Lymphocyte development/Effector Lymphocytes (T cells) Flashcards
___ and ___ are the transcription factors responsible for B cell development and they work in the bone marrow
EBF and Pax5 are the transcription factors responsible for B cell development and they work in the bone marrow
(EBony and Pax are having their 5th Baby)
How do Pax5 and EBF aid in VDJ rearrangement?
*Note that these are two of the transcription factors that mark the chromatin so that the RAGs can rearrange the heavy chain genes and not the T cell genes*
Describe the process of T cell maturation in the thymus
At what point does T and B cell lineage commitment occur? Before or after VDJ rearrangement?
What is the role of NOTCH1?
CLP = common lymphoid progenitor. These will go to the thymus and (under the influence of the stromal cells in the bone marrow where they came from) they’ll upregulate the transcription factor for T cell development: Notch 1
The NOTCH family of receptors are the one involved in embryogenesis (something about cells making binary decisions)
The CLPs express NOTCH1 which interacts with ligands in the thymus, then the intracellular piece of notch1 goes to the nucleus and upregulates T cell gene expression
The early thymic precursor can still give rise to other cells until Notch turns off the potential for those programs
The cells go through the “double negative” stage and then they’ll mature into CD8+ or CD4+ T cells
**note that lineage commitment happens BEFORE VDJ rearrangement**
Explain the process of T cell development from a pro T cell in the thymus to a naive CD4/CD8+ T cell
At the proT or proB cell stage, there’s a requirement for IL7 (so there’s an importance of the common gamma chain)
RAG is first turned on in these pro cells. The DJ rearrangement of the heavy chain happens in the pro B cell and in the pro T cell, the DJ rearrangement of the T cell receptor beta chain happens, along side the y/d genes as well. Depending on which set of genes “win” in this process, you’ll either have gamma/delta T cells proliferating or alpha/beta T cells proliferating
Following gene rearrangement, the next step is the pre-T or B cell level. At this level is when the newly synthesized chains are expressed on the cell’s surface with the surrogate chain (recall the one who’s function it is to send the feedback signal to stop RAG activity if the chain that’s been produced is functional). The cells are called “large” pre T or B cells because they’re dividing
After this point, the cells stop dividing, at which point, they’re double positive because they’re expressing both CD4 and CD8 (in the case of T cells, that is)
Now the second rearrangement occurs in which the genes for the light chains (B cell) and the alpha chain (T cell) are rearranged
If all the genes are rearranged properly, we can express the appropriate receptors on the surface.
Explain the process of B cell development from the pro B cell coming from the bone marrow
**note that the B cell development process is essentially the same as T cell development, but he didn’t mention that B cells undergo negative selection so remember that for Step**
At the proT or proB cell stage, there’s a requirement for IL7 (so there’s an importance of the common gamma chain)
RAG is first turned on in these pro cells. The DJ rearrangement of the heavy chain happens in the pro B cell and in the pro T cell, the DJ rearrangement of the T cell receptor beta chain happens, along side the y/d genes as well. Depending on which set of genes “win” in this process, you’ll either have gamma/delta T cells proliferating or alpha/beta T cells proliferating
Following gene rearrangement, the next step is the pre-T or B cell level. At this level is when the newly synthesized chains are expressed on the cell’s surface with the surrogate chain (recall the one who’s function it is to send the feedback signal to stop RAG activity if the chain that’s been produced is functional). The cells are called “large” pre T or B cells because they’re dividing
After this point, the cells stop dividing, at which point, they’re double positive because they’re expressing both CD4 and CD8 (in the case of T cells, that is)
Now the second rearrangement occurs in which the genes for the light chains (B cell) and the alpha chain (T cell) are rearranged
If all the genes are rearranged properly, we can express the appropriate receptors on the surface.
At the point following pro B and T cell, why are the cells called “large cells”?
They’re called large because they’re dividing as in they’re doing a transient proliferation, the point of which is to make sure that each cell after this point has a functional heavy chain/beta chain that can then be linked to the light chain/alpha chain that’ll be rearranged and synthesized in the next steps
Explain what’s happening here
Note that at the point where the B cell is an “immature B cell” after having expressed a functional heavy and light chain, its still sensitive to apoptosis via self antigen (that’s the negative selection stuff from Pathoma). Apparently, they’ll comb through the body and get used to other molecules (those that are outchea just randomly recognizing self gon get kilt), and the cells that pass the negative selection process express IgM and IgG in the lymph node
OR
I think what’s actually happening here is that the negative selection process involves the autoreactive B cells undergoing receptor editing for the light chain (within 3 or 4 days) and the cell will put up a new receptor with a new light chain that *hopefully* won’t be autoreactive. If it’s still autoreactive, the cell will undergo apoptosis, or if the light chain can’t associate will the heavy chain, it’ll die by neglect (also probably apoptosis)
Why can you only do receptor editing with light chains and not heavy chains?
Between the heavy and the light chain, you can only rearrange the light chain a second time around to correct an autoreactive receptor because unlike the heavy chain that has D genes that, once those are arranged with their respective J’s cant be moved out the way, the light chain only has V genes being paired with J genes (another thing to note is the light chain locus is all 12’mer and 23’mers, which is the combination you want for rearrangement) so its so much easier to re-do those and make a new light chain
What’s the function of the kappa deleting element?
Basically, when you make the light chain, you typically make the kappa light chain first (and in higher quantities). If that’s the autoreactive one, then you delete that out and you put in a lambda there and hope it works
The thing that’s responsible for that is the kappa deleting element (circled in red)
When in the human body do gamma/delta T cells appear?
What is the function of these cells?
Right after birth. They disappear after.
The function of those is still being elucidated but basically they act as a first line of defense in case of infection
T/F: Most gamma delta cells stay double negative b/c they don’t recognize MHC, neither do they need it for development.
Truth.
*see image below*
Describe the migration of alpha/beta T cells thru the thymus
see image below
note the following:
DN1=CD44+/CD25-
DN2=CD44+/CD25+
DN3+CD44-/CD25+
DN4=CD44-/CD25+
T/F: The TCR cannot undergo receptor editing the same way B cells do with the light chain. (if true, how does this editing happen and what is the outcome/point of the editing?)
Falsehood. T cells can totally receptor edit as well.
TCRs can also undergo rearrangement of the alpha chain gene, which can result in sort of making up/repairing a heterodimer that wasn’t functional/was autoreactive, or serving as almost a tag for the cell to be deleted
Describe the process of T cell extravasation into the tissues (note that this is just like what the neutrophils do)
Here:
Chemokines involved in getting a naïve cell into the lymph node
Recall that CCR7 is a T cell receptor that binds CCL19 and CCL21
You have to enough signaling before the cell can actually slow down in response to the chemokines
Step 1:
Tethering by selectins – here CD62L is expressed by endothelial cells and tethers the T cell down (note that this is NOT a strong interaction)
Step 2:
Rolling – the T cells rolls on the surface of the endothelium, meanwhile the endothelial cells are releasing chemokines
Step 3:
Arrest – the chemokine CCL21 or 19 is released and are bound by CCR7 on the T cell. This prompts the T cell to bind to ICAM1 and then it stops. It’ll then go thru the usual squeezing thru the vasculature and go to the site where its needed
The molecule responsible for T cell exit from the lymph nodes is called___
sphingosine 1 phosphate
How does S1P control the timing of T cell exit from a lymphoid organ?
T cell exit from the lymph node is very precisely timed
In the blood and lymph is a lot of Sphingosine 1 phosphate, which is what drives T cell exit from lymph nodes (S1P is degraded by enzymes in the lymph node
Because the concentration of S1P is high outside of the lymph node, all cells will downregulate the receptor for it
When the T cell is in the blood and lymph, it doesn’t signal for S1P because again, there’s a high conc of it around but once it gets in to the lymph node, then the receptor is expressed and it becomes sensitive to S1P so then it leaves again to go get some
(the point: the lack of S1P in a lymphoid organ drives the T cell out of the organ and out back into circulation)
Describe the functions of the following proteins in leukocyte adhesion deficiency:
Kindlin 3
SLC35C1
CD18/Integrin beta2
Kindlin 3 - activation
SLC35C1 (glycosylation) - rolling
CD18 - adhesion (its a integrin)
Remember: 2..3..1 (so you’re 24)
(rolling >> activation >> adhesion)
Which process is affected by LAD2 deficiency which affects SLC35C1?
Lad II (2 lads glycosylatin) (mutation in SLC35C1) – infants develop recurrent bacterial infections, no pus at infection site, Bombay blood type hh
A mutation in ___ results in LADIII, which is characterized by recurrent bacterial infections and a presentation similar to Glanzmann thrombasthenia (presentation with bleeding issues at birth)
Lad III (involved in rolling – you, Yas and Chimmy O walking home from the library – 3 lads just Kindlin - mutation = disease process resembling Glanzmann thrombasthenia, and recurrent bacterial infections. Bleeding issues present at birth)
Mutations in CD18/Integrin beta2 result in which LAD?
What is the presentation?
Lad I (The beta2 kinds just turned 18 and they have so much integrity) – mutation in CD18/Integrin beta2
Slow wound healing
Delayed attachment of the umbilical cord and infection of umbilical cord stump
No pus at infection site
How is a T cell supposed to know where to go to go grab a bug that’s invading the body if the T cells are only found in specific spots i.e. lymph nodes?
T/F: (the answer to the above) uses the same molecules as the T cell to go to the lymph node
The dendritic cells are basically the T cell’s hired snitch that tells it if it’s a bug in town. They always snitching too, always going to the lymph nodes and what not
Note that dendritic cells use the same CC19/21 and CD62L to migrate to the lymph nodes (makes sense that you use the same chemokines because you’re going to the same place)
How does the T cell know that the molecule being presented is self or its from a bug that needs to be killed?
The dendritic cell not only gets antigen from the bug and chops the proteins up, when you PAMP binding to PRRs, you also have downstream expression of co-stimulatory molecules, lie B7, that are the “2nd signal” for the T cell and tell it if the antigen being presented is a bug (note that self antigen won’t do the same because there’s no PAMPs right)
Describe how CD3 signaling works via ITAMs and ITIMs
You bind your antigen or whatever and your CD3 coreceptor gets a signal: SRC is a kinase that’ll phosphorylate the ITAMs and then SYK kinases are recruited/bind to that phosphorylated ITAM
Note that ITIMs also get phosphorylated by SRC kinases but they recruit phosphatases instead
Binding of CD4/8 to the MHC molecule leads to recruitment on ___, an SRC kinase. Following this, there’s phosphorylation of ITAMs on the nearby CD3 molecule. This leads to recruitment of ___, a SYK kinase.
Binding of CD4/8 to the MHC molecule leads to recruitment on Lck, an SRC kinase. Following this, there’s phosphorylation of ITAMs on the nearby CD3 molecule. This leads to recruitment of ZAP70, a SYK kinase.
Describe the 3 pathways leading to NFKB, AP1 and NFAT activation
Initially, the SRC kinase is recruited to CD4 (here its Lck, a type of SRC), then the kinase phosphorylates the ITAM on the CD3 molecule. Following that, you have recruitment of ZAP70 (the SYK kinase) then you have downstream phosphorylation cascades activating all kinds of stuff
Option 1: ZAP70 pathway leads to recruitment and phosphorylation of phospholipase C and then that is clipped into IP3 and DAG. Recall that IP3 leads to an increase in intracellular calcium , the calcium of which activates calcineurin, which leads to activation of the NFAT transcription factor pathway
Option 2: ZAP70 activity can also lead to recruitment of adaptor proteins. Then you have GTP/GDP exchange of RAS/Rac proteins, which leads to recruitment or activation of JNK or ERK, whose downstream pathway is mediated via NFKB
OR
Option 3: ZAP70 activity leading to activation of PI3K which activates PIP3 which then leads to activation of Akt and mTOR whose downstream pathway is mediated by AP1
Binding to CD28 is ___, whereas binding to CTLA4 and PD1 is ___
What are the ligands of each of these?
Note that CD28 binding by B7 is a STIMULATORY signal, and binding to CTLA4 and PD1 are INHIBITORY signals
CD28 again sees CD80 or 86
CTLA4 also sees CD80 or 86
PD1 sees PDL1 or PDL2
What are the functions of the following:
Nivolumab/Opdivo
Belatacept
Abatacept
Nivolumab/Opdivo is an anti-PD1 or inhibits its ligands (so you induce stimulation) **I niver liked that PD1 life so I’m bouta Opd out**
Belatacept (makes it easier to accept): Anti-CD28/recombinant CTLA4 for transplant rejection prevention
Abatacept (about to accept): Similar to belatacept
What are two differences between T cell and B cell activation?
The main difference in the B cell is that the B cell doesn’t need to do all that fancy signaling. Instead the BCR/antibody can just bind free antigen and then the coreceptor is Igalpha/beta which also has those ITAMS (remember SRC-ITAM-SYC, then everything else are transcription factors you know)
Where the T cell has Lck come in following CD4/8 binding to MHC, the B cell has ___, ___ or ___ binding to IGalpha/beta
ZAP70 is unique to T cells whereas the B cells use___
Where the T cell has Lck come in following CD4/8 binding to MHC, the B cell has Fyn, Lyn or Btk binding to IGalpha/beta
ZAP70 is unique to T cells whereas the B cells use SYK
What is the significance of CD45? Which CD45 is expressed on naive vs effector vs memory T cells?
CD45 is a marker expressed on T cells and different types of CD45 mark which T cell stage we’re talking about
CD45RA –Naïve
CD45RO – Memory T cell
Complete the following:
IL12 >> naïve T cell >> ___transcription factor >> Th1 >> ___
IL4 >> naïve T cell >> ___ transcription factor >> Th2 >> IL4 + ___
TGFbeta + IL6 >> naïve T cell >> ___ transcription factor >> Th17 >> ___
IL6 + IL21 >> naïve T cell >> ___ transcription factor >> Tfh >> ___
IL12 >> naïve T cell >> Tbet transcription factor >> Th1 >> IFNy
IL4 >> naïve T cell >> Gata3 transcription factor >> Th2 >> IL4 + IL13
TGFbeta + IL6 >> naïve T cell >> RorYT transcription factor >> Th17 >> IL17
IL6 + IL21 >> naïve T cell >> Bcl6 transcription factor >> Tfh >> IL21
The downstream effects of Th1 cell activation is secretion on IFNy, whose signaling leads to killing of ___ pathogens, activation of macrophages and class switiching to ___
The downstream effects of Th1 cell activation is secretion on IFNy, whose signaling leads to killing of intracellular pathogens, activation of macrophages and class switiching to IgG3
The downstream effects of Th2 activation are secretion of IL4 and IL13, whose signaling leads to class switching to __, ___ and ___, killing of (intracellular/extracellular) pathogens and antibody production by B cells
The downstream effects of Th2 activation are secretion of IL4 and IL13, whose signaling leads to class switching to IgE, IgG1 and IgG4, killing of extracellular pathogens and antibody production by B cells
The downstream effects of Th17 activation are IL17 release, whose signaling leads to killing of ___ (intracellular/extracellular) bacteria and fungi and ___ activation (immune cell)
The downstream effects of Th17 activation are IL17 release, whose signaling leads to killing of extracellular bacteria and fungi and neutrophil activation (immune cell)
The downstream effects of Tfh activation are IL21 release, whose signaling leads to ___
The downstream effects of Tfh activation are IL21 release, whose signaling leads to long term humoral immunity
What is the difference between Tcm’s and Tem’s? Which two kinds of molecules does each cell express?
Tcm – central memory cells. Almost like stem cells but for memory cells, they keep making new memory cells. They express CCR7 and CD62L
Tem – effector memory cells are partially “armed”. They’re not at the level of regular effector cells but they’re still able to fight. These ones mostly circulate in tissues and express little or no CCR7 or CD62L
Describe the process of beta selection
The cell undergoes allelic exclusion of the TCRbeta chain, the alpha chain rearranges so that means RAG is turned back on, the cell expresses either CD4/CD8, and the cell proliferates
(so you had already made a beta remember, so now you just want to make an alpha to pair with the already functional beta that you made earlier
IPEX is a disease that results from a mutation in ___ which is necessary for the development of Tregs
IPEX is a condition in which there’s a mutation in Foxp3, which is required for development of Tregs
