MODULE 1 - ALEX'S LECTURES Flashcards
what is a payoff of having an adaptive immune system and why?
autoimmunity
because it involves rearranging DNA in B and T cells
what are key components of an adaptive immune system?
MHC molecules, T and B lymphocytes
what are some selection pressures that have shaped our immune systems and how have we coped/responded to this?
selection pressures = unknown emerging diseases
responses = generation of diversity in B and T cells (adaptive immune system)
what is a key problem with somatic cell DNA rearrangements of gremlin encoded receptors in B and T cells?
autoreactivity
what was the Cambrian explosion and what might have lead to mass extinctions following this?
a great increase in multicellular life thus coinciding with an increase in innate and adaptive immunity
lack of adaptive immune system may have lead to extinctions after this due to emergence of things like viruses
also could’ve been due to decreasing oxygen/increasing sulphur
what are immunoglobulins?
similar shaped proteins which make up the backbone of TCR and BCR systems
what are variable lymphocyte receptors (VLRs)?
structures in agnathans (jawless fish) which have LRRs and similar functions to immunoglobulin
do agnathans have toll-like receptors?
yes
how do you know if a fish has an adaptive immune system?
if it has a jaw
i.e. NOT an agnathan
why did adaptive immunity evolve in jawed fish?
jaw allows increased prey range so more microbial exposure
skeletal meals increase risk of gut/tissue perforation
longer lifespan and extended reproductive age so greater chance of infection
how did agnathans and normal vertebrates benefit from whole genome duplication (when you get an extra copy of a chromosome)?
extra copy of chromosome allows some of the genes to mutate and take on new functions e.g. developing MHC
what are genome duplications often accompanied by?
morphological and functional innovations
this is because genetic changes in one copy of a gene allows diversification of function in a new ‘paralogue’
what is a paralogue and what aspect of the adaptive immune system do they form the basis of?
the genetically different copy of a gene following genome duplication
likely form the basis of the MHC system by allowing new functions of classical lipid-binding MHC allowing it to bind peptides
what is RAG?
recombinase activating gene
an enzyme which allows for rearrangement of DNA and catalyses immunoglobulin recombination which is necessary for TCR and BCR rearrangements
likely derived from ancestral transposon
RAGs are very specific to rearranging BCR and TCR
how did a transposon go on to form RAG?
original transposon encoded transposase enzyme which allowed it to move and integrate transposase recognised sequences
it jumped into our genomes and took on new function and also duplicated into RAG1 and RAG2 which both catalyses rearrangement of T and B cells
they are also separated from original integration sites
when are RAG genes most expressed/active?
during B and T cell development when they get their first receptors
it was thought agnathans such as hagfish have no adaptive immune response. what was recently discovered which disproved this?
it was found they didn’t miss out on an Ig-based adaptive immune systems, they just developed totally different receptors called VLRs
what are VLRs (variable lymphocyte receptors)?
VLRs are leucine rich repeat proteins (similar to TLR structure) which are in gremlin configuration in hagfish T and B-like cells prior to diversification
they undergo recombination with flanking sequences which involves homology as opposed to looping out like us
ultimately hagfish/lamprey lymphocytes (which are similar to our B and T cells but different) secrete soluble VLR in their blood (just like Ig in us!)
what are the two hagfish lymphocyte-like cells and what are their functions?
two distinct types of cell - VLRA and VLRB
VLRA seems to act like a T cell with cell surface receptors acting as a trigger
VLRB seems to act like a B cell by secreting VLRs (as if its Ig antibody)
TLRs and mannose receptors of the innate system are germline encoded, what does this mean?
they don’t change and are expressed all through your body in many cells
this works as they sense conserved microbial structures?
antibody and TCRs of the adaptive system are in germline state in most cells of your body and so are not expressed, so how are they expressed in B and T cells?
in B and T cells they have mechanisms for rearrangement of germline genes allowing them to be expressed as proteins
expression can only occur once rearrangement occurs
this gene rearrangment involves looping out variable genes (requires RAG enzyme) thus bringing together other genes which can be transcribed as a single transcriptional unit in B and T cells
hagfish VLRs (variable lymphocyte receptors) are not rearranged like human antibody and TCRs, so how does their expression occur?
they undergo gene conversion where germline genes fold together and some homology occurs between VLR subunits leading to gene conversion rather than looping
gene rearrangement and gene conversion are both examples of what?
somatic cell DNA alterations (also remember these can lead to autoimmunity, the big pitfall of adaptive systems of immunity)
what is DSCAM?
a gene in drosophila which is involved in neuronal wiring but also host defence by opsonising bacteria to facilitate uptake by phagocytes
splicing of the clusters of exons which are in DSCAM can produce thousands of isoforms, so why is this not an adaptive system?
because for it to be adaptive you need a lymphocyte to replicate that isoform (cloning) rather than just randomly produce them
i.e. if you immunise a drosophila it won’t have a stronger immune response next time
sea urchins have 222 TLRs well we have 10, why have they still not got an adaptive immune system?
for it to be adaptive the sea urchin phagocytes would need to divide keep select TLRs on their surface not just everyone i.e. expression is not clonally distributed
so if you immunise a sea urchin it will not change its immune response
what do the drosophila and sea urchin examples tell us about adaptive immune system requirements?
no clonal selection = no memory response = no adaptive system
in immature T or B cells, the TCR/BCR genes are in germline state. What does rearrangement of these genes do?
rearrangement generates diversity by looping out variable genes allowing others to be brought together and be expressed as a single unit
this is how mature (naive) T and B cells express unique antigen receptors
this also means in germline state Ig genes not expressed (BCR genes)
what is clonal selection?
selective expansion or lymphocytes that interact with antigen
one B or T cell has one type of receptor on its surface with thousands of copies of it. If that receptor is for the right antigen then that lymphocyte will undergo clonal expansion
what is a neutrophil?
produced in the bone marrow
the most abundant leukocyte but also short-lived
produce ROS and neutrophil extracellular traps (NETS)
what is the major component of pus?
dead and dying neutrophils
what does ROS production by neutrophils lead to?
breakdown of the neutrophil and thus the release of DNA and histones (neutrophil extracellular traps or NETS)
what do neutrophil extracellular traps (NETS) do?
bind bacteria
what are dendritic cells?
APCs which can activate naive T cells
express both MHCI and II (upregulate MHCII especially after activation) and also express costimulatory molecules
migratory function as they ferry antigen from the periphery to the lymph node
why are dendritic cells the best APC for activating naive (mature) T cells??
they are the most potent APC
when dendritic cells migrate to the lymph node what is the first section of it that they go to?
the T cell zone (makes sense cause they wanna present that antigen asap, get there via chemokinetic signals)
what is the main immune cell involved in transplant rejection?
dendritic cells
what are the dendritic cell subsets derived from?
common myeloid progenitor cells
what are the three main subsets of dendritic cells?
langerhans cells
dermal dendritic cells
thymic dendritic cells
all these have primary roles which they are best suited for
what are langerhans cells?
a subset of dendritic cells which are found in the epidermis
what are dermal dendritic cells?
dendritic cells specialised in cross-priming
what are thymic dendritic cells?
dendritic cells which mediate central tolerance
what is cross-priming?
allows peptides from exogenous antigen being processed in the endosome to leak into the cytoplasm of the dendritic cell and be presented very quickly onto MHCI to activate cytotoxic (CD8) T cells
what does MHCII-peptide activate?
helper (CD4) T cells
what are conventional dendritic cells?
the main subset of DCs involved in stimulating naive memory T cells
what cytokines do plasmacytoid dendritic cells release and why?
release large amounts of interferon type I (IFNa) which tells neighbouring cells to downregulate protein transcription and upregulate MHC expression
IFNa is very effective against viral infections
why are plasmacytoid DCs called that?
cause they look like plasma cells as they have a lot of golgi in them which allows for production of lots of cytokines
what does lack of co-stimulation lead to?
anergy (non-responsiveness) or cell death (apoptosis)
they would have received signal one (MHC-peptide presentation) but signal two (costimulation) is required for activation
signal 2 (costimulation) only occurs if the dendritic cell has been activated
this guards against autoimmunity and is a mechanism of peripheral tolerance
just signal 1 =
OFF
signal 1 + signal 2 =
ON
how are dendritic cells activated?
stimulation by signals from stressed cells or microbes (via TLR) causing the DC to express costimulatory molecules (CD80/86) on its surface as well as upregulate MHC expression
this activation can also be thought of as maturation, where the DC becomes competent to activate naive T cells
what are macrophages?
have many functions in the body, mainly antigen clearance
precursor is monocyte in blood
inappropriate differentiation of macrophages can lead to atherosclerosis (heart disease) as they can express coagulation factors
outline the interaction between a CD4 (helper) T cell and a macrophage?
presentation of intracellular antigens by macrophages leads to interactions with CD4 T cells which then release IFN-gamma which activates anti-bacteria activity in macrophage
so macrophage activation by CD4 T cells enhances antimicrobial immunity
what do natural killer cells do?
recognise inhibitory receptors (MHCI) on normal cells
positive signal builds up and unless inhibited by signal from MHC NK cell becomes activated and lyses target cell
are primarily an innate cell but are essential for development of tumour immunity
can infiltrate lymph nodes and contribute to T cell activation
why are natural killer cells considered innate cells?
they don’t undergo generation of diversity like T and B cells do
what is antibody-dependent cellular cytotoxicity (ADCC)?
the other way NK cells can kill infected or cancerous host cells
NK cells have CD16 Fc receptors which are good at recognising and binding the Fc domain on cell-bound antibodies (ABs which have bound antigen on surface of target cell)
this binding causes cross-linking of CD16 triggering degranulation into a lytic synapse killing the infected/tumour cell via apoptosis
this could be how giving someone therapeutic antibodies can help cancer patients
other than ADCC, what else are Fc receptors critical for?
complement
what is the name of the Fc receptor on NK cells involved in antibody-dependent cellular cytotoxicity (ADCC)?
CD16
when might we need to use engineered T cells (CAR T cells)?
if a cancer has gotten too big or the tumour isn’t very hot (doesn’t mutate as much so fewer peptides on surface so illicits a weaker immune response)
how do you make CAR T cells?
take a bunch of blood from patient, cycle it through aphaeresis machine so it spins out the plasma, grow up the T cells from this in vitro
put crippled lentivirus in which has CAR (chimeric antigen receptor) which is a spliced antibody component with the cytoplasmic domains CD3 (involved in signal 1) and CD28 (involved in signal 2)
how do CAR T cells work?
you can splice the antibody component (CAR) to be specific for whatever antigen you want to target e.g. tumour antigens
so the CAR T cells have their original TCRs but now also have a chimeric receptor which when triggered activates the T cell allowing it to target the cancer cell
this is proven to be very effective against B cell lymphomas and relapsed/refractory disease
where is complement made?
the liver
where are Toll-Like receptors (TLRs) most active?
the endosome
but we also have some in the cytoplasm looking for microbial nucleic acids which looks different to our mRNA which you might find in the cytoplasm
what is the convertase for most complement pathways?
C2b and C4b
what is the broad idea behind the complement pathways?
different pathways which lead to activation of C3 complement via cleavage to C3b which is deposited on microbial surface thus stimulating membrane attack complex which leads to lysis of cell
outline the classical complement pathway?
antibody (especially IgM) activates this pathway by triggering C1 molecules to bind to microbial cell surface which activates proteases that cleave C2 and C4 to form C2b-C4b convertase which then cleaves C3 to C3b (active complement) which is deposited on cell surface leading to formation of membrane attack complex
outline the lectin complement pathway?
carbohydrates (e.g. LPS) activate this pathway by triggering mannose-binding lectin molecules to bind to the microbial cell surface which activates proteases that cleave C2 and C4 into C2b-C4b convertase which cleaves C3 to active complement (C3b) which can then be deposited on microbial cell surface leading to formation of membrane attack complex
outline the alternative complement pathway?
occurs via spontaneous hydrolysis (of C3 to C3b which then becomes its own convertase by complexing with some molecules) so is always occurring unless inhibited by transmembrane molecules called complement inhibitors in our membranes which deflect any complement from our cell surface
microbes don’t have complement inhibitors which is why they get fucked up by complement and we don’t
so our way of switching off the alternative pathway is complement inhibitors
what happens to someone who has a deficiency in the enzyme that locks complement inhibitors into our membranes?
they piss red cause of all the dead lysed RBCs that end up in their urine
what is occurring on a molecular level when complement binds to cell surfaces?
C3 binds to microbial membrane once its thioester domain (TED) which sits in the C3 alpha domain is activated
TED activation is inhibited by the inhibitory beta domain which blocks it. Once C3 cleaves beta-chain this exposes highly reactive alpha chain TED creating the active complement molecule C3b. C3b is then immediately bound to adjacent microbes or inactivated by hydrolysis
what happens to any C3b that has nothing to bind to?
it gets inactivated quickly by water (via hydrolysis)
what is beneficial about the TED being so reactive?
it will react with and bind pretty much anything on the microbial cell surface
what happens with C3a and C5a (leftovers which float away after cleavage of C3)?
they act as inflammatory signals allowing other innate cells like neutrophils to come and help clean up the mess
what do complement inhibitors do?
prevent complement from binding and/or inactivate the complement
what happens from CD59 deficiency?
decreased complement inhibition causing paroxysmal nocturnal haemoglobinuria (PNH) which is where you piss red in the morning cause of your urine retention exposing all the lysed RBCs
what is CD59?
it is a complement inhibitor in the membrane of host cells which prevents the assembly of the membrane attack complex (i.e. inhibits the later components of complement which form the complex/pore)
what happens when bacteria stimulate the release of IL-6 from macrophages?
IL-6 goes and acts on the liver to induce release of acute phase reactants which are inflammation markers such as C-reactive protein (CRP)
what is C-reactive protein (CRP) and what does it do?
it is an acute phase reactant which binds phosphocholine which is common on bacterial cell surfaces
it is also an important biomarker in clinical scenarios for bacterial infections (not really for viral infections)
how did Toll-like receptors (TLRs) get their name?
they look very similar to drosophila toll receptors
what are toll-like receptors (TLRs)?
dimers with leucine-rich repeat (LRR) domains that bind PAMPs and DAMPs (pathogen and damage associated molecular patterns)
do TLRs only recognise and bind pathogen associated molecules?
no they also do so for commensals however we usually have firewalls up keeping the commensals from becoming invasive
however if body is compromised (e.g. immunosuppressants) then commensals may become more invasive like pathogens making them opportunistic pathogens
what is similar and different in the immune responses to gram-neg (pink) and gram-pos(purple)?
they display different molecules so are recognised by different TLRs in the innate system
gram-negative cell membranes have LPS so are detected by TLR-4
gram-positive bacteria cell membranes have lipoteichoic acid so are detected by TLR-2
both types of bacterial membrane are destroyed by lysozyme, they just have different recognition systems
so the innate system can distinguish between different classes of microbes (also like fungi and shit)
what is lysozyme?
an important enzyme of the innate system that can destroy both classes of bacterial membrane
why is the innate system distinguishing between types of microbe important?
so it can have an effective and specialised adaptive response (i.e. different T cells for different microbes)
how can we detect so many different molecules with only 10 different TLR’s?
TLRs are homodimers (TLR3, 4 etc.) but they can also form heterodimers which changes their secondary and tertiary structure allowing recognition of lots of molecules
why are TLRs that recognise nucleic acids most efficient in the endosome/lysosome?
because the low pH protonates the microbial nucleic acids making recognition by the TLRs easier and more efficient
what is the TIR domain of TLRs?
the TLRs recruit different adapter proteins to their TIR domain allowing them to activate different signalling pathways
what are some of the key signalling pathways activated by TLRs?
NF-kappaB transcription factor activation
MAP kinase pathway leading to downstream signalling to activate transcription factor AP-1
interferon regulating factor (IRF) pathways (ramps up the interferon response e.g. down regulate protein transcription and up regular MHC expression so more commonly activated by viral infections)
the first two pathways are more generalised activation pathways associated with inflammation
why might you find the IRF pathways to be more active for TLRs that detect nucleic acids?
cause it ramps up interferon responses which is important for viral infections
what is the general process of TLR activation and signalling?
LRRs detect and bind ligands
TIR domain recruits adaptor molecules
signal transduction mediated via phosphorylation leads to activation of transcription factors
transcription factors translocate across nuclear membrane into nucleus and initiate transcription of usually silent genes
are DCs and innate immune cell or an adaptive immune cell?
neither
they are more like a bridge between the innate and adaptive response
this is cause they have lots of molecules involved in adaptive immunity (e.g. MHC) but also lots involved in innate immunity (e.g. TLRs)
they are also very involved in kicking off inflammation via IRF pathways (especially plasmocytoid DCs)
which immune cells have TLRs?
pretty much all of them I think
