How does the immune system detect infection ? Flashcards
What does the innate system detect ?
PAMPs and DAMPs
What are PAMPs and DAMPs ?
PAMPs (pathogen-associated molecular patterns), DAMPs (damage-associated molecular patterns)
What are some features of the innate system ?
- Recognises generic danger signals
o Common evolutionary conserved pathogens molecules (PAMPs)
o Molecules produced by damaged host cells (DAMPs) - Limited receptor diversity
- Not adaptable; receptors germline encoded
- Cells of same and different innate lineages share same receptors and recognise same molecules
What are some features of the adaptive immune system ?
- Can recognise almost any microbial or non-microbial molecule (antigens)
- Very large (almost infinite) receptor diversity
- Adaptable; receptors created by somatic recombination of gene segments
- Each cell has one unique receptor that is highly specific for a particular molecule
How does innate sensing work ?
The complement system: collection of proteins working together as an early warning system and to destroy pathogens: (proteins can recruit immune cells, label for phagocytosis, lyse pathogens)
What are the 3 ways of pathogen recognition ?
Direct pathogen recognition; alternative pathway and lectin pathway
Adaptive immunity: classical pathway
What is the alternative pathway ?
: 1) C3b spontaneously produced, 2) C3b binds to amino and hydroxyl groups on the microbes, 3) complement effector mechanisms activated
- amino and hydroxyl on host cell too, host cells must block C3b activity or autoimmunity will occur
What is the lectin pathway ?
1) MBL (mannose binding lectin) binds to mannose on the surface of the pathogens (bacteria, yeast, virus, parasites), no mannose on host cell. C3b activates the mechanism
What is an example of a PAMP ?
Mannose
How does the innate cells recognise PAMPs ?
PRRs (pattern recognition receptors), MBL
What cells have PRRs on them ?
Macrophages and neutrophils
What is phagocytosis ?
Phagocytes: Macrophages and Neutrophils
- way of sample the environment for microbes
- talk to T cells and show them any microbial molecules they’ve detected by becoming an APC (antigen presenting cell)
- activates T cells
What is the difference between macrophages and dendritic cells ?
Macrophages:
- don’t move from infection site
- talk to T cells at infection site
- good killer
- good all rounder
Dendritic cell (DC):
- migrate from infection site to LN
- talk to t cells in LN and infection site
- doesn’t kill
- specialised in talking with t cells
What is the use in neutrophils ?
type of granulocyte and are the most abundant white blood cells in the body. They are part of the innate immune system and are primarily responsible for phagocytosing (engulfing and destroying) pathogens, especially bacteria. Neutrophils are usually the first cells to arrive at the site of infection and are involved in the initial, rapid immune response.
Macrophages are … ? in their resting state … ?
sentinels: found in all barrier tissue (skin, intestine, lungs)
- in their resting state:
o mop up apoptotic cells
o remove debris
o sample the environment
o scan for danger via PRRs
What is the first danger signal ? (yellow)
= tissue damage:
- PRRs on innate recognise molecules released from damaged or necrotic cells
- Damaged-associated Molecular patterns (DAMPs)
- Potential break in barrier
- Pathogen that is causing damage whilst invading
Damage is a warning (yellow alert) but not necessarily infection
What is the second danger signal ? (yellow)
: PAMPs
- All microbes have these conserved molecules that differ from host
- Different classes of microbes = different PAMPs
- PAMPs evolutionary conserved
PAMPs are evolutionary conserved, what does that mean ?
- Receptors can be germline encoded, allow for a fast response
- One innate cell can express multiple PRR and so can recognise and respond to a wide range of microbes
- Innate cells can directly tell whether you have been exposed to a microbe
What are some PAMPs ?
e.g., Gram -ve: LPS (lipopolysaccharide), flagella, viruses = ds RNA + ssRNA, fungi – cell wall glucans
A single innate cell can express …. different PRRs so can instantly recognise many different types of pathogens
multiple
How do pathogens avoid recognition ?
- Modification of PAMPs – salmonella can modify LPS reducing its ability to activate PRRs
- Inhibition of PRR signalling pathways – vaccinia virus, ebola, hepatitis C, influenza A
What is the red alert ?
- Increase in size
- Enhanced phagocytosis
- Release toxic molecules
- Better killer
- Release cytokines (TNF alpha)
What is inflammation ?
- Recruit immune cells to infection site
o (neutrophils – phagocytose, release destructive chemicals)
o NK cells – cytokine production, killing infected cells - Activate immune cells (yellow alert)
- Production of acute phase proteins (CRP)
- Tissue redness/swelling/heat
- Fever
This initiates the adaptive immune
System and killing of the pathogen
How is inflammation resolved ?
- Neutrophils are short-lived and apoptose
- Macrophages apoptose or revert back to resting state
- NK cells apoptose or revert back to resting state and continue patrolling body
How can PAMPs cause sepsis ?
PAMPs set up a very powerful feedback loop which is good at attacking a localised infection, if systemic then PAMPs can act as a toxin (sepsis)
PAMPS –> macrophages –> cytokines (IFN-alpha) –> sepsis: inhibits heart contractions, fluid leaks into tissues, increased blood clotting, cachexia (Muscle wasting) –> reduced blood pressure –> septic shock
What is the PRR for LPS ?
TLR4
What does TLR4 polymorphism lead to ?
Increased susceptibility to sepsis
What are some advantages of innate sensing ?
- PAMPs allow you to distinguish microbes from self
- PAMPs indicate to the immune system the type of invading microbe
- Recognise essential evolutionary conserved PAMPs makes it difficult for pathogens evade detection
- A small number of different PRRs can detect a wide variety of different microbes
- Receptors are germ-line
- One cell = multiple PRRs
- Different cell types can express the same PRRs
What are some disadvantages of innate sensing ?
- Not very specific – only gives a rough idea of microbe type
- Not adaptable (except through evolution), the receptors your born with are the ones you keep
- Does not allow the development of immune memory
What are some features of adaptive immunity ?
- Can recognise almost any microbial or non-microbial molecule (antigens) with a high degree of specificity
- Very large (almost infinite) receptor diversity
- Adaptable; receptors created by somatic recombination of gene segments
- Each cell has one unique receptor that is highly specific for a particular antigen
What do antigens bind to ?
Antigen: a molecule recognised by adaptive immune cells. Will bind either a T cell receptor of antibody (B cell receptor), or both
What is an epitope ?
Epitope: the precise part of the antigen recognised by the T or B cell receptor. An antigen can have multiple epitopes
What is the paratope ?
Paratope: The part of the antibody or T cell receptor that binds the epitope
T cells only recognise …
Ag presented to them by professional Antigen Presenting Cells (APC) e.g., macrophage or DC
- B cells recognise Ag on its own
TCR
membrane bound, T cell receptors
What are some features of B cell antigen receptor ?
- Membrane bound and secreted
- Secreted form has immune effector functions
- Secreted form called antibody (Ab) or Immunoglobulin (Ig)
- Membrane form called B cell receptor (BCR) or surface Immunoglobulin (slg)
T cells Ag recognise … whereas b cell Ag recognise …
T cell Ag (recognise proteins only) –recognise linear peptide (8-25 amino acids long) sequences, presented by APC, proteins have to be broken down itno peptides
B cell Ag (detect pretty much anything organic) – conformational (can be linear), epitope can cross loops (discontinuous), native molecule, recognise shape rather than sequence
Linear epitope vs discontinuous epitope
Linear: one end of the protein antigen
Discontinuous: binds to separate areas on the protein antigen
What are some parts of the antibody ?
Light chains, heavy chains, antigen binding region (Fab), Fc region
What is the alpha chain ?
part of Fab that is the heavy chain
What is the beta chain ?
The part of the Fab that makes up the light chain
T cell receptors have … Ag binding sites, antibodies have … Ag binding sites
1, 2
Antigen binding domains are modular, what does that mean ?
They can be independent and interchangeable
How are antigen receptors created ?
somatic recombination, the process of going from an immature B cell DNA to a mature B cell DNA recombines the gene segments for the alpha chain genes
- VDJ recombinase is used to recombine the different gene segments
What is junctional diversity ?
rearrangement of V, D and J genes gives a few million antibody specificities
- Good but not enough
- Need another way of increasing diversity
How does junctional diversity happen ?
1) Joining of v, d and j are not always precise RSSs (recombination signal sequences to align V, D and J segments
2) Addition of bases: creation of P-nucleotides (hairpin must be nicked in order to leave an overhang producing a palindromic sequence), random addition of N nucleotides (TdT – terminal deoxyribonucelotidyl transferase)
3) Deletion of bases
4) Sequence aligns
5) Fill in the gaps
A new DNA sequence at the V, D and J regions
What is productive and non-productive rearrangement ?
- Majority of rearrangements will not result in a functional protein
- Only b cells that produce a functional rearrangement survive, those that do not die via apoptosis
- 2x sets of V, D and J so each has 2 changes to rearrange the receptor
- Each B cell specific for one Ag, so 2x chromosome can lead to 2 different Ag so allelic exclusion (block gene rearrangement on the other chromosome)
What is clonal expansion
The number of T and B cells able to responds to one antigen is very low
- T/B cells sees it Ag and becomes activated
- Activated cells divide
- All daughter cells have identical Ag specificity
- The time required to activate and expand Ag-specific T/B cells to an effective number makes adaptive response slow
What are some examples of antigenic variation to evade the immune system ?
- Influenza: surface proteins
- Trypanosomes and Malaria: switch between multiple versions of the same molecule
- HIV: high mutation rate, prevents adaptive immunity, difficulties in vaccine development
What is central tolerance ?
Central tolerance: a mechanism by which T and B cells are capable of recognising self-antigens are deleted before they are released systemically to fight infection
- Most potentially dangerous self-reactive T cells are deleted before they can cause damage, but this process is not perfect
- Also, does not remove T cells that can recognise innocuous. Antigens such as food
What are some advantages of adaptive sensing ?
- Very adaptable, somatic rearrangement of gene segments allows the creation of receptors that can recognise almost any possible antigen
- Highly specific
- Having a receptor that can identify a particular species or strain of microbe allows toy to remember that microbe
What are some disadvantages of adaptive sensing ?
- Slow, requires time to activate and clonally expand cells with relevant receptor
- High specificity means its relatively easy for a microbe to evade recognition changing its antigenic structures
- Receptor cannot tell what it is recognising and cannot distinguish pathogens from self or innocuous molecules (e.g., pollen or food)
Who decides if something is friend or foe ?
Innate immune cells
What do T cells recognise ?
short 8-25 amino acids, cant recognise Ag on its own, must be given an APC
What cells can be professional APC made ?
DC, macrophages
What are the Naive T and B cells ?
never seen an Ag before
What is the size difference between the 2 different classes of MHC ?
Class I – 7-11 amino acids long
Class II – 13-25 amino acids long
How does the MHC, antigen and the T cell receptor interact ?
The antigen lies in the groove of MHC, they can bind different peptides. T cell receptors bind both MHC and peptides, Thus, T cell can only recognise peptides when combined with the MHC.
- Each MHC molecule can bind to a range of different peptide sequences
One MHC can bind to … peptides
multiple
MHC are … expressed
codominantly
What is the MHC haplotype ?
MHC haplotype is the set of MHC alleles present on each chromosome
- MHC molecules are the principal factor in defining acceptance or rejection of grafts
- Foreign MHC molecules on graft activate the recipients T cells that then kill the graft
- Need to match the MHC molecules (haplotypes) between host and donor as much as possible – tissue typing
Extracellular Ag are presented by …, causes ?
MHC class II
Th cells, regulatory T cells –> only see Ag presented on MHC class II, express CD4 on the surface –> coordinate immune responses
Intracellular Ag are presented by …, causes ?
MHC class I
Cytotoxic T cells/ lymphocytes (CTL) –> only see Ag presented by MHC class I, express CD8 on surface –> killed cells infected with intracellular pathogens
CD4 bind to … and CD8 bind to
class II, Class I
What is the role of DC ?
Dendritic cells naïve T cells whether or not to activate
- Present in all barrier tissues
- Immune sentinels, similar to macrophages
- Express PRRs (Like innate cells)
- Do not kill (unlike macrophages)
Their role:
- scan for infection via PRRs
- sample environmental antigens
- take Ag to lymph nodes to talk with T cells (Macrophages stay at infection site)
3 phases of the life of a dendritic cell ?
1) Sample: takes up and spits out extra-cellular fluid and molecules, expresses PRRs to detect DAMPs and PAMPs, not very good at presenting Ag (good as they present self-antigens)
2) ‘Traveller with cargo’: takes in more environment molecules/ antigens, stops sampling the environment, carriers’ antigens to the LN to present them to T cells
3) Presenter: mature antigen presenting cell in the LN; good at presenting Ag, up-regulates MHC class II, up-regulates molecules like B7, CD80, CD86 required for signal 2
How do DC communicate danger ?
- MHC class 2 used to present Ag to helper T cells – control specificity
- But, MHC on DC (and other APC) will also present self-Ag and harmless Ag
T cells require what 2 signals >
- Communicates with the specific AG
- Co-stimulation: PAMPs up-regulate B7 on APC, B7 signals to the T cell via CD28
o B7 tells the T cell that the Ag is from a microbe
Signal 1 alone shows
innocuous molecules (food or self-Ag)
Why doesn’t Th cells have many receptors ?
The reason why one Th cell doesn’t have lots of receptors, because if one is activated like pathogen-specific TCR but it will also activate other receptors like self-Ag specific
What are CTL ?
Cytotoxic T cells (CTL)
- Only recognises Ag presented by MHC class I
- CTL kills infected cell
- MHC class I/ Antigen identifies infected cell
- Handshake between infected cell and CTL allows very precise killing
What cells i best at activating Naive T cells?
DC
What is the role of macrophages APC ?
Activated Th cell goes to infection site, macrophages asks for help presenting Ag, Th responds by producing IFN-gamma, tells Th cell infection still present
How is a B cell recognised?
B cells require permission from activated Th cells to gain full effector potential
- Activated Th cells have passed the DC test, are assumed to be pathogen-specific, and so competent to decide whether B cells are Ag specific
T-dependent Ab response vs T-independent Ab response
T-dependent Ab response: full effector functions, can switch isotype (Fc region of Ab that defines effector function), affinity maturation - can increase its affinity for Ag
T-independent Ab response: limited effector functions, no isotype switching, no affinity maturation, stimulated by repeating epitopes, usually against carbohydrates or nob-proteins
How do B APC work ?
B cells presents the Ag it recognises to the Th cell, If Th cell recognises it then it means the Ag is from a pathogen, Th cell gives permission to B cell to respond
Immune memory
- More pathogen specific T and B cells
- Memory T and B cells easier to activate
- Memory T cells can be activated by more APC types (not just DC)
memory T cells patrol the tissues focussing on location of last infection (skin), and do not need activated in the LN - Memory T cells and B cells have established effector functions
What happens when the infection clears ?
o Danger signals reduce – innate cells loose activation signals
o Antigen reduces – innate cells can no longer activate T cells, B cells no longer see Ag
o Immune regulatory network develops – Treg cells and inhibitory cytokines such as IL-10
o Innate cells die or return to resting state
o Majority of T and B cells die without Ag
o Some T and B cells survive to become memory cells
IL-1
Promotes inflammation and fever
IL-6
Stimulates immune responses and is involved in inflammation and infection.
IL-10
An anti-inflammatory cytokine that inhibits immune responses
IFN-alpha
Produced in response to viral infections and enhance immune cell activity
IFN-gamma
Important in activating macrophages and enhancing the antigen presentation of MHC molecules.
TNF- alpha
Plays a key role in inflammation and is involved in autoimmune diseases like rheumatoid arthritis.
TNF-beta
Important in immune responses and tumor regression
which cytokine activates macrophages ?
TNF-α and IFN-γ
which cytokine is secreted macrophages ?
TNF-α
which cytokine recruits NK cells and neutrophils ?
TNF-α
Which cytokine is an early warning sign
TNF-α
Which cytokine is secreted by NK cells ?
TNF-α and IFN-γ
Which cytokine, when over expressed, leads to septic shock
TNF-α
which cytokine causes fever and cachexia ?
TNF-α
What are some key features of PAMPs ?
conserved across various different bacterial groups, essential for bacterial infection, different to human patterns
Germline encoded, but can be adapted to recognise current infection, true or false ?
germline encoded is correct, not adapted to current infection as it is innate
Linear peptides are recognised by b or t cells ?
both
Native structure molecules are recognised by b or t cells ?
B cells
Repeating epitopes are part of T or B cells ?
B cells
T or B cells recognise host molecules ?
T cells and B cells
Do BCR or TCR have immune effector function ?
BCR
Do BCR or TCR recognise only APC
TCR
T cell clonal expansion is driven by TNF-alpha, true or false ?
False, driven by IL-2 not TNF-alpha
What processes are involved in creating Ab diversity?
Imprecise somatic recombination of V, D, and J gene segments, Addition or deletion of nucleotides at joins of V, D, and J genes, Joining of multiple randomly selected V gene segments to a D or J gene segment
What activates naive T cells ?
Dendritic cell
Are macrophages or DC activated first
both at the same time
Do DC respond to DAMPs and PAMPs via PRRs ?
yes
Which MHC present intracellular antigen
MHC class 1
Which MHC present extracellular antigen
MHC class 2
What MHC class is expressed on all nucleated cells ?
MHC class 1
Which MHC class is presented to CD4+ cells ?
MHC Class 2
Which MHC class is presented to CD8+ cells ?
MHC class 1
How does a DC communicate to a T cell that the Ag it is presenting is from a pathogen?
Signal 2 (B7 on DC binds CD28 on T cell). The DC upregulates B7 to complete signal 2 only when its PRRs recognise danger signals.
What is true if T cells receive signal 1 but not 2 ?
The antigen presented is a self-antigen, The T cell deactivates or dies, The PRRs on the DC have not detected PAMPs.
What is signal 1 and 2 in terms of T cell activation ?
Signal 1: Antigen-specific recognition
The T cell receptor (TCR) on the T cell binds to dendritic cell.
For CD4+ T cells, the antigen is presented on MHC class II.
For CD8+ T cells, it’s on MHC class I.
Signal 2: Co-stimulatory signal
The B7 molecule (CD80/CD86) on the dendritic cell binds to CD28 on the T cell.
This is the co-stimulatory signal.
The dendritic cell only upregulates B7 if its pattern recognition receptors (PRRs) detect a danger signal, like a PAMP (e.g., LPS from bacteria).
What immune arm co-ordinates immune responses ?
Adaptive immune system
Which type of communication allows a cell to send a message systemically ?
cytokines
Which type of communication is good for local communication ?
cytokines and cell-to-cell
Which barrier is classified as both physical and chemical?
skin
Which of the following cell types bridges the innate and adaptive immune systems?
Dendritic cells
How do NK cells recognise infected cells
recognise the absence of MHC 1
Which PRR is located in endosomes and recognizes viral RNA?
TLR3
TLR4 detects
LPS
What is NOT a cardinal sign of inflammation?
Itchiness
Which enzyme is critical for V(D)J recombination?
RAG1/2
Somatic hypermutation occurs in:
Germinal centers
What is the role of MHC I molecules?
Present intracellular peptides to CD8+ T cells
MHC II molecules present peptides to:
CD4+ cells
Which cells undergo negative selection in the thymus to prevent autoimmunity
CD4+ and CD8+ cells
MHC class 2 is only presented on …
Antigen presenting cells
