MODULE 2 - ROS KEMP'S LECTURES Flashcards
what are some things effector T cells do?
move to different places in the body
kill infected cells (in different ways)
support antibody production
enhance innate immune system by enhances bacterial killing
make different types of cytokines
remember the antigen for next time
why are different effector responses needed to fight different pathogens?
different types of organisms
different routes of infection
different site of infection
different molecules etc.
what are the main subsets of CD4+ T cells?
mainly:
Th1
Th2
Th3
Th17
Treg
also:
T follicular helper
Th9
how do cytokines lead to different effector functions?
APCs produce cytokines
cytokines activate T cells
T cells produce cytokines (could be more or the same or different kinds). These go off and act on immune cells including T cells
cytokines act on T cell to initiate downstream functions e.g. more cytokines, killing enzymes, chemokine, metabolic products, survival proteins etc.
what immune cells do cytokines act on?
phagocytes
T cells
B cells
non-immune cells
what are polarising cytokines?
produced by other immune cells (not T cells) (usually innate cells such as APCs)
bind to receptors on naive T cell surface
help drive differentiation into different T cell subsets
what are effector cytokines?
produced by different T cell subsets
bind to receptors on other cells
leads to effector functions in other cells and are usually suited for whatever pathogen initiated the response
outline the process of polarising cytokine acting on naive T cell leading to Th1 effector functions?
APC produces IL-12 based off of signals it receives
IL-12 receptor (dimer) on T cell picks this up leading to activation of T-bet transcription factor resulting in production of IFN-gamma
IFN-gamma acts on macrophages to increase phagocytosis/enhance bacterial killing, acts on CD8 T cells to kill infected cells and acts on B cells to make/improve antibody to enhance phagocytosis
what type of infection is IFN-gamma effector cytokine most useful for?
intracellular infections (virus, bacteria)
outline the process of polarising cytokines acting on naive T cell leading to Th2 effector functions?
APC produces IL-4 which is received by IL-4 receptor
this leads to activation of GATA-3 transcription factor leading to production of cytokines such as IL-4, IL-5 and IL-13 which are very good for extracellular infections such as worms and parasites
these effector cytokines promote mast cell eosinophils to destroy worms, tell CD4 T cells to produce more IL-4, 5 and 13 and tell B cells to make antibody to bind pathogens
outline the process of polarising cytokines acting on naive T cell leading to Th17 effector functions?
APC produces TGF-beta and IL-6 which go and act on their given receptors on the naive T cell
these polarising cytokines act on ROR-gammaT transcription factor leading to production of IL-17 which causes neutrophils to cause inflammation. Also tells T cells to produce IL-22 which is causes a positive feedback loop for Th17
Th17 is a pro-inflammatory cell as IL-17 causes inflammation
Also responsible for most autoimmune inflammatory diseases such as MS and IBD
generally good for extracellular infections such as fungus and bacteria
is it just CD4 T cells that have subsets?
No!
So do CD8+ T cells and they are similar to CD4+ subsets
Tc1, Tc2, Tc17
are T cell subsets mutually exclusive?
nah we just learn it like that cause we aren’t fucking smart enough
T cells can low-key maybe display more than one effector phenotype and change from one phenotype to another
different effector strategies are important for dealing with different pathogens, but what can uncontrolled effector responses lead to?
immunopathologies
different subsets associated with different pathologies
how can Th1 cells contribute to autoimmune diseases?
they secrete IFN-gamma which is pro-inflammatory. This is good for activating cell mediated immunity e.g. killing infected and cancer cells but
IFN-gamma activates inflammatory mediators and other cells. IFN-gamma receptor on many cells in body, this can result in tissue damage. IFN-gamma also promotes antibody class switching to IgG which is a more potent antibody i.e. more damage
this contributes to autoimmune diseases such as lupus and type I diabetes
how does Th2 contribute to allergy?
Th2 secretes IL-4, IL-5 and IL-13 which help clear parasites by stimulating mucus production, smooth muscle contraction and antibody class switching to IgE
however this contributes to respiratory issues cause smooth muscle contraction and excess mucus production is fucked if its in the respiratory tract (asthma)
IgE binds to mast cells and basophils leading to activation of macrophages in lungs, degranulation, release of pro inflammatory modulators and allergic inflammation
how can Th17 contribute to autoimmune disease?
Th17 secretes IL-17 which is good for immunity to extracellular bacteria such as Klebsiella pneumoneae. It recruits and activates neutrophils which are essential for Klebsiella clearance. Also involved in tissue immunity in the gut, skin, lints however can be associated with tissue specific AI disease e.g. IBD
IL-17 is a pro-inflammatory cytokine and IL-17 receptors are present on epithelial tissues. It also promotes production of enzymes that can cause tissue damage
generally outline the process of signal transduction?
extracellular molecule activates a cell surface molecule (receptor)
this receptor alters intracellular molecules
amplification of the signal
ultimately you get gene transcription and protein production
what are the first messengers of signal transduction?
natural inter-cellular ligands that bind and activate receptors e.g. cytokines
need receptors in the membrane
a bit different in the case of TCR as it is not the thing activating it as MHC is
what are the second messengers of signal transduction?
enter the cytoplasm and trigger response within the cell
chemical relays from plasma membrane to cytoplasm
intracellular signal transduction
tend to just be a shit load of proteins in the cell
what are membrane receptors in signal transduction?
external influences determine what happens inside target cell
cell membrane impermeable to influences, so receptors in the membrane allow molecules to get through
these are needed for signal transduction to occur
basically takes signal from outside cell inside cell e.g. TCR
what is affinity?
strength of binding (e.g. of interaction between MHC and TCR)
what is avidity?
total strength of interaction (e.g. total impact of everything binding like the interaction between a T cell and an APC with all the MHC-TCR interactions and other ligands together)
what is a way of stopping signal transduction?
down regulating a receptor
outline the TCR structure?
two chains - alpha and beta
variable region and constant region
membrane bound only (unlike BCR)
what part of the TCR binds antigen and MHC?
the variable region
although this and the constant region of the TCR have no signalling capacity
the signalling comes from the CD3 molecules around it which have the capacity to transmit a signal and join up with the TCR to form the TCR complex
outline the molecules/interactions involved in T cell activation?
TCR-MHC (signal 1) - antigen-specific
CD4/CD8-MHC - co-receptor
LFA1-ICAM - adhesion
CD28-CD80 (signal 2) - co-stimulation
APC-IL-12 - inflammatory signals
what occurs during the antigen-specific interaction between TCR and MHC (signal 1)?
T cell recognises specific antigen in the context of MHC
what occurs during the interaction between CD4/CD8 co-receptors and MHC?
CD4-MHCII
CD8-MHCI
co-receptors stabilise low-affinity interaction between the TCR and MHC keeping the cells together by stabilising cell-cell binding
what occurs during the interaction between adhesion molecules LFA-1 and ICAM and which cell has which molecule?
LFA-1 on T cell
ICAM on APC
these are adhesion molecules which further stabilise cell-cell binding between T cell and APC
what occurs during the interaction between co-stimulatory molecules CD28 and CD80?
CD28 on T cell
CD80 on APC
signal 2
co-stimulatory receptor sends extra activation signal
what occurs during the interaction between the APC secreted IL-12 and the T cell?
IL-12 not only makes the T cell more likely to become Th1 but also provides the inflammatory signals which reinforce other interactions and signals occurring making them more likely to result in activation
outline the intracellular signalling that leads to T cell activation?
phosphorylation of ITAMs
co-receptor signal
activation of ZAP-70
involvement of scaffold proteins and adaptor molecules
activation of PLC-gamma
activation of transcription factors
how does phosphorylation of ITAMs occur during intracellular signalling of a T cell?
when TCR binds with MHC-peptide it undergoes conformational change which exposes ITAMs of CD3 molecules
two tyrosine kinases called LCK (attached to bottom of CD4/CD8) and FYN (just chills in the cytoplasm around CD3) phosphorylate the ITAMs as soon as their phosphorylation sites are exposed following conformational change
FYN is the first tyrosine kinase to phosphorylate the ITAMs
where are LCK and FYN located?
LCK is constitutively associated with cytoplasmic domains of CD4 and CD8
FYN associates weakly with cytoplasmic chains of zeta and CD3 chains
how does the co-receptor signal contribute to intracellular signalling of a T cell?
CD4/CD8 binds to MHCII/MHCI to stabilise interaction
because LCK bound to bottom of co-receptor, it moves LCK over to where TCR is allowing it to phosphorylate the ITAMs
how does activation of ZAP-70 occur during intracellular signalling of T cell activation?
once ITAMs phosphorylated they provide a binding site for ZAP70
this allows ZAP70 to get phosphorylated by LCK
what is the role of scaffold proteins in T cell intracellular signalling?
once ZAP70 gets phosphorylated and activated it recruits and phosphorylates the scaffold proteins LAT and SLP76
this leads to recruitment of phospholipase C-gamma (PLC-gamma) to the membrane
how is PLC-gamma activated?
once PLC-gamma is recruited to the membrane by LAT and SLP76 then it is phosphorylated by the CD28 signalling cascade
PLC-gamma activation causes it to move to the nucleus to activate three pathways that activate different transcription factors such as NFKB
what is the outcome of T cell intracellular signalling?
activation of transcription factors which regulate gene expression including:
- IL-2 production (T cell proliferation and survival)
- perforin/granzyme production (T cell cytotoxic function)
- cytokines (activate other cells depending on type of infection)
remember that the actual T cell isn’t activated yet as that requires the co-stimulation signal from CD28 which comes soon via another pathway
what do T cells need to do once activated and what is this driven by?
survive, proliferate quickly, up-regulate metabolism and acquire functions such as cytokine production and killing molecules
all of this is driven by IL-2
this means that the first thing a T cell must do is is get IL-2 made and also get IL-2 receptor made
what happens if there is no CD28 signal?
T cell won’t get activated
it needs co-stimulation from CD28-CD80 as this is signal 2
one of the jobs of TCR signalling is recruiting PLC-gamma to signalling complex, what causes PLC-gamma activation?
CD28 co-stimulation
what does PLC-gamma do following activation?
splits PIP2 into two secondary messengers called DAG and IP3
outline the CD28 signalling cascade?
LCK phosphorylates CD28
PI3-kinase binds to phosphorylated CD28 and gets activated
Activated PI3-kinase leads to recruitment of Itk
Itk activates PLC-gamma
what is the role of IP3?
IP3 increases intracellular Ca2+ conc. which leads to activation of calcineurin which then activates a transcription factor called NFAT
NFAT controls genes encoding a bunch of cytokines and T cell effector functions including IL-2
what is the first role of DAG?
DAG recruits protein kinase C-0 (PKC-0)
PKC-0 activates CARMA
CARMA leads to activation of transcription factor called NFKB
NFKB controls a lot of stuff, mainly IL-2
what is the second role of DAG?
DAG recruits RasGRP
RasGRP activates Ras
Ras activates MAP kinase cascade
MAPK activates Fos which is a component of the transcription factor AP-I
AP-I controls mostly IL-2 and some other cytokines
what is the main cytokine produced by the three possible pathways resulting from PLC-gamma activation?
IL-2
what T cell functions does IL-2 control?
survival
proliferation
metabolism
cytotoxicity
cytokine production
T cell death following immune response
what is the main downstream effect of TCR binding and CD28 co-stimulation?
production of IL-2 and IL-2 receptor
this leads to a positive feedback loop for T cell proliferation, survival and growth)
what is the IL-2 receptor?
is needed for IL-2 to work which is why activated T cells make both IL-2 and IL-2R
IL-2 receptor has three components; alpha chain, beta chain and gamma chain. The receptor works best with all three
IL-2 is shaped to allow interaction with two receptor chains
IL-2R can functionally signal through intermediate or high affinity receptors only
what is IL-2Ralpha?
the alpha chain of IL-2R (also called CD25)
is upregulated upon T cell activation and doesn’t do anything on its own (not responsible for signal transduction)
what is IL-2Rbeta?
the beta chain of IL-2R (also called CD122)
always present on the T cell but not sufficient enough to drive T cell functions alone
responsible for signal transduction
what is IL-2Rgamma?
the gamma chain of IL-2R (also called gammaC)
responsible for signal transduction
what is an intermediate affinity IL-2 receptor composed of?
IL-2Rbeta and IL-2Rgamma
can allow IL-2 signalling but not really enough to drive CD4 T cell functions
what is a high affinity IL-2 receptor composed of?
IL-2Ralpha, IL-2Rbeta and IL-2Rgamma
what does it mean if the IL-2 receptor is transiently expressed?
means the receptor isn’t expressed all the time e.g. in effector T cells
this probably means you don’t want that cell proliferating or carrying out its functions all the time
what does it mean if the IL-2 receptor is constitutively expressed?
means the receptor is expressed all the time
probably means you want that cell carrying out its function all the time
what does the kind of IL-2 receptor expressed on cell tell you?
tells you the kind off effect IL-2 production will have
for example IL-2 signals through:
- constitutively expressed IL-2Rabgamma in Tregs
- constitutively expressed IL-2Rbgamma in NK cells
- transiently expressed IL-2Rabgamma in effector T cells
why can Tregs outcompete effector T cells?
cause they constitutively express high affinity IL-2 receptor well effector T cells only transiently express high affinity IL-2R
reminder that high affinity IL-2 receptor has alpha, beta and gamma chain
outline the interaction between IL-2 and IL-2R?
IL-2 interacts with IL-2Ra
IL-2 undergoes conformational change that allows it to interact with IL-2Rb
gamma chain is recruited
IL-2 binding leads to dimerisation of IL-2Rb and gammaC
this dimerisation is required for signalling to occur
many cells respond to IL-2, but what does the variation in sensitivity depend on?
types of IL-2R expressed (high affinity, intermediate affinity)
induced (transient) vs constitutive expression of IL-2R
what are the three IL-2 signalling pathways?
JAK-STAT pathway
RAS-MAP kinase pathway
PI3K pathway
outline IL-2R signalling via JAKSTAT?
IL-2R has no intrinsic protein kinase domains and so relies on janus family kinases (JAKs) to initiate signalling
JAK activation leads to phosphorylation of beta chain of IL-2R
SH2 domains on STAT proteins bind phosphorylated receptors
transcription factors called STATS get phosphorylated, dimerise and translocate to nucleus
the main outcome of this is expression of IL-2R alpha chain (CD25) so more receptor available for more interaction and thus more activation
also activates FasL (cytotoxicity) and FOXP3 (Tregs)
what are the main outcomes of the IL-2 signalling pathways PI3K signalling and Ras-MAPK signalling?
main outcome is production of more IL-2
also production of cell cycle proteins (proliferation) and CTLA4 (negative feedback)
what does IL-2 control?
T cell:
activation
proliferation
survival
polarisation
death
what gene expression is induced by IL-2?
more IL-2
more IL-2 signalling
proliferation and cell cycle
glucose uptake (energy)
more cytokines and cytokine receptors
death pathways
all this leads to more T cell activation
outline the IL-2 - IL-2R autocrine loop?
TCR activation via TCR and costimulation results in activation of NFAT, NFKB and AP1 which leads to expression of IL-2 and IL-2R alpha chain
IL-2 binds to the IL-2R alpha chain intimating IL-2 signalling which activates STATs leading to expression of IL-2 and IL-2R
how do you stop the autocrine loop of IL-2 - IL-2R and decrease T cell activation?
IL-2 negative feedback
signals from dendritic cells via TCRs are different after antigen clearance meaning that the signalling pathways within the T cell are different
downstream effect is signals saying do less to the T cell
what are the two ways in which a T cell can undergo negative feedback to reduce IL-2 and IL-2R production?
SOCS
PTEN/BLIMP
outline the SOCS method of IL-2 regulation?
SOCS = suppressor of cytokine signalling
- activation signal
- end of infection signal = SOCS transcribed
- SOCS inhibit IL-2 signalling
SOCS are induced by STAT activation from IL-2 signalling and inhibit JAKS binding stopping IL-2 signalling following the end of infection signal
many cytokines self-regulate by expressing SOCS proteins
the main point is they inhibit cytokine signalling after the cytokine has had its effect
outline the PTEN and BLIMP-1 methods of IL-2 regulation/negative feedback?
IL-2 induces PRDM1 gene that encodes a transcription factor called BLIMP-1
BLIMP-1 then represses IL-2 transcription thus stopping the feedback loop
in contracting T cell you’ll see lots of BLIMP and not so much IL-2 production
what are T cell subsets classified based on?
cytokines that induce differentiation
transcription factors that control gene expression
cytokines produced by the cells
outline the process of JAK-STAT signalling?
- binding of cytokine to receptor causes receptor to dimerise
- this brings receptor associated JAKs in close
- JAKs phosphorylate each other on tyrosine residues (cause no phosphorylation sites on cytokine receptor so has to be done via JAKS)
- activated JAKs phosphorylate receptor
- receptor phosphorylation creates binding sites for STATs
- STATs bind, get phosphorylated by JAKs, then dissociate
- STATs dimerise and translocate to nucleus to make shit happen
outline the molecular process from activation to effect of Th1 cells?
pathogen activates APC indicating IFN-gamma response will be best to get rid of it
APC takes pathogen antigen to specific TCR activating it and giving costimulatory signal leading to proliferation and IL-2 and IL-2R expression. At the same time APC making IL-12 which binds IL-12R
IL-12R signals via JAK protein causing dimerisation of two STAT4 TFs which go off to nucleus inducing mild IFN-gamma expression and Tbet expression
Once Tbet expressed you can get v effective IFN-gamma production from the IL-12R signalling leading to more Tbet and more IL-12R (positive feedback)
IFN-gamma causes increased TLR and MHC expression, increased chemokine secretion, increased macrophage activation, increased phagocytosis
outline the molecular process from activation to effect of Th2 cells?
parasite activates APC which takes antigen to specific TCR activating it and giving costimulatory signal leading to proliferation, IL-2 and IL-4 expression
IL-4 binds IL-4R activating JAK protein which causes STAT6 to dimerise and go to nucleus inducing mild production of IL4, 5 and 13 and activating GATA3
Now that we have GATA3 the IL-4R signalling leads to strong expression of the cytokines (IL-4, 5 13) starting positive feedback loop where more GATA3 expressed leading to more cytokines
IL-4 stimulates B cells to make IgE, IL-5 activates mast cells and basophils, IL-13 stimulates mucus production; the idea of this is that you can fuck up a parasite and then clear it out with mucus
Th2 response also associated with atopy and allergy
outline the molecular process from activation to effect of Th17 cells?
Th17 cells have two receptors that need to be activated: IL6R and TGFbetaR (we ignore this one cause signalling weird)
IL6R signals through JAKSTAT causing dimerisation of STAT3 leading to production of IL-17 and expression of RORgammaT. Also expression of IL21 and IL21R
so now getting positive feedback but also second signal through IL21>IL21R>STAT3>RORgammaT. This leads to production of IL-17, 21, 23 and 23R
So IL21R reinforcement leads to IL23R reinforcement and ultimately makes Th17 super stable phenotype
IL-17 recruits neutrophils, promotes inflammation
IL-22 stimulates epithelial cells to make antimicrobial peptides
IL-23 promotes maintenance of Th17 phenotype
Th17 in general associated with chronic inflammatory diseases e.g. MS, IBD
what do Tregs do?
immune responses cause damage to us too so need to control scope and size of immune response
also need to control autoreactive cells which escape regulation in development and need to control autoimmune responses
Tregs do all this
what is the difference between thymic and induced Tregs?
thymic Tregs come from thymus and already are a Treg
induced Tregs develop from naive T cells in periphery in response to antigen activation and cytokine signals (these ones are a type of T cell subset?)
how do you define a Treg?
constitutively expresses IL-2Ra (CD25) chain all the time (makes sense cause they need be ready to respond to IL-2)
in conjunction with low IL-7Ra chain (CD127) expression (used to define human Tregs)
this is the case for both tTregs and iTregs
can also look at FOXP3 TF which is master regulator for Treg function; represses transcription of pro-inflammatory genes (e.g. IL-2, IFN-gamma), enhances transcription of anti-inflammatory genes (e.g. IL-10, CTLA-4)
demethylation of the FOXP3 locus only occurs in Tregs with stable expression of FOXP3 (not conventional T cell that upregulate FOXP3 transiently after activation)
why is it kinda hard to identify Tregs using CD25 and FOXP3?
FOXP3 an intranuclear protein so not always possible to identify
CD25 and FOXP3 alone cannot be used to identify Tregs as conventional T cell population can upregulate both markers after activation
outline the molecular process from activation to effect of induced Tregs?
DC presents something like commensal antigen or damaged self antigen which suggests might be time to tone down immune response to specific TCR
signalling via TGFbetaR>JAK>STAT3 and also activation of STAT5 from IL2R leading to production of FOXP3, IL-10 and TGFbeta
the Treg then can suppress effector T cell function, activation and proliferation and also promote healing
why might you get a lot of weird hybrids of both Th17 and Tregs?
they both need TGFbetaR
outline what cytokine mediated suppression by IL-10 does?
Tregs make IL-10 which shuts down a bunch of immune response functions e.g.
inhibits: antigen presentation by macrophages, pro-inflammatory cytokine production by macrophages, costimulation signals by macrophages
enhances production of anti-inflammatory IL-1 receptor antagonist
down-regulates IFN-gamma and IL-2 production
induces anergy
stimulates secretory IgA production by B cells
outline cytokine mediated suppression by TGFbeta?
As well as IL-10, Tregs make TGFbeta which:
converts naive T cells to Tregs
inhibits activation of T cells and activation of macrophages
heals intestinal epithelial barrier
outline Treg immune suppression by cell surface molecules CTLA4?
Tregs can upregulate CTLA4 which preferentially binds same ligand (CD80/CD86) as CD28 (signal 2) thus inhibiting TCR signalling
So if lots of Tregs in system where APCs activating T cells they will get in the way cause they upregulate CTLA4 which binds CD80 with more affinity than CD28 so slow immune response
shortens dwell time between naive T cells and APCs and has similar effect to ICOS
outline Treg immune suppression by metabolic control?
T cells need a shit load of glucose/energy for activation which is supported through IL-2 signalling so Tregs can constitutively express IL-2Ra (CD25) which outcompetes other T cells for IL-2
Tregs can also induce T cell anergy (I think this might be through the above method tho??)
Tregs can produce tryptophan metabolites which inhibit T cell growth
why do T cells display plasticity and heterogeneity and how is this important?
throughout immune response T cells needed for different jobs e.g. inflammation to healing. Many disease require multiple layers of immune response, these differences usually influenced by cytokines (which also change over immune response)
this is clinically important as T cell phenotypes determine disease progression/patient outcome and immune therapies try to target this. Diseases like IBS show a lot of T cell heterogeneity/plasticity
what is T cell plasticity?
the ability of a T cell to take on characteristics of many subsets simultaneously or at different times
basically T cells change
what is differentiation/polarisation of T cells?
reversible maturation based off early cytokine signals that allows cells to undergo alternate fates depending on environment
this differentiation is then reinforced by master transcription factors
remember that differentiation can then be reprogrammed based off of other signals (plasticity)
what do we see lots of in transition phases of T cells?
co-expression
what are the four ways that T cell subsets are regulated?
cytokine mediated inhibition
transcriptional inhibition of T cell subsets
epigenetic control of T cell subsets
TCR signalling
what are the four ways that T cell subsets are regulated?
cytokine mediated inhibition
transcriptional inhibition of T cell subsets
epigenetic control of T cell subsets
TCR signalling
what are the ways cytokines control T cell subsets?
cytokine combinations can drive hybrid T cells
cytokines can inhibit activation of other T cell subsets (e.g. Th1 making IFN-gamma can inhibit Th2 and Th17 development) (direct inhibition)
cytokine inhibition of T cell subsets via APC’s (e.g. Th1 cytokine prime DC to not be able to make Th2) (indirect inhibition)
what is transcriptional control of T cell subsets?
during T cell differentiation toward one lineage the other lineages are suppressed as their is mutual exclusivity among master transcription factors (the one that gets primed first wins) and further cross regulation occurs through repression of TFs
what are the master regulators of the main T cell subsets?
Th1 - Tbet
Th2 - GATA3
Th17 - RORgammaT
Treg - FOXP3
what are the six main types of transcriptional regulation?
pioneer
antagonism
synergy
competition
redistribution
what is pioneer transcriptional regulation?
initial polarising signal (STATs coordinate cytokine signal to get transcription of more cytokines)
what is antagonism transcriptional regulation?
transcription factors competing for binding sites
this could be due to two cytokine activating two STATs making them compete for the binding site
what is synergy transcriptional regulation?
transcription factors finding friends to help them bind
this occurs in the form of TF needing a co-factor to help it bind
what is competition transcriptional regulation?
transcription factors fighting over their friends
this occurs when common molecules required for binding e.g. FOXP3 and RORgammat both need the same co-factor so might have to scrap for it
what is redistribution transcriptional regulation?
transcription factors moving to new places
occurs when two different transcription factors expressed and can bind in different places
what is modulation transcriptional regulation?
transcription factors change activity of other molecules
occurs when one transcription factor can change the binding of another transcription factor
what is epigenetic control of T cell subsets?
epigenetic control activation and repression of genes
differentiated T cells divide and daughter cells keep the same differentiation programme by (a) self reinforcing transcription factor networks and (b) epigenetic mechanisms (stable and heritable programme BUT with ability to change)
mechanisms of epigenetic control works by two major substrates:
- methylation of DNA (usually repressive = gene silencing)
- chromatin/histone remodelling (activation or repression)
how do we know epigenetics is involved in controlling T cell subsets?
inhibit histone modification in naive T cells and it makes IFN-gamma and IL-4
inhibit DNA methylation in naive T cells and it makes IFN-gamma
this indicates somewhere in these cells things are being told not to be made but if you take away inhibitory signal they make it
give an example of epigenetic control of T cells via histone modification?
if you activate a cell under Th2 conditions you get a stop signal for IFNgamma but if under Th1 you get a go signal and start making it
i.e. there are lots of repressive histone modifications keeping lots of genes silent without changing DNA sequence
give an example of epigenetic control of T cells via methylation?
if you add IL-12 to naive T cell and it becomes Th1 you get demethylation of Tbet and IFN-gamma
at what levels do T cell changes occur?
cytokine level, binding level and epigenetic level
outline how TCR signalling strength is involved in controlling T cell subsets?
TCR affinity generates different signalling strength pathways in cell
this can lead to activation of different transcription factors and therefore different cytokine genes e.g.
- tuning receptiveness of cell to different cytokines
- inducing expression of specific cytokine receptors
- impinging directly on activation of specific STATs
T cells with different functions use different metabolic pathways to do what?
- generate energy stores to promote survival
- produce everything they need for growth and proliferation
cytokines can promote different metabolic pathways in T cells and these metabolic pathways are closely linked by shared fuel inputs
what are some of the major metabolic pathways in T cells?
glycolytic metabolic pathway
fatty acid oxidation
fatty acid synthesis
outline glycolysis in T cells?
relatively inefficient but supports anabolic growth (so uses lots of energy very quick)
pro-growth signal pathways (e.g. PI3K and MAPK) promote use of glycolytic metabolism
most important metabolic pathway for rapidly proliferating cells
outline the TCA cycle/OX-PHOS in T cells?
highly efficient meaning cells can stay alive without using many resources
used in most quiescent/non-proliferating cells
supports oxidative phosphorylation (OX-PHOS)
outline fatty acid oxidation (FAO) and fatty acid synthesis (FAS) in T cells?
FAO = conversion of fatty acids into products the cell uses to generate energy (i.e. using stuff to get energy which is then used for stuff like FAS)
FAS = lets cells make lipids as building blocks for cell growth and proliferation (i.e. what u need to build the stuff you need to make more T cells)
what does metabolism determine in T cells?
ability to transition from naive to effector to memory phenotype
this is because specific T cell subsets require distinct metabolic pathways to match their functional requirements and to allow survival
outline the molecular metabolic process behind activation of T cells?
during activation T cells switch to aerobic glycolysis (and glutamine catabolism)
this switch is mediated by signalling pathways downstream from TCR, co-stimulation and cytokines
these pathways include MAPK/ERK, PI3K, mTOR, NFKB
this leads to activation of TFs like HIF-1alpha which induce genes important for glycolysis (the main metabolic pathway for activated T cells)
all of this is mediated by mTOR
outline the metabolic switch during naive to effector T cell transition?
naive T cell (quiescent) - OXPHOS, low lactate, low nutrient uptake
activated T cell - up regulates glycolysis, OXPHOS, mTOR, HIF-1alpha and cell gets bigger in general
outline the metabolic switch during transition from effector to memory T cell?
glycolysis main pathway in activated cell
when you transition to memory you just dial this back and bring out fatty acids a bit more
so memory cells are small and quiescent like naive cells but they have to retain their phenotype so that can respond quickly
like lying down but with their running clothes on
what are the metabolic pathways in T cell activation controlled by?
TCR signalling cascade
presence of cytokines
availability of nutrients
what is the glucose receptor when do T cells upregulate this during activation?
GLUT-1
upregulate very early on in activation cause lots of energy required for activation
what is GLUT-1?
glucose transporter/receptor
expression upregulated upon T cell activation
expression dependent on activation of PI3K
what does PI3K do?
activates mTOR
what does mTOR signalling do?
augments glycolytic metabolism to support growth and proliferation
it is the main controller of the switch to the glycolytic pathway
what are the key energy sources for T cells?
glucose (particularly important in early activation)
glutamine (T cells increase expression of glutamine transports and deletion of these impairs transition to effector)
lipids or fatty acids (component of cell membranes and provide a high yielding energy source, also supply substrates for cell signalling; demand rapidly increases following activation for membrane synthesis)
what are the main metabolic pathways in use in the main effector T cell subsets, memory and Tregs?
Th1, 2, 17 - aerobic glycolysis
memory, Treg - fatty acid oxidation (FAO)
what happens if you make a knockout with no GLUT-1?
T cells can’t grow and proliferate and can’t differentiate in Th1, 2 or 17
they can however still differentiate into Tregs (therefore Treg differentiation doesn’t require the glucose pathway)
what is mTOR?
mediates the switch to glycolysis
two different mTOR complexes which do different things and are regulated by different stimuli
mTORC1 controls cell growth and division and responds to nutrient availability
mTORC2 responds to growth factors and cytokines and controls response to those cytokines (i.e. differentiation pathways)
one or both of these will be activated depending on signals coming in and the ratio of expression dictates what subset the T cell becomes
outline the specific mTOR activations the main T cell subsets, what does this show?
Th1 - mTORC1 upregulated
Th2 - mTORC1, mTORC2 upregulated
Th17 - mTORC1, HIF1alpha upregulated
Treg - AMPK upregulated
shows that different T cell subsets do different jobs and so the way they get and use energy is different from one another
why is it that Tregs don’t need much mTORC1?
cause mostly use OXPHOS and fatty acid oxidation (FAO) to produce energy
different metabolic requirement to the effector T cells which use glycolysis and fatty acid synthesis (FAS)
