Immunology Test 3

2 Major Lymphocytes

2 major lymphocytes: B lymphocytes (BCR) and T lymphocytes (TCR) TCR: Processed antigen (peptides) have to be presented with MHC 1 or 2 CD4 T cells/helper T cells produce cytokines to help regulate and coordinate immune response CD8 T cells when activated differentiate into cytotoxic t cells (produces perforin, granzymes B Cells differentiate into plasma cells

MHC I and MHC II have all the following in common except: A Both are comprised of two different polypeptide chains B Both have a nonspecific peptide binding groove C Both are used to present endogenous peptide antigens D Both are recognized by the antigen receptors of T lymphocytes E Both are expressed by professional APCs

Both are used to present endogenous peptide antigens

Which statement about BCR is false? A BCR recognizes and binds to native extracellular antigens B BCR can be endocytosed after binding to antigen C BCR is used to present a processed antigen to a helper T (TH) cell D Antigen binding to BCR generates an intracellular signal

C BCR is used to present a processed antigen to a helper T (TH) cell

Fc region of Immunoglobulin

Fc (Crystallizable/constant) Region: Just made up of constant region of the heavy chains (looks the same for all antibodies) When you produce antibodies, they can be produced as one of 5 Isotypes (IgA, IgD, IgE, IgG, IgM) What makes each one different is the Fc region (stem) - while it's still constant, it's just slightly different version of fc region Each one of the different regions means each Ig interacts with immune system in different ways. IgM and IgA (dimer) can form multimers- multiple antibodies can link together through fc region through interaction called J chain, you can even get IgM pentamer (5 IgM molecules connected together= 10 antigen binding sites)- increases/drives binding affinity because you are concentrated a lot of binding sites in a small area - increasing tightness/binding ability - increase minetics IgA: linked by J chain, made as dimer - secreted antibody, produced in blood but secreted into places like mucosal surfaces (portals of entry) IgE slightly longer stem Involved in important molecular interaction Binds to FcR (Fc Receptor) Phagocytic cells express FcR Any antibody that binds to any antigen is still going to have constant region that can be recognized by any immune cells C1q; Another thing that recognizes the Fc region - (Triggers classical COMPLEMENT cascade This is the complex that binds to any antibody that's bound to an antigen on the surface of the microbe and this triggers the classical complement cascade

Which statement about the Fc stem of immunoglobulins is false? Each of the five Ig isotypes has a unique Fc Fc binds to C1q and initiates the classical complement pathway Fc binds to the Fc receptor (FcR) on phagocytic cells Fc is comprised of one heavy chain and one light chain

Fc is comprised of one heavy chain and one light chain

Selection

First step in creating mature lymphocytes (T cells and B cells) that are ready to fight infection (naive and waiting to be exposed to antigen) is making receptors Next step: Because of the frameshifts we created, we can get premature stop codons, run on sentences, lots of garbage) (Also, out of the antigens that our receptors can recognize, some of those antigens are self, and if we make mature lymphocytes that recognize self antigens, we will attack our own tissue - autoimmunity - we need to eliminate those)

Cross Presentation (What if the virus does not infect pAPC (eg DC))

First time you see virus, we need PAPC to become infected so they can present the viral antigens to naive T cells that will produce the proper cytotoxic response If they aren't infected, we don't get endogenous pathway or presentation of MHC 1, There are a lot of viruses that are incapable of infected DC or macrophages, but we still need cytotoxic response, so if the virus does not infect PAPC, we do cross presentation Cross presentation of exogenous antigens from extracellular virus with MHC 1 Cross over pathways If the virus does not infect DC cell (for example), there is another way for DC to present viral antigens (through phagocytosis- present antigens with MHC 2, activate helper response to CD4 t cell), but how would you activate cytotoxic response? Cross presentation: Take phagocyte in via exogenous pathway from extracellular virus, but process / present with endogenous pathway/MHC 1 Crossover pathway: presenting antigen with "wrong" mhc If it's presented to naive cell, cytotoxic t cell becomes activated, now it can recognize other cells infected This way you can still trigger cytotoxic response Normal pathway: MHC 2 pathway to CD4 T cell (helper response) But we need cytotoxic response too - also shoves antigen to MHC1 to present to CD8

Exogenous Pathway

For presentation of exogenous antigens from extracellular microbes (any microbe) with MHC 2 (CD4) Could be virus in extracellular phase (anything outside of cell at that time) The CD4 T cell will differentiate into a helper T cell 1. Extracellular (floating around) antigen engulfed- (like bacterial antigens) through Phagocytosis and endocytosis (bring in for processing) Endocytosis: Like phagocytosis, but phagocytosis is bringing in big things from the outside, endocytosis is bringing in small things from the outside - both ways of bringing antigen into cells Digestion in phagosomes/endosomes creates peptides 2. Antigen processing in endosome/phagosome (membrane enclosed compartment, that seperates inside of compartment from cytosol) 3.MHC 11 synthesis in RER Antigens are in compartment, MHC 2 is being synthesized in RER, so how do we get them together? Bring MHC to the antigen. Chaperone proteins chaperone MHC 2 to antigens in endosome/phagosome (in the endogenous pathway, we brought antigen to the MHC)- no passing through golgi WITH antigen Binds to chaperone molecule called invariant chain in RER (Invariant chain blocks binding site while it could be exposed to endogenous peptides- makes sure peptides don't get loaded on improperly/at the wrong time Why is invariant chain important? In mhc 1, loading occurs in RER, but we don't want that to load the peptide antigens on MHC2 there MHC passes through golgi without antigen- eventually packaged into vesicles 4. Chaperones and peptide loafing in endosome/phagosome Fusion to vesicles from golgi containing MHC 2 (stabilized by invariant chain (Ii) in RER) Vesicle fusion: Antigens and MHC will combine together, and then the vesicle becomes acidified (drop in pH) - Invariant chain molecule will be broken down by acid into CLIP Invariant chain is digested into CLIP Invariant chain broken down into CLIP by acidic pH Exchange of CLIP for peptide antigens HLA DM exchanges CLIP for peptide in binding grove on MHC 2 MHC peptide complex transported to cell surface/membrane 5. MHC - peptide complex transport -The cytoplasmic vesicle containing the MHC II-peptide complex is transported to the cell membrane, where the exogenous peptide antigen will be displayed on the surface of the APC.

For activation of T cells and formation of long-term memory, T cells require three signals during antigen presentation. The three signals include - (signal 1) antigen binding to the T cell receptor, (signal 2) <CHOOSE ANSWER> and (signal 3) cytokine signaling from the APC and other innate cells.

co-stimulation by CD28

Professional antigen-presenting cells use MHC I and MHC II to present antigens to and activate mature naive T lymphocytes. Which pair of leukocytes are professional APCs? A dendritic cells and macrophages B B and T lymphocytes C neutrophils and macrophages D basophils and mast cells E helper and cytotoxic T cells

dendritic cells and macrophages

If a virus infects a dendritic cell (DC), the <CHOOSE ANSWER 1> antigens will be processed and presented with <CHOOSE ANSWER 2> to a naive T cell. A endogenous ; MHC I B endogenous ; MHC II C exogenous ; MHC I D exogenous ; MHC II

endogenous (Newly created inside infected cell) ; MHC I Presenting to CD8 T cell (CD8 is co-receptor to MHC 1)

What consist of an antigen binding site:

has to be where two different chains come together (alpha/beta or heavy/light), and then it also has to be in variable region (near the top of molecule) 2 antigen binding sites on BCR (looks like the letter Y), TCR only has one

What happens to a single-positive CD4 thymocyte whose TCR does not bind to a peptide presented with MHC by a thymic dendritic cell (DC)?

it becomes a mature naive CD4 T lymphocyte

How does a double-positive thymocyte know which co-receptor (CD4 or CD8) to express when it becomes a single-positive thymocyte? A whether it binds to MHC I or MHC II on cTEC B whether it binds to MHC I or MHC II on mTEC C whether it binds to MHC I or MHC II on thymic DC D whether it binds to self or nonself antigens on cTEC

whether it binds to MHC I or MHC II on cTEC -cTEC (happens in cortex- outer surface of thymus- that's where MHC restriction happens) -mTEC (next step: happens in thymic medulla: Testing for binding to self antigens and getting rid of the ones that bind)

APCs with MHC 2

(almost all present with MHC 1- all listed for MHC 2 also present for MHC 1) Thymic epithelial cells -Positive and negative selection of immature T cells DCs and macrophages (professional APCs) -Activate mature naive CD4 T Cells -Helper response B cells (professional APCs- can present with MHC one or two) Its job is not to activate naive cells, but becomes activated by Th (helper cells) B cell presents using MHC 2 but to becomes activated by t cell Interacting with previously activated t cells - different from Dc and macrophages which interact with immature cells

T-Cell Development

-Antigen presentation in the thymus -Bone marrow cells become Common lymphoid progenitors (CLPs = precursors to T cells and B cells) migrate from bone marrow to thymus -Before birth, APCs in the thymus use MHC to present random peptides to immature T lymphocytes, called thymocytes, Thymocytes undergo: -TCR gene rearrangement (VDJ segments) and expression (2 checkpoints) -Co-receptor expression (CD4 and CD8) -Positive selection for MHC Restriction: (Binding is good, think positive, negative is bad - would not work with immune system= die off) -Determine which ones possess TCRs that recognize/bind to self MHC (keep these). -Negative selection for SELF TOLERANCE (All lymphocytes undergo this process) Thymus cells present self-peptide antigens to determine which TCRs specifically recognize self. If the T-cells that bound to self survived, every time they saw self they would attack (autoimmunity) Binding of self-antigen to TCR generates a signal that triggers apoptosis in the thymocyte. If this thymocyte were to mature, it would attack host tissues that express that self antigen (i.e. autoimmunity). This checkpoint creates immune tolerance to self-antigens. -Self tolerance = opposite of immune response We don't want them to recognize self- antigens, but we want them recognize self MHC -Double negative, to double positive, to single positive Only 1-3% leave thymus and become peripheral T cells

T-Cell Development: Positive selection

-Positive selection for MHC Restriction: (Binding is good, think positive, negative is bad - would not work with immune system= die off) -Determine which ones possess TCRs that recognize/bind to self MHC (keep these). A signal is generated by antigen presentation that allows thymocytes that bind a peptide-MHC combination to survive. This checkpoint in T cell development is called MHC RESTRICTION (ensures that host TCRs will work with host MHC) -B cells don't have to go through this process because they bind to native antigens, don't respond to MHC presentation of antigens -Double positive (DP) thymocytes that express TCR and both CD4 AND CD8 (present MHC 1 and MHC 2 simultaneously) -APCs= cortical thymus epithelial cells (cTEC) present random peptides with self MHC 1 and MHC 2 simultaneously -Thymus made up of cortex and medulla (cortex is outer, medulla is inner) -We want low affinity binding to either MHC 1 or MHC 2 (2-5% of cells) (Positive selection) -We want weak binding to either MHC 1 or MHC 2 because strong binding indicates that the T cell receptor binds to self MHC like its an antigen (It's recognizing self as an antigen) -Strong bind= negative selection = cell death (2-5% as well, the others just die of neglect (no binding= no signal)- over 90% of cells you created are wastes) - part of self tolerance -If cells pass this step, they choose whether to keep CD4 or CD8 as their co-receptor

CAR T cell therapy

-Scientists genetically engineering a patients own T cells -Mix collected T cells with disabled virus so T cells grow artificial receptors that are called chimeric antigen receptors -Certain types of cancers bear cd19 antigen - modified T cells attach on to this and release chemicals that trigger cell death T cells are removed from a patient and modified so that they express CAR receptors specific to the patient's particular cancer. The T cells, which can then recognize and kill the cancer cells, are reintroduced into the patient through IV

B-Cell Activation

Activated B cells differentiate into plasma cells, which produces antibodies Antibodies are immune protein that recognize/bind/tag antigens) = (Basically just more BCR, with out transmembrane region (antibodies secreted from cell, float around, looking for antigens to tag) -BCR recognizes antigens that are native/soluble (whole form, not processed/presented) Antigens typically floating around (extracellular), B cell recognizes portion of antigen (for example, a protein that is part of viral capsid, b cell recognizes segment of amino acids on that protein) Naive b cell- exogenous antigen binds to receptor, b cell becomes partially activated B cell can also endocytose the exogenous antigen bound to the BCR, and then process and present peptides with MHC II. The B cell, acting as the APC, will interact with a CD4 T cell previously activated by the same antigen. The TCR of this helper T cell will specifically recognize the peptide-MHC combination displayed by the B cell and the CD4 co-receptor will recognize MHC II. Always present antigens to T cells Activated helper cells produce cytokines to help fully activate B cell -Endocytosis -> break down exogenous peptides, combined with MHC 2, displayed on the surface of cell

Antibody

Another important antigen binding molecule that you produce: antibody Antibody also made up of four chains, two heavy and two light Difference betweeen antibody and BCR: BCR is anchored to the B cell membrane, by transmembrane region, but antibody is soluble, its released from cell/not attached to cell

When the TCR of a mature naive T lymphocyte binds to its specific peptide-MHC complex, intracellular signalling in the T cell will result in all the following EXCEPT: Activation of effector function Apoptosis Proliferation Cytokine secretion and/or cytotoxicity Survival

Apoptosis

T dependent activation of naive B lymphocytes

B lymphocytes have antigen receptors that can recognize native antigens (antigens don't have to be broken down, processed, or presented with MHC - antigen can be recognized just floating around) Only enough to partially stimulate B -cell T-dependent activation = Helper T cells are going to help activate it Naive cd4 T cells are activated, differentiate into helper T cells, which help activate b-cells The antigen presenting cell is the b- cell (APC) The antigen is being presented to t cell (helper t cell) Helper cell produces cytokines to help fully activate b -cell

BCR Polypeptide Chain

BCR: Made up of four chains (Light chain and heavy chain (2 of each) Anchor regions, constant regions, variable regions (makeup antigen binding site) 2 antigen binding sites on BCR (looks like the letter Y), TCR only has one

Checkpoints for TCR Expression

Beta chain gene starts to rearrange first If it rearranges successfully (VDJ C), beta chain expressed on surface of thymocyte Step 1: Before we express alpha chain gene, we make sure beta chain is expressed/functional (energy saver) - we test it by producing surrogate alpha chain (Pre T-alpha): Takes the place of alpha -Step 1: Pre TCR (Beta chain + pre T-alpha): Not functional: Only job is to see if everything looks good/should go to next step -CD3 complex sends signals (Stops further beta chain rearrangement (2nd beta (copy of gene on other chromosome turned off), stimulates proliferation and expression of CD4 and CD8 co-receptors (Double positive), cell allows TCR alpha chain locus rearrangement) -Testing first copy of gene - If that doesn't work: Second copy on other chromosome = take two (If signal never happens/neither work, we get cell death) -Step 2: Alpha chain undergoes rearrangement/expression, remove surrogate alpha chain, combine alpha and beta and see if they work together (see if alpha works). This is where double negative becomes double positive (Formation of Alpha beta TCR) Gamma delta T cell: Not important (Alpha beta dominates after birth, gamma delta before birth)

HLA variants are inherited as haplotypes but both alleles are expressed. This type of <CHOOSE ANSWER> expression produces the unique HLA allotype of each individual.

Co-Dominant The alleles carried on one maternal or paternal chromosome represent a MHC/HLA haplotype. The combination of class I and II alleles expressed in a diploid individual creates a MHC/HLA allotype.

Extra

CD3 complex: signaling complex on TCR Antigen receptors Self versus nonself: Do not distinguish between harmful and harmful (that's really the job of PAMPs and PRRs) BCR and TCR - both recognize epitope of antigen, but in different ways T Cell receptor will only recognize self MHC- Even if t cell receptor recognized antigen, if it doesn't recognize MHC itself, it won't become activated Communication between helper cells and CD8 T cells during activation - if DC cell is going to present exogenous antigens with MHC 2 to CD4 t cell (helper), that cell will produce cytokines, like IL 2, which will bind to a receptor found on the naive Tc cell, so that when you get cross presentation, cytokine response will help activate cell Binding groove holds peptide of a certain size (only binds certain type, but a wide variety) Size and charge distribution of peptides are critical for determining what binds

What is the co-receptor expressed by T cells that recognizes MHC I? A CD3 B CD4 C CD8 D MHC I E beta-2-microglobulin

CD8

Two different populations of T-Cells/T-Lymphocytes

CD8: MHC 1 triggers cytotoxic response: CD8 co-receptor for MHC 1 Endogenous = Produced inside antigen presenting cell (intracellular infection) -More Common -Cytotoxic T cells kill infected cells displaying MHC 1 plus that antigen (specific response) - Recognizes particular endogenous antigen (sign of intracellular infection) Cytotoxic response: Cell killing response (killing virus infected cell) CD4: MHC 2 triggers helper response: CD4 Co-receptor for MHC 2 T-cell is receptor and helper to TCR (CD4) is co-receptor Type of antigen presented: Exogenous antigens (Antigens produced outside APC, brought into APC, usually through endocytosis or phagocytosis, antigen was processed into peptides, which are then loaded onto MHC 2 molecules, which are then displayed on the surface of the APC, presenting exogenous peptide antigen)

MHC/HLA Loci

Class 1 genes: Coded in three ares A, B, C Loci encode different versions of alpha chain of MHC 1 From one chromosome, you can produce three different version of MHC 1 alpha chain B2 Microglobulin is invariant and encoded on different chromosomes. Class 2 Genes: DP, DQ, DR (These are the main loci) Loci encode different version of alpha and beta chain of MHC 2 Multiple versions ( DP alpha, DP beta, DQ alpha and DQ beta....) Each ABC and DP, DQ, DR are co-expressed

Arrange the following steps for the endogenous pathway in the correct order:

Cytosolic protein is tagged with ubiquitin Cytosolic protein is processed into peptides by the proteasome Peptide is transported by TAP into the RER Peptide is processed by ERAP to get optimal peptides for loading on MHC 1 Peptide is loaded on to MHC 1 and replaces tapas in-calreticulin-ERp57 complex Peptide MHC 1 complex is transported to the cell surface

Car T cell Article

Cytotoxic T cells (TC cells) target tumors, which can contain a lot of self antigens We have to hope that antigen originally produced inside tumor cell gets tagged with ubiquitin - kinda an imperfect system So, with CAR-T therapy, we are taking t-cells and modifying them genetically to have a receptor to target tumor cells better and more effectively CAR T Cell (displays CAR receptor- has properties of both B-cell receptor and T-cell receptor): antigen receptor looks more like BCR (this is because BCR doesn't need antigen presentation) Antigen binds, signal generated intracellularly (has to be TCR to produce cytotoxic response- TCR inside, BCR outside) On tumor cell, we aren't looking for antigen presentation, we are looking for tumor specific antigens that are expressed on the surface of the cell naturally (not displayed with MHC) - these are native antigens, BCR will recognize a single epitope on the surface of tumor cell We need something to differentiate tumor from healthy cells Mucin (MUC1) antigen expressed in abundance on tumor cells We created a receptor that recognizes this antigen - highly specific -Used this method to target breast cancer cells (CAR.MUC1) Tumors are also good at down regulating immune responses so they don't get eliminated Cytokine produced by tumor cells (IL4) - down regulates activity of T cells (T cell exposed to IL4 doesn't do its job) - even if we can design something to recognize tumor, it won't do any good What CAR is made of: Chimeric means its made up of two parts -At one end, the gene sequence has a signaling domain (t cell receptor- TCR component), then the transmembrane, hooked up to antigen binding domain ( made up of VH and VL - V stands for variable (antigen binding site always in variable region) VH and VL (Heavy and light): Come together to form antigen binding site for BCR- just taking one arm of BCR - hooked up to signaling domain of TCR Anti - IgG makes anything with CAR florese (fluorescent) - they found 78% of cells in engineered t cell population expressed CAR - that's pretty good Now we can test these cells out - test them against different tumor cells - use control #1 (cell not expressing MUC 1 to ensure that car t cells aren't killing normal cells) Tests measure cytotoxic activity at different effector (T cell) to target (tumor cell) ratios More car t cells = more tumor killing Negative control #2: Non engineered T cells (won't recognize tumor cell) Tumors produce IL4 - binds to IL4 receptor on T cells and down-regulate activity (even if the cell recognizes tumor cell, it won't produce cytotoxins) 4/7 ICR: Inverted cytokine receptor One end : IL4 receptor, then signaling region in IL7 -IL7 binding to IL7 causes upregulation/stimulation, so what if we could make IL4 cause stimulating response too instead of down-regulation So, when tumor binds sends IL4, it actually stimulates Compare old version and new version of t cells in IL2 and IL4: With the 4/7 ICR, the activity was the same as if IL4 wasn't there

In terms of both structure and function, the αβ-TCR is most similar to: A membrane-bound monomeric IgM (BCR) B soluble pentameric IgM (antibody) C Fc stem of monomeric IgM D Fab arm of monomeric IgM

D Fab arm of monomeric IgM

In the article by Bajgain et al. 2018, what was the source of the T cells that were engineered to make CAR T cells? A tumor cells from a breast cancer patient B hematopoietic stem cells from a healthy bone marrow donor C hematopoietic stem cells from umbilical cord blood donors D peripheral blood mononuclear cells from healthy human donors E peripheral blood mononuclear cells from healthy mouse donors

D peripheral blood mononuclear cells from healthy human donors

An important checkpoint during B cell development is the formation of the pre-BCR, which is comprised of the mu heavy chain and:

D surrogate light chain

What segments are used in antibody heavy chains only?

D Segments

An individual with a defect in RAG will be born with SCID, or severe combined immunodeficiency. Which statement describes the immune deficiency in a patient who has a defect in RAG? A Does not produce antigen presenting cells B Produces mature B lymphocytes but not mature T lymphocytes C Produces mature T lymphocytes but not mature B lymphocytes D Does not produce mature B and T lymphocytes

D. Does not produce mature B and T lymphocytes SCID: Bubble boy disease: Defect that causes immune system not to be able to function normaly (Severe-combined immunodeficiency) -RAG defect (No functional T or B cells) -No T or B cells: you can't fight off infection

thymocyte does not bind to cTEC thymocyte binds with low affinity to cTEC thymocyte does not bind to mTEC thymocyte binds with high affinity to mTEC

Death by neglect (apoptosis) positive selection of MHC-restricted thymocyte positive selection of self-tolerant thymocyte negative selection of auto-reactive thymocyte (apoptosis)

Immature T cells that express functional TCR are called <CHOOSE ANSWER> because they express both CD4 and CD8 co-receptors.

Double Positive

Regulatory T Cells (Treg) and Tolerance

During negative selection in thymic medulla... -Some SP thymocytes bind self-antigens with LOW AFFINITY -These autoreactive cells might survive negative selection and become mature naive T cells -However, some of these become a different T cell type called a REGULATORY T CELL, or Treg Whereas, HELPER T CELLS use cytokines to ACTIVATE immune responses REGULATORY T CELLS use cytokines to DOWN-REGULATE (INHIBIT) immune responses So, regulatory T cells produce SELF TOLERANCE by recognizing self antigens and SUPPRESSING any immune response that might accidentally occur

Each chain is encoded by a:

Each chain is encoded by a modular gene (made up of individual segments) The chains are polypeptides/proteins (all proteins inside of cells are encoded by genes, so how can we make TCR and BCell receptor? We must have in our DNA, chains for these genes We must have an alpha chain gene, beta chain gene, heavy chain gene and light chain gene so we can make these receptors

When an extracellular virus particle is phagocytosed by a dendritic cell, the exogenous antigens are processed and presented with: A MHC I to a CD8 T cell B MHC II to a CD4 T cell C Either A or B D Neither A nor B

Either A or B Either one can happen because of cross presentation. B is the normal thing that would happen if a DC cell phagocytosed an EXOGENOUS antigen (MHC 2 to CD4). The abnormal thing associated with viral infection is cross presentation / MHC 1 presentation. Every time you have a viral infection, you HAVE to activate both helper and cytotoxic responses

Immunoglobulin (Ig)

Either b cell receptor or antibody Protein Can be broken up into two regions Region where arms are connected to stem = hinge region (susceptible to enzymatic cleavage) Fab( fragments of antigen binding): Antigen binding site -Two arms contain antigen binding sites - same binding site on each arm(each made up of light and part of heavy chain Fc (Crystallizable/constant) Region: Just made up of constant region of the heavy chains (looks the same for all antibodies) 5 Isotypes (IgA, IgD, IgE, IgG, IgM) Ig Alpha andIg Beta are signaling complex for BCR

In which cellular location is a peptide antigen loaded on to MHC II?

Endoplasmic Reticulum

In the endogenous pathway, peptide antigens are loaded on to MHC I molecules in the: A cytosol B endoplasmic reticulum C Golgi complex D endosome E nucleus

Endoplasmic Reticulum (RER) Loading does not occur in same location for MHC 2 (EXOgenous pathway = ENDOsome

In the exogenous pathway, peptide antigens are loaded on to MHC II molecules in the: A cytosol B endoplasmic reticulum C Golgi complex D endosome E nucleus

Endosome

An antigen receptor binds to an (_____________), which is a specific portion of the antigen (sometimes called the antigenic determinant) recognized by the receptor.

Epitope

Which cell type does not expresses MHC molecules (neither MHC I nor MHC II)? A dendritic cell B B lymphocyte C T lymphocyte D erythrocyte E nucleated cell

Erythrocyte (red blood cell) No nucleus Transport important blood gasses They dont need MHC because viruses don't infect and multiply in blood cells (because there's no nucleus, no machinery to reproduce inside) -Malaria can reproduce inside (parasite) - thats bad because RBC has no ability to alert immune system that it's being infected (can't express MHC)

Which part of an immunoglobulin (Ig) molecule contains the antigen-binding site?

Fab

Combinatorial Diversity

Gene regions encoding antigen binding site are comprised of multiple variable segments (Each gene region/segment is variable) Before gene is expressed, it is recombined/rearranged into new combination One segment from each region is randomly recombined to make functional gene (Within the same gene) Gene rearrangement creates enormous diversity of antigen binding V(D)J regions encode the antigen binding site for each receptor chain TCR Beta and BCR-H (Similar) Each of the four regions (VDJC) are all made up of multiple variable gene segments : V (variable) region (made up of 52 segments (TCR beta chain: vbeta 1, v beta 2, v beta 3, ..... V beta 52), one is picked) D (Diversity) (TCR Beta Made up of 2, one is picked J (junctional) (pick 1 of 13 for TCR Beta chain) VDJ all combined together - makes up variable region of the protein C (constant ) region (pick 1) (where carboxy terminus is) Beta 52X2X13 = 1352 possible combinations Alpha: 70 V segments, 61 J segments = 4270 possible combinations TCR alpha and BCR Light (very similar) - No D region VJ C Alpha: 70 V segments, 61 J segments = 4270 possible combinations To make the TCR, one random alpha + one random beta chain to make antigen binding site (1352X 4270 = 5.8 X 10^6 possible combination) (still just starting with two genes, alpha and beta) -But this won't cover enough (there are more than 6 million antigens, not even thinking about how many different epitopes on each antigen)

MHC/HLA variation

Genes are inherited as haplotypes from each parent Two chromosome number 6 = double copy of alleles (maternal and paternal) Alleles found on one chromosome = ½ of alleles Haplotypes are all unique, even though everyone has MHC 1 and MHC 2 Alleles are codominant (both are expressed)- mixture of alpha and beta chains combining Creates slight variations in MHC antigen binding sites, which is good because now we can present a wide variety of peptide antigens Each locus has many alleles (Just in HLA locus A (alpha chain for MHC 1), there are 1500 different alleles, and you only need 1, 2000 for B locus, 1110 for C locus) Thousands of different HLA allotypes Allotype: What is the type of alleles you have for both MHC 1 and MHC 2 (Thousands and thousands of different allotypes can exist - most closely related would be a sibling) For identical twins, same alleles, same allotype

Junctional Diversity

Happens during lymphocyte development, before we have mature T cells that express receptors (process of making genes for those receptors first) When we are cutting out VD and J segments (using RAG) and starting to recombine them, their is an enzyme that is expressed during lymphocyte development caled TDT Terminal Deoxynucleotidyl transferase (TdT) inserts random ACGTs (nucleotides) at the ends of fragment junction sites (V segrement, insert 1, 2, or 3 bases, add D segment, add a few segments, link to J, add a few segments, link to C) Inserting random nucleotides- creating mutants by inserting bases at random (mutagenesis) What are genes? Instructions for making proteins. ACGT are spelling out instructions on how to make protein - when you translate genes, you translate three nucleotides at a time (each three letter combo= amino acid) Greatly influences reading frame which will influence final product (what does this polypeptide look like) - frame shift DNA protein kinase (DNA-PKc), artemis and others help join segments (insert more random ACGTs bases/ also serve as repair enzymes that compete the joining of DNA segments ) This random adding of bases creates 10^13-10^14 possibilities

Which immunoglobulin isotypes are co-expressed as B-cell receptors (BCR)?

IgD & IgM

What event causes positive selection, i.e. survival, of immature B lymphocytes during their development?

Immature B cell expresses BCR with functional heavy and light chains

Why is it easier to find a compatible blood transfusion than a compatible bone marrow transplant?

In order to have a compatible blood transfusion, two people need to have the same blood type. However, there are only eight different blood types (A, B, AB, and O positive/negative), so your odds of finding a match are relatively high. Finding two people with the same HLA type, on the other hand, is much more difficult. In order for a bone marrow transplant to occur, two people need to have the same human leukocyte antigen (HLA) type. Half of the HLA markers are inherited from ones mother and the other half are from ones father, so the best chance of finding a close HLA match would be to look at ones siblings. However, even then, just in HLA locus A (alpha chain for MHC 1), there are 1500 different alleles, and you only need 1. There are also around 2000 different alleles for B locus, and 1110 for the C locus. Basically, there are thousands and thousands of different HLA allotypes, so finding two that match up is incredibly rare. -Blood doesn't have MHC so no allotype

Bridging Innate and Adaptive Immunity

Innate immunity works better with adaptive immunity (makes responses more targeted) T cells react to cytokines produced in response to PAMPs Antigen presenting cell (APC) uses MHC to present peptide antigen T cell use TCR to recognize MHC peptide complex PAMPs and PRRs give context to what non-self antigen is : Some non-self antigens are not harmful, PAMPs let you know what is harmful Antigens can still be presented for non-harmful, but there's no t cell activated (Non-self antigens but no pamps = no response) PAMPs tell us general classification of what type of microbe (can tell antigens if its from bacteria, fungi, etc.) T cell helps generate specific/adaptive response like antibody production, phagocytic responses, ect

Which endonuclease is involved in producing combinatorial diversity in anitgen receptors by recombining V(D)J segments of antigen-receptor genes to create millions of possible antigen binding sites? A Artemis B C3b C RAG D TdT E DNA-PKc

RAG - this is happening in both T cells and B cells

What happens to a double-positive thymocyte whose TCR binds with high affinity to a peptide presented with MHC I by a cortical thymic epithelial cell (cTEC)?

It undergoes apoptosis

What are the types of light chains?

Lambda and Kappa -Only one is recombined and expressed at a time -Each has 70 V segments, but kappa has 5 J segments and lambda has 4 J segments. A light-chain gene is transcribed and processed to produce a VL-JL-CL mRNA. The heavy chain V-D-J and light chain V-J combinatorial diversities are 10,530 and 630, respectively. When one random light chain and one random heavy chain interact to form a B- cell receptor, it has the potential to create one of 6.6x106 (over six million) possible antigen- binding sites.

MHC 1 vs MHC 2

MHC 1 = Alpha Chain (A1,A2,A3) + Beta2 microglobulin (between A3 and A1) -MHC I alpha chain is a membrane-bound polypeptide encoded by six loci (each represents a co-dominant allele). Each individual may have up to 12 distinct alpha chain alleles because the loci are carried on both the maternal/paternal chromosomes. -This variation is critical because binding groove of MHC I resides on alpha chain. Peptide binding group only on one of the chains (Between a1-a2) β2-microglobulin, is an invariant polypeptide chain encoded on another chromosome, it does not have a transmembrane domain and does not contribute to peptide loading. MHC 2 = Comprised of two membrane-bound chains: Alpha chain (a1 and a2) + beta chain (b1 and b2) Peptide binding groove between a1 and b1 - combo of two different chains MHC 1 presents endogenous, MHC 2 presents exogenous

MHC 1: ___________genous: CD_: Differentiates into _________ MHC 2: ___________genous: CD_

MHC 1: Endogenous: CD8: Differentiates into cytotoxic T-cell MHC 2: Exogenous: CD4

MHC

Major histocompatibility Complex (Histo = tissue) proteins AKA Human Leukocyte antigen (HLA- used when referring to tissue compatibility) MHC = molecules used for antigen presentation to T cells MHC is what makes something nonself to you A genetic locus on chromosome 6 was discovered that played a key role in tissue compatibility (Where the MHC 1 and 2 genes are located = MHC locus). -MHC appeared to act as cell-surface antigens that were variable enough to be recognized by the immune system as self (compatible w/ host) or nonself (rejected by host) T-lymphocytes use T-cell receptor to recognize antigen (antigen HAS to be presented using MHC, without MHC nothing happens) Most important part of MHC molecule = binding site The MHC locus codes for two distinct classes of polypeptide chains: MHC 1 and MHC 2

T cell Responses

Mature naive T cells are activated and differentiate into effector cells (TH or TC (cytotoxic T cells)) If you want to get a TH cell, you have to present with MHC 2 If you want a TC cell you have to present with MHC 1 (virus has to infect DC) -Antigen-specific Cytoxic TCs will bind to the peptide-MHC combination displayed by infected cells, which will trigger the release of perforin and granzymes from the cytotoxic T cell. These cytotoxic factors will induce apoptosis of the infected host cell. Exogenous antigen (phagocytosed by DC (extracellular)) -Co-receptor = CD4 -The activated CD4 T cell will differentiate into helper T lymphocytes (TH cells), which will secrete cytokines to activate other immune cells (B lymphocytes)

Macrophages

PAPC too, but DCs can migrate Macrophages can't migrate, antigens have to come to macrophage activated T cells can travel to macrophages, and macrophages can stimulate them there

Where in the antigen-presenting cell (APC) are MHC molecules synthesized? A cytosol B nucleus C rough endoplasmic reticulum D smooth endoplasmic reticulum E Golgi complex

Rough endoplasmic reticulum MHC is a membrane associated carrier protein Eventually transported to Golgi, where MHC will be modified Then, pieces transported to membrane, where they are inserted (sticking out) - antigen then binds to groove sticking out

Peptide

Peptide = piece of protein/ protein antigen is digested into peptides -Displayed on the surface of antigen presenting cell

T cell receptor (TCR) forms molecular interactions with: A native antigen B peptide anitgen C self MHC D A & B only E B & C only

Peptide Antigen and Self MHC (B and C only)

The pre-T cell receptor (pre-TCR) is comprised of functional beta chain and: Pre BCR:

Pre T alpha Surrogate light chain (Same thing happens as TCR- Heavy chain is like beta chain in TCR - rearrange heavy chain first, test with surrogate light chain, then make pre BCR, then step 2: Make light chain, then make functional BCR)

Central vs. Peripheral Self Tolerance

Presentation of self-antigens that are native to the thymus (CENTRAL) mTECs present self-antigens that are normally expressed by cells of the thymus DCs present self-antigens that are expressed outside the thymus but circulate through the thymus (and be phagocytosed by DCs) Therefore, TCRs that recognize these CENTRAL antigens are eliminated from the population before they become mature naive T cells Presentation of self-antigens that are NOT native to the thymus (PERIPHERAL) mTECs present self-antigens that are not normally expressed by cells of the thymus Aire (autoimmune regulator) is expressed by mTECs during T cell development Aire turns ON expression of genes that are normally OFF in the thymus (e.g. brain proteins) In this way, thymocytes do not have to leave thymus to be tested against peripheral self-antigens Therefore, TCRs that recognize these PERIPHERAL antigens are eliminated from the population before they become mature naive T cells

PAPC (professional antigen presenting cells):

Presenting antigens with a purpose - to activate naive T cells (first time you see antigen, you have to activate cell that has never seen it before but is equipped with receptor that recognizes antigen) - Macrophages and dendritic cells (can use either MHC 1 (to activate naive CD8 T cells) or 2 (To activate naive CD4 T cells))

T-cell Activation

Professional APC (eg Dendritic cell) uses either MHC 1 or MHC 11 to present non-self antigens DC (which will process microbial antigens and combine these peptides with MHC) cell migrates from where it encountered microbe to lymphatic circulation with digested microbe, then it presents antigen to T cells in secondary lymphoid tissues (lymph node = place where naive lymphocytes hang out) Basically, bring antigens to secondary lymphoid tissues were naive T cells are to present antigens DC's are PAPC (professional antigen presenting cell) - means that it presents to NAIVE t cell to trigger first adaptive response Naive cell can only be triggered if PAPC presents TCR recognizes MHC-antigen complex

Antigen Presentation to T Cells

Selection of immature T lymphocytes during development happens before you are born (when you developing t lymphocytes) T lymphocytes originate from bone marrow like everything else, then in an immature state they go to thymus (surrounds the heart) Antigen presenting cells in the thymus that are presenting antigens to immature t cells before they become mature - helping them develop Antigens being presented are not antigens from microbes, they are called SELF ANTIGENS (this is important because how can you recognize non self if you don't know what self is?) - when you attack self = auto immunity Activation of naive CD4 and CD8 lymphocytes (getting the response started) Stimulating responses from helper and cytotoxic t lymphocytes Effector cells = cell that does something in terms of immune response (activated) Tcell knows through TCR interaction with MHC, that antigen being presented is non-self, but co-receptor recognizes that its exogenous T cell receptor job: Recognize nonself peptide antigen (doesn't care where it came from as long as its non self), and recognizing self MHC (Doesn't care what type, as its long as its self) Antigen presenting cells use MHC to present to TCR on t - lymphocyte The reason we present antigens to T cells is because they play an important role in dealing with intracellular infection versus extracellular

Self Tolerance

Self Tolerance Why?: Make sure TCR does NOT interact with self antigens Where?: Medulla of thymus Who?: SP thymocytes (alpha/beta-TCR and CD4 or CD8) How?: mTECs and DCs present SELF-peptides with MHC I and self-MHC II High-affinity binding of TCR to self-antigen produces apoptosis signals (negative selection) No binding of TCR to self-antigen = survival and thymocytes become mature naive CD4 or CD8 T lymphocytes (go to secondary lymphoid tissues)

RAG (Combinatorial Diversity)

Set of enzymes that are encoded by recombinase activating gene (RAG-1 and 2) - encode endonucleases (enzymes that cut DNA/ V(D)J segments to be rearranged/recombined) -Codes for enzymes that are involved in recombination -Recombination driven by enzymes (make chemical reactions happen) -Way to create diversity in antigen receptors

B-Lymphocyte Development

Similar in many ways to T cell development except for chain names and no MHC/co-receptors involved Why?: make sure B cells produce functional BCRs that do not bind to self-antigens Where?: bone marrow stromal cells Who?: immature B cells (pro-B and pre-B) How?: BCR expression (2 checkpoints) and then selection BCR: Heavy chain rearrangement first and then tested with surrogate light chain (checkpoint 1) -If successful, proceed with light chain rearrangement -If unsuccessful, rearrange 2nd heavy chain allele -If unsuccessful again, cell death Kappa or Lambda light chain rearrangement (checkpoint 2) If 1st kappa allele rearrangement successful, immature B cell is expressing functional BCR (IgD or IgM) If unsuccessful, try other alleles (kappa 2, lambda 1, lambda 2) until cell death Negative selection/Self tolerance -Bind to self antigens in the bone marrow or in circulation on the way to secondary lymphoid tissues = cell death (negative selection) -Surviving cells become mature naive B cells

Why is HLA diversity important for antigen presentation?

So you can present many different types of peptides - make sure you are able to present lots of antigens Microbes can change over time (mutation) - they can change their antigens over time, so creates new varieties of peptides- as long as human population has variation, some of us will be able to present antigen - Those who can present antigens die because they cant activate adaptive immunity Those who can present antigen live on and breed Variation is critical because microbes are always changing

Antigen presenting cells use MHC to present peptide antigens to:

T Lymphocytes (only type of cell that gets antigen presented to it) A T lymphocyte expresses a membrane-associated receptor, or T-cell receptor (TCR), that recognizes and binds to the peptide-MHC combination displayed by the APC. Once the TCR is bound, an intracellular signal is generated, which causes the T lymphocyte to respond according on the situation. T cell responses, and therefore, adaptive immune responses, are dependent on antigen presentation. Antigen presentation used for linking second and third line of defense (link between innate and adaptive immunity)

TCR Polypeptide Chain

T cell receptors made up of two different polypeptide chains (alpha and beta chain- not the same chains as MHC) Both chains have transmembrane region, constant regions, and variable regions (different in different t cells - every cell has a different variable region - this is antigen binding site) Every cell has a different variable region: One t cell has one variable region that recognizes one antigen - millions of antigens, millions of different T cells

Double Negative (DN) Thymocytes

T lymphocytes originate, like all leukocytes, from multipotent stem cells in red bone marrow. First, common lymphoid progenitors (CLPs) are formed, which give rise to T cells, B cells and innate lymphoid cells (e.g. natural killer cells). During their development, some CLPs leave the bone marrow and travel through the blood until they reach the thymus. These immature precursors, or thymocytes, do not yet express T-cell receptors. They also do not express CD4 or CD8 co-receptors, so they are termed double-negative (DN) thymocytes.

All the following cells can express both MHC I and MHC II except: A B lymphocytes B T lymphocytes C dendritic cells D macrophages E thymic epithelial cells

T-Lymphocytes

Match the host molecule with its role in antigen processing. TAP Invariant chain Proteasome ERp57 ERAP HLA-DM

TAP: Transport peptides into RER Invariant chain: Block peptide binding site of MHC 11 Proteasome: Process cytosolic proteins into peptides ERp57: Block peptide binding site of MHC 1 ERAP: Process peptides in RER (to correct length) HLA-DM: Exchange CLIP with peptide in MHC-11

The binding of peptide to MHC is much less specific than the binding of peptide to T cell receptor. So, why is creating variation in the peptide-binding region of MHC chains important (i.e. why are there so many MHC allotypes in the human population)?

TCRs recognize and specifically bind to each individual peptide antigen, but MHC is designed to nonspecifically bind only certain recognizable peptides. Variation in the peptide-binding grooves of MHC ensures that a great diversity of peptide antigens can be bound, allowing presentation to specific TCRs. There are many alleles at each MHC locus and there are thousands of unique MHC allotypes in the human population because microbes are constantly changing and mutating, so it is essential that we also maintain diversity in our ability to present antigens. Some people may not have MHC capable of binding a new peptide antigen, but people who do are best suited for survival and will be favored for reproduction, passing on those favorable alleles to future generations. Basically, MHC variation guarantees that functional immune systems in humans will evolve and survive along with microbial mutation.

Which factor is involved in creating junctional diversity during TCR and BCR gene rearrangement?

TDT

Both MHC I and II are comprised of two polypeptide chains each. While both chains of MHC II are created by genetic recombination, only one chain of MHC I is recombined. Why is the second chain of MHC I, called beta-2-microglobulin, invariant? Hint: Compare the structures of MHC I and II.

The second chain of MHC 1, called beta-2-microglobulin, is invariant because unlike the alpha Chain on MHC 1 and MHC 2 and the beta chain on MHC 2, beta-2-microglobulin does not connect to the binding site. This means that beta-2-microglobulin serves as a stabilizer, and is on a separate chromosome. It also does not have a transmembrane domain and does not contribute to peptide loading.

Endogenous Pathway

Taking antigens that have been produced within cell (Intracellular) (virus), and loading onto MHC 1, which presents antigens 1. Intracellular antigen synthesis (viral protein) 2. Antigen processing in cytosol of infected cell Abnormal intracellular proteins (viral antigens) are tagged in ubiquitin- separates them from normal proteins (tagging says to start breaking things down/gives a warning) -Tagged proteins get shuttled into proteasome (Looks like a cylinder), where proteins are broken down into peptides (like a paper shredder) 3. The assorted peptides are transported from the cytosol into the lumen of the rough endoplasmic reticulum (RER) by an ATP-driven transport protein called TAP (transporter associated with antigen processing). Fragmented antigens are further processed by an RER enzyme called ERAP (endoplasmic reticulum aminopeptidase) to produce peptides of the correct size for loading into the antigen-binding groove of MHC I. 4. Meanwhile, MHC 1 synthesis in RER (both types of MHC are synthesized here) -Before combining with β2-microglobulin, the MHC I alpha chain is anchored to the RER membrane and stabilized by forming a complex with two chaperone proteins, calnexin and ERp57. 5. Chaperones (helpers) makes sure peptide gets loading on to MHC molecule properly (all occurs in RER) ERp57, calnexin, tapasin, and calreticulin stabilize MHC1 complex for peptide loading (In the lumen of the RER where MHC1 peptide loading occurs) ERp57 blocks the antigen-binding groove of MHC I until endogenous peptides are ready for loading. ERAP processes peptides to optimal size for peptide-binding groove of MHC 1 Might have to trim some peptides down. When peptide has the right size (8-17), chaperone proteins affinity not stronger to block anymore Chaperone protein stuck over the top of alpha chain (peptide binding groove) - puts a lid on peptide loading zone (eventually, chaperone proteins will be replaced with second chain, B2 microglobulin- then its actually MHC 1) A peptide is exchanged for ERp57 6. MHC-peptide complex transport Now antigen presenting cell is presenting RER to Golgi to cell membrane, complex that is transported is then displayed using MHC 1 Two main location for processing and loading Processing: cytosol (tag, process, transport) Loading: RER (MHC 1 synthesized, some processing, transport) The thing that made us know that this peptide needed to be loaded onto MHC 1 was tagging

If a virus cannot infect a dendritic cell (DC), the virus will be phagocytosed and its antigens will be cross presented with MHC I, so that CD8 T cells can be activated for a cytotoxic response. How does the DC know that these phagocytosed antigens should be cross presented?

The DC cell knows which viruses to engulf and cross present because they are stimulated by viral PAMPs and cytokines produced by TH cells TLR: pattern recognition receptors that recognize conserved molecules of microbes, such as viruses have certain molecules are recognized by these receptors An antigen is eaten, DC just eat stuff they don't know what they are eaten, then they get signals from TLR (viral Pamps bind to TLR means we need cross presentation)

Describe the similarity of chain structures that BCR and TCR share.

The TCR alpha/gamma chain is similar in structure to the BCR light chain; VJ segments encode for the regions. The TCR beta/delta chain is similar in structure to the BCR heavy chain; VDJ segments encode for regions.

In the research article by Bajgain et al. 2018, what host molecule was the chimeric antigen receptor designed to recognize. Why was this target chosen?

The host molecule that the chimeric antigen receptor was designed to recognize was Mucin (MUC1), because scientists needed to identify an antigen that tumor cells expressed in abundance, but that healthy cells did not. Mucin is a glycosylated neoantigen that is readily expressed by tumor cells and whose expression has been correlated with a poor prognosis. Scientist needed to create a highly specific receptor that recognizes this antigen in order to ensure that CAR-T cells were not killing normal cells, and instead only targeted tumor cells. In the paper, they were using this method to specifically target breast cancer cells (CAR MUC1).

APC's with MHC 1

Thymic epithelial cells (cells within the thymus, where T cells develop) Positive and negative selection of immature T cells Select t cells that have receptors to interact with self MHC but don't recognize self antigens Development of the cell/how we make mature T cells - part of the process involves thymic epithelial cells DCs and macrophages (professional APCs) Activate mature naive CD8 T cells Only naive cells can be activated by PAPC Cytotoxic response (activation of CD8 T cells) All nucleated cells (pretty much any immune or tissue cell: Kidney, liver, etc) Target cells from cytotoxic response Excludes erythrocytes Only viruses can infect and multiply within nucleated cells of body

Aire is a factor expressed in mTECs that promotes the development of peripheral tolerance. Why is this factor called the "autoimmune regulator?"

To expose single positive thymocytes to antigens not native to the thymus, mTECs express a gene called AIRE (autoimmune regulator). SP thymocytes that bind to the self-antigens will be negatively selected, creating peripheral tolerance. AIRE is called the "autoimmune regulator" because it is part of the mechanism that eliminates T cells that are self-reactive and would cause autoimmune disease. After selection in the thymus, the remaining pool of thymocytes consists of cells with a TCR that is MHC-restricted and specific to nonself antigens. If immature thymocytes are not exposed to ALL self-antigens of the host, then some autoreactive (self-reactive) thymocytes will mature into mature naive autoreactive T lymphocytes. These autoreactive lymphocyte will then recognize and attack these self-antigens (e.g. brain proteins) on cell/tissues/organs of the host and cause damage (e.g. brain damage). This improper immune response is called AUTOIMMUNITY.

Exam Question: Why are there two different MHC's?

To tell the difference between antigens that are exogenous or endogenous- that's important because of the response that you would have to it - endogenous/exogenous tells us how they reproduce - in fluids? In cells? - we can't have the same response to all the different mechanisms - very difficult to fight both with same response - Two different of MHC for presenting two different types of antigens to two different types of T cells (CD4 and CD8) - by activating those t-cells, we get two different responses (Response for intracellular or response for extracellular) 2 different MHC related to how MHC comes across microbe (phagocytosis or infection)

Why did Bajgain et al. 2018 engineer their CAR T cells to express an inverted cytokine IL-4 /IL-7 receptor (4/7ICR) in addition to the antigen receptor?

Tumors produce IL4, which binds to IL4 receptor on T-cells and down-regulates their activity, meaning that even if the T-cell were to recognize a tumor cell, it would be inactivated and would not produce cytokines to trigger apoptosis. However, 4/7 inverted cytokine receptor (ICR) contains an IL4 receptor on one end, and in the signaling region it contains IL7. IL7 binding to IL7 receptors causes up-regulation or stimulation, so scientists engineered CAR T cells to express this inverted cytokine receptor (4/7 ICR) because it causes IL4 to bring about a stimulating response instead of leading to t-cell down-regulation. This appeared to be an effective strategy, because when comparing old version and new version of t-cells in IL2 and IL4, with the addition of the 4/7 ICR, the activity was the same as if IL4 was not present.

What are the region gene segments?

Variable (V), Diversity (D), Joining (J), and Constant (C) region genes

Variant and Invariant Chains

Variant: One individual will produce varieties (not identical) Alpha Chain on MHC 1, Alpha chain on MHC 2, and Beta chain on MHC 2 (3 of the four chains) Involved in binding site because so many different types of antigens have to presented - create variants of MHC ( a bunch of types of MHC 1 and 2, you use a variety of these to present a bunch of different types of antigens ) Variants of MHC: Different MHC 1s, different MHC 2s: Variations of MHC used to present variation of antigens - This variation is important because there are a variety of antigens out there (somewhat non-specific)- Why this is important: MHC needs to be able to present a wide variety of peptide antigens Invariant: B2 microglobulin: Does not connect to binding site Basically just stabilizes

MHC Restriction Why is creating MHC restriction important during T cell development?

Why?: Make sure TCR can interact with self MHC Where?: Cortex of thymus Who?: DP thymocytes (alpha/beta-TCR and both CD4 and CD8) How?: cTEC present peptides with self-MHC I and self-MHC II Low-affinity binding of TCR to self-MHC produces survival signals (positive selection) If T cell binds MHC I, it will become SP CD8 thymocyte If T cell binds MHC II, it will become SP CD4 thymocyte Creating MHC restriction is important during T-cell development because it makes thymocytes that only work with the MHC allotype of their host. This process eliminates any T-cells that would bind to self antigens, causing an autoimmune disorder.

Activation of CD4

a little more complicated : most of what they do deals with extracellular pathogens Antigen presenting cell, like dendritic cell, phagocytizes antigen, processed, and presented with MHC 2 (antigen originally outside, but brought inside) - CD4 t cell gets activated by DC, and then CD4 t cell becomes helper t cell = Helper response Helper T cells produce cytokines to help communicate with other immune cells (hey, there's any extracellular pathogen floating around, can tell b-cells to produce antibodies, can activate eosinophils for parasitic response...) Helper cells also help cytotoxic response Helper Cell has to know what type of pathogen we are dealing with - viral, bacteria, parasite Conveys this info to cells during antigen presentation by PAMPs

Why do we need great antigen diversity?

because this is happening before you are born, before you have seen antigens before We have to create receptors for antigens we may not see Create so many combinations of antigen receptor genes that you will account for every antigen you will see in the future - account for every possibility (better to have too many than not enough) A lot of leftovers, that are essentially useless Done at random, because you don't know what you are looking for There are only like 20-30,000 genes in the human genome, so even if we devoed ever gene to making a unique antigen binding receptor, we still wouldn't have nearly enough genes

How does a pAPC know whether to present a microbial antigen with MHC I or MHC II? A antigen is bacterial or viral B antigen is endogenous or exogenous C antigen is encountered in tissues or on mucosal surfaces D antigen is protein or carbohydrate E the MHC type is randomly chosen

antigen is endogenous or exogenous

What happens to a double-positive thymocyte whose TCR binds with low affinity to a peptide presented with MHC I by a cortical thymic epithelial cell (cTEC)?

it becomes an immature single-positive CD8 thymocyte MHC restriction is created in the thymic cortex. Thymocytes that bind to self MHC with low affinity survive because these cells have shown they can recognize antigens presented with self MHC. By recognizing MHC I, the cell begins to preferentially express CD8, which is the co-receptor specific for MHC I.

BCR and TCR have all of the following in common EXCEPT: receptor consists of multiple polypeptide chains receptor has multiple antigen binding sites receptor has a transmembrane anchor receptor has constant and variable regions

recepter has multiple antigen binding sites