed from C2b and C4b fragments. C4b oponiser
Mannose-binding lectin: Binding firectly cleaves C2 and C4. C3 convertase is then formed from C2b and C4b fragments. C4b oponiser
Alternative: C3 cleaved spontainously in C3b and C3a. C3b binds to pathogen surface and is activated by factor B to form another C3 convertase
C3 convertase cleave C3 into C3a and C3b.
C3a is an anaphylatoxin.
C3b is an oponiser and goes on to combine with C3 convertase to form C5 convertase which cleaves C5.
C5 cleaved by C3a into C5a and C5b.
C5a is an anaphylatoxin
C5b goes on to trigger and partake in complement membrane lysis with C6-9
In general “a” are anaphylotoxins while “b” are oponisers and cleavers of further complemments
List all the innate immune cells
Phagocytes:
Neutrophils
Macrophages
Dendritic
Allergic/parasites:
Eosinophil
Basophil
Mast cell
Virally infected:
NK Cell
Which of the innate immune cells are phagocytes?
Phagocytes:
Neutrophils
Macrophages
Dendritic
Which innate immune cells are involved in allergic reactions and parasite response?
Eosinophil
Basophil
Mast cell
Which innate immune cells are involved in killing virally infected cells?
Natural killer “NK” cells
Comparing the phagocytes
What is Extravasation?
Neutrophils need to get from the circulation to the site of inflammation - process of
extravasation
- Endothelium of blood vessel altered by inflammatory cytokines
- Neutrophil starts to roll along endothelium, then firmly adheres, and exits between
endothelial cells (diapedesis) - Follows chemokine gradient to site of inflammation.
Describe the process of phagocytosis
- Phagocyte detects pathogen and
engulfs it - forms phagosome - Lysosome fuses with phagosome
- lysosome contains toxic products
to kill/degrade pathogen - Now called phagolysosome
- Phagolysosome “matures” as
more lysosomes fuse with it and
H+ ions are pumped in - acid!
What is the phagosome, lysosome and phagolysosome
Phagosome - vesticle containing the munch
Lysosome - vesticle containing digestive chems and enzymes
Phagolysosome - fused phagosome and lysosome
How are macrophages activated to become phagocytes?
- Activation can come from danger signalling or cytokines,
especially IFNγ - IFNγ from other cells - NK cells, other activated macrophages, but
in an established immune response, from helper T cells.
What is a Neutrophil NETs
Neutrophil Extracellular Traps
- Neutrophils can extrude their DNA, acting like
a net which traps pathogens. - = “Netosis” (vs apoptosis and necrosis)
- Primarily seen in extracellular fungal infections.
What is a dendritic cells main purpose?
Antigen presentation
How does a dendritic cell present antigens to T cells?
When dendritic cells in the
periphery they are
constantly taking up antigen.
* If they sense danger they
“mature”
* Get better at antigen
presentation, and
upregulate different
chemokine receptors
* This results in their
migration to the
lymphatics, and into the
draining lymph node,
where they will present
antigen to T cells.
Difference between B and T cell antigen recognition
T cells must have their antigen chopped up in peptides and then loaded on
Major Histocompatibility Complex (MHC) molecules on another cell (dentritic cell)
T - fancy fucks
Three signals involved in antigen presentation?
Signal 1: the antigen peptides on the MHC
Signal 2: B7 receptor (only there if the dendritic cells sensed PAMPs/DAMPs) that binds to the CD28 ligand on the T cell. This is required for a presentation
Siganl 3: cytokine signal to signal the quality of the immune response. A way for the dendritic cell to convey more information about what it saw
Which cytokine is initially raised during exercise and muscle contraction? What are the effects?
IL-6
- Reduces TNF from macrophages and therefor reduces inflammation
- Mobilises NK cells
- Improves T-cells
What are the six sentinels of the innate immune system in homeostasis.
4 are non-inflammatory
How does ageing inhibit your natural immunity?
Inhibitions
- Reduced lymphocyte diversity (marrow and thymus atrophy)
- Exausted immune system from chronic infection or scared severe historical infection
Effects
Reduced response to new antigens:
* More susceptable to infections
* Worse vaccine efficacy
Reduced survailence of self:
* re-emergence of latent viruses
* increased cancers
Why does an increasing age contribute to increasing inflammation?
There is an accumalation of danger signals of danger signal that trigger the innate immunity e.g. cell debris, cytokines etc.
What happens in inflammation in metabolic syndrome (meta-inflammation)
Obese adipose tissue is stressed and releases inflamatory cytokines
What cytokines are involved in healthy lean adipose tissue and what are in obese adipose tissue?
Lean:
IL-4
IL-10
Obese:
IL-1beta, IL-6, IL-12, IL-18
What is inflammaging?
Inappropriate persistent inflammation with ageing
What is immunosenesence?
Specific immunity declines with ageing
How to T-cells get around the brain?
They enter through the sinuses, search for immune signals then drain through the lymphatic vessels
How do the intestines keep microbes away
– Goblet cell mucus (gel of glycoprotein + water)
* Physical barrier
* Holds antimicrobial peptides (epithelium, Paneth cells) and immunoglobulin (IgA)
– IgA (intestinal plasma cells) transcytosed across epithelium
* coats microbes and toxins
* shapes the microbiome by selective targeting & supports some symbionts
– Steady state low level neutrophil emigration to luminal surface
What is a key antibody in mucous?
IgA (Immunoglobulin A)
What happens in IBS
dysbiosis (=altered gut microbiota including bacteria, fungi, yeasts, viruses)
* reduced diversity with accumulation of pathobionts (symbionts which cause disease under
changed conditions, including bacteria, fungi, viruses)
– microbes accumulate near epithelium, penetrate into lamina propria promoting
inflammation
– cycles of inflammatory damage, barrier breakdown, further dysbiosis
What happens to your metabolic state during an immune response?
The immune cells switch from a metabolic state to an anabolic state as they are required to synthesise more proteins etc.
What is exudate?
This is the cells, fluid and proteins delivered to tissues by vessels during inflammation
What happens to capillary beds during inflammation?
The become leaky
Blood fills the capillary beds (redness and heat)
Interstitial matrix fills with fluid (swelling)
Perivascular mast cells degranulate & release cytokines through
projections into vessels. Incoming leucocytes take over
WHat are mast cells?
They are a type of sentinal cell that sits in tissue.
They are have IgE antigens and hence are recognised by IgE antibodies. The binding of IgE is a common method whereby mast cells are activated (the one involved in allergies)
Other activation triggers include cold and complement
Once activated they then degranulate releasing various mediators such as cytokines and histamines
What is the antibody involved in triggering mast cells in allergies?
IgE
What things can be released by mast cells as they degranulate?
- Histamines (vasodilation, vascular leak)
- Leukotrienes from arachidonic acid (bronchoconstriction)
- Cytokines (other leukocyte recrutment)
Basophil vs Mast cell
Both can release histamines and are involved in allergies however mast cells are more important int his regard
Mast cell:
* found in tissues
* releases histamines in allergies but also leukotrienes in asthma and cytokines to attract other immune cells
Basophils:
* Found in the blood
* Releases histamines but it’s primary role is anti-parasitic
How do neutrophils enter tissue?
Think glycocalyx, selectins, cytokines, platelets and fibrin
What is Chemotaxis
Directed migration up a concentration gradient
Once a neutrophil has oass the endothelium into tissue how does it continue to find the injury site?
It follows the rigitity of the injury site aka the fibrin scaffold
Phagocytes need a fibrin scaffold in order to crawl
What is cloaking?
During minor injury resident macrophages can hide injury from neutrophils and prevent them trigger happy cunts from shooting up the place
If the neutrophil never actually makes contact with the injury it can’t create a the swarming effect
What does a neutrophil look like in histology?
Kinda like a tiny clump of frogspawn
What is the order of arrival of exudate out of neutrophils, monocytes/macrophages, fluid?
What are 4 exudates you see in clinical practice and their constituents?
4 outcomes of inflammation with increaseing severity?
- Resolution - complete healing
- Organisation - healing with scarring
- Dissemination - sepsis
- Chronic inflammation - inflammation persists
What happens with inflammation resolution?
Danger signal wane:
- Neutrophils undergo apoptosis
- pro-inflammatory mediator are catabolised
Anti-imflammatory mediators predominate:
- IL10
- complement and cytokine inhibitors
- pro resolving lipids
What happens in Organisation?
Exudate is replaced with granulation tissue that remains to form a collagen scar.
Prone to disease progression as stiff tissue makes it easier for leukocyte adhesion
Difference between regeneration and repair
- Regeneration – renewal or compensatory growth to
replace damaged tissues - Repair – fibrous scar production (fibrosis) to patch
damaged tissues
What are Labile cells
These are cells that are capable of regeneration in homeostasis such as a the skin and gut
What are stable cells?
Cells which are non-proliferative in homeostasis but that are instead capable of regenerating after injury (liver, kidney)
What are permanant cells?
Permanent cells – unable to regenerate (neurons,
cardiac myocytes)
With regard to regeneration skin cells and GI tract cells are examples of what?
Labile cells
With regards to regeneration, liver and kidney cells are examples of what?
Stable cells
With regards to regeneration, neurons and cardiac myocyte are examples of what?
Permanent cells
What kind of healing is associated with TGF-alpha (transofrming growth factor) and which TGF-beta
TGF-alpha - signal which promotes regeneration of cell capable of regeneration
TGF-beta - signal which promotes repair, it produces fibroblast
migration & proliferation
What collagen is involved in scar formation
fibrillar type I
/III
Three stages to scar formation
- Fibroblast migration and proliferation
- Extracellular matrix deposition - collagen
- Tissue remodelling
What breaks down the ECM in order for remodelling to occur?
Matrix metalloproteinases
(MMPs)
What is liver cirrhosis?
Even though the liver can regenerate there is still some scarring, repeated injury leads to irreverible scarring known as liver cirrhosis
Definition of sepsis
Life-threatening organ dysfunction caused by a dysregulated host response to infection
What is the first stage in sepsis?
Cytokine storm
Main cytokines involved in the cytokine storm relating to sepsis?
TNF + IL-18
Ifn-γ
IL1-β
Main effects of sepsis
Extreme vasodilation leaky vessels leading to fluid build up and bleeding
Glycocalyx degradation leads to coagulation & platelet deposition which cause wide spread thrombosis
Hyperclotting then depletes clotting
factors/platelets leading to haemorrhage
What is endothelial glycocalyx
Is is a protective layer on the endothelium
What kicks of the hyper thrombitic activity in sepsis?
Glycocalyx degradation
Why does sepsis keep exaggerating itself?
Tissue necrosis (such as the loss of glycocalyx) and inflammation perpetuates danger signals leading to sequential organ failure (lung, cardiovascular, CNS, renal, marrow, liver)
Blood test result for septic shock
High blood serum lactate.
This is due to a build up of lactic acid as a result of anaerobic respiration due to widespread hypoxia
Ongoing problems after sepsis recovery
- Fatigue
- Mental health issues
- Immediate immonosuppression due to immune rebound (immune system exhausted)
- Sepsis survivors have lingering immune suppression
What is granulation tissue?
Granulation tissue is a type of new connective tissue made up of fibroblasts, vessels, lymphatics.
It willl eventually become a collagen scar
Surrounds dead tissue, pus or irritants
What is an inflammatory sinus
Abnormal tract in an epithelial surface lined by granulation tissue.
A sinus ends whereas a fistula link two epithelial surfaces
What is an inflammatory fistula
Abnormal tract in an epithelial surface lined by granulation tissue.
A sinus ends whereas a fistula link two epithelial surfaces
What is an ulcer
A localised defect in epithelial tissue caused by the shedding of inflammatory nectrotic tissue
What is an abscess
Pus in a newly formed cavity surrounded by granulation tissue
What is a granuloma
Organised cluster of mature activated macrophages, in response to persistent stimuli
Low turn over granuloma vs high turnover granuloma
Low turnover:
Foreign body present, inert and indigestable leads to a persistant long lived macrophage population
High turnover:
Due to infection or toxic agents. Short-lived macrophages with continual replenishment. T cells & other immune cells also present
How does TB take advantage of macrophages?
It encourages it’s own phagocytosis avoiding lysosomes, once inside a macrophage the infected marophage undergoes apoptosis.
New macophages come and consume the aopoptitic infected macrophages and get infected themselves
This eventually forms a granuloma
What are unactivated T/B cells called?
naive T/B cells
What are activated T/B cells called?
effector T/B cells and some become memory T/B cells.
Where are the majority of T/B cells found?
Spend most of their time in the secondary lymphoid organs (eg
spleen and lymph nodes)
* Recirculate via the lymph and blood, then back to secondary
lymphoid organs
What is the function of a B cell
Once activated they become plasma cells where they make antibodies for specific antigens
What is a B cell called once activated?
Plasma cell
or
Effector B cell
What are the two main types of T cell
CD8+ Cytotoxic T Lymphocyte (CTL)
* kills infected/mutated ‘self’ cells
CD4+ T helper cell (Th cell)
* Organise immune responses - produce different cytokines
* can differentiate into different types - Th1, Th2, Th17, Treg
What is the job of a Cytotoxic T Lymphocyte (CTL)
kills infected/mutated ‘self’ cells
What is the job of a T helper cell (Th cell)
Organises immune responses by producing produce different cytokines
What are the 4 different types of T helper cell?
Th1, Th2, Th17, Treg
How are T/B cells trained?
Each T/B cell in the pool of naive T/B cells has a randomly generated anti-gen receptor
If this binds to antigen it then proliferates
Some remain after in the pool of naive as memory cells for a faster response in the future
What is the difference between a B cell antigen receptor and a T cell antigen receptor
B cells are just an embedded antibody with light chain and heavy chain
T cells are straight
What is the difference between the variable region of an antigen receptor and the constant region?
Variable region - different on every naive cell
Constant - the same on every type of that cell
How is BcR and TcR diversity acheived?
The variable regions are made up of one of each of the VDJ gene segments (variable, diversity and joining).
By randomly selecting one of each you get considerable variation
Each receptor is made up of two creating further diversity e.g. alpha/beta in TcR and light/heavy in BcR
Lastly when joining the genes joining nucleotides can be added or removed
Two types of diversity creating BcR and TcR diversity
Combinational: varying VDJ combinations
Junctional diversity: random error in joining the genes
Class 1 and class 2 MHC
MHC (Major
Histocompatibility Complex) is the things that presents antigens to T cells.
CD8+ CTLs only bind antigen on class I MHC which are found on all nucleated cells except for neurons> They will kill tumors and virally infected cells
CD4+ T helper cells only bind antigen on class II MHC which are only found on dendritic cells
What is MHC polymorphism?
Variations of the gene amoungst the whole population (most polymorphic of all human genes)
This is a common cause of transplant rejection (1 in100,000 chance of matching an unrelated donor)
What is tolerance?
The process of training T and B cells to not recognise self
Self reacting T cells are deleted in the thymus
Self reacting B cells are deleted in the bone marrow
There is also some peripheral tolerance, once lymphocytes have passed the self/non-self test and are in the lymph nodes, if they recognise an antigen without danger they get deleted (stop allergies)
Regarding T cell selection in the thymus what is positive and negitive selection?
To test cells they have to pass two criteria, do they work and are they harmful
They have to be able to bind MHC to some degree (positive selection)
If they bind the testing MHC too well then they are considering self reacting and are deleted (negative selection)
Peripheral tolerence
T cells are killed in the lymph nodes if a dendritic cell presents an anti-gen with out the danger signal
Overall picture of T and B cell map (just for looking at)
Five forms of antibody
Antibody = immunoglobulin = Ig
5 forms of antibody: IgM, IgG, IgA, IgE, IgD
Hint: GAMED
5 Different purposes of antibodies
- Neutralisation (binds to viruses and prevents them from infecting IgA)
- Oponisation (marks fro phagocytosis IgA and IgG)
- Pro inflammatory (IgE when bound to mast cells triggering allergic response)
- Complement activation (IgM and IgG)
- ADCC (Antibody-dependent cell cytotoxicity) (marks cells for kill by NK cells and neutrophils
What is B cell class switching?
Naive B cells express IgM (& IgD): early response dominated by IgM
Activated B cells can class switch to make IgG, IgA and IgE
Which different types of Fc receptor bind to whic antigens
- Fcɣ receptor for IgG,
- Fcε receptor for IgE
- Fcɑ receptor for IgA
- Fcμ receptor for IgM
Where these receptors are determines the function of antibodies e.g. mast cells have Fcε receptors therefore IgE is the allergy one
Simple as it’s alphabetical
Best antibody for activating complement?
IgM
Best antibody at neutralising intestinal pathogen
AgA
Best antibody at opsonising, neutralising & ADCC ( a wee bit of compliment activation)
IgG
somatic hypermutation
This is where the variable region of a B-cell antibody receptor can mutate upon activation creating strong or weaker binding to antigens
What determines the type of T helper cell that a naive T cell becomes
Signal 3 (cytokines)
What are the different functions of T1,T2,T17 and Treg T helper cells
4 jobs of T helper cells
How do T helper cells help B cells to activate?
If a B cell presents a T helper cell with a peptide/MCII that they recognise then in return the T helper cell provides signal 2 which activates the B cell.
Thus, CD4+ T cells effectively only provide help to B cells that
recognise the same antigen as they do - called ‘linked
recognition’
As activated T helper cells have already made sure there is danger associated with the peptide this insures that B cells don’t recognise self/ benign antigens
How do T helper cells drive affinity maturation of B cells?
Following somatic hypermutation, linked recognition by
CD4+ T cells allows selection of those B cells expressing
receptors/antibodies that bind antigen most strongly
Hence, the requirement for help from CD4+ T cells is
essential to drive affinity maturation of B cells
How do CD4+ T cells select the appropriate class
of antibody during class-switching
Cytokines from CD4+ T cells select class of antibody
How do Th1 cells do their job?
They signal to macrophages who have engulfed a pathogen to digest the pathogen if the Th1 recognises it
How to Th2 cells do their hob?
They activate mast cells and plasma cells
How to Th17 cells do their job?
They make signals to attract neutrophils
How do Treg cells do their job?
They inhibit dendritic cells preventing further T cell activation
How do CD8+ Cytotoxic T
Lymphocytes (CTLs) kill a cell
They are presented with peptides on MHC1 which the infected cell gave to the dendritic cell. The CTL then uses these to recognise the infected cell.
CD8+ CTL kill through FAS
ligation and perforin and
granzyme release.
* FAS ligation directly signals
to induce apoptosis
* Perforin forms pore
allowing granzyme to
enter.
* Granzyme activates
caspases, DNAase
activation and
mitochondrial break down.
What cells make IF-gamma (interferon gamma)
NK cells and ILC1 (innate lymphoid cells type 1) cells make it to activate and polarise the immune response to a virus
What do innate lymphoid cells type 3 do?
ILC3 are are responsible activation of the immune system in response to extracellular bacteria and fungi. This response is antigen non-specific. They secrete interleukin-17 and 22.
Shapes of the 5 antibodies?
All Y shaped
IgE,IgG,IgD -> single Y
IgA -> double Y
IgM -> pentamer
