MCB 150 Midterm 2

syngenic

genetically identical at all loci (inbred strains of mice)

congenic

mice differing in only one gene locus while being genetically identical at all other loci; obtained by backcrossing

backcrossing

a way to generate a congenic mouse with a specific gene of interest; a way to move a gene or group of genes from one line of mice to another; achieved by breeding F1 hybrids back to the parent line you intend to move the gene to; if your gene of interest is in mouse line A and you want to move it to mouse line B, you will breed A with B and then breed the F1 offspring back to line B

allele

a variant form of a gene; many genes occur in several (or more) different forms within the general population

polymorphic

existing in a variety of different forms; applied to a gene, occurring in a variety of different alleles; these genes have multiple alleles (termed haplotypes) and each allele is able to bind a slightly different set of peptides (having multiple alleles for each gene within a population helps protect the population as a whole from a wide array of pathogens)

polymorphism

variability at a gene locus in which all variants occur at a frequency greater than 1%

polygenic

containing several separate loci encoding proteins of identical function; applied to the MHC

haplotype

group of linked genes that are (usually) inherited as a group; MHC genes

co-dominant expression

both alleles for a given gene are expressed; like MHC alleles, contrast to allelic exclusion

MHC restriction

the fact that peptide antigen can only be recognized by a given T cell if it is bound to a particular self MHC molecule; a consequence of events that occur during T cell development where only T cells that recognize self-MHC are positively selected; T cells from a given individual only recognize MHC molecules from the same haplotype

alloreactivity

the recognition by T cells of MHC molecules (with loaded peptide) different than self-MHC molecules; MHC diversity between individuals leads to problems with transplant rejections as a result of MHC mismatch: the MHC is recognized as "non-self" and the tissue is destroyed by the immune system

allograft

a transplant of tissue from an allogeneic donor of the same species; such grafts are invariably rejected unless the recipient is immunosuppressed

MHC I:peptide pathway

peptide loading in the ER; MHC class I bound to TAP1/2 and chaperone proteins (calnexin/preB2m, calreticulin binds alpha:B2m, tapasin binds MHC to TAP) until peptide is loaded which stabilizes MHC and releases it from TAP

MHC II:peptide pathway

acidification of endocytic vesicles activates proteases that degrade proteins into peptide fragments which are loaded on to MHC class II molecules; alpha and beta chains associate in the ER; MHC class II sorted into vesicles in trans golgi network; deliver MHC class II to specialized compartments for peptide loading called MIIC

TAP1/2

transporters associated with antigen processing; ATP-binding cassette proteins that form a heterodimeric complex in the endoplasmic reticulum membrane through which short peptides are transported from the cytosol into the lumen of the ER where they associate with MHC class I molecules; pump peptides into ER; transporters associated with antigen processing; form channel from cytoplasm to ER lumen

ERAAP

an ER resident protease that trims the NH2 termini of polypeptides to a size at which they can bind to MHC class I molecules (8-9 amino acids)

NK cells

a type of ILC that is important in innate immunity to viruses and other intracellular pathogens and in antibody-dependent cell-mediated cytotoxicity (ADCC); express activating and inhibiting receptors but are not antigen-specific receptors of T or B cells

ADCC

lysis directed by antibody recognizing antigen on target cell; NK cell is activated through binding of antibody to Fc receptor (cells that perform this must have Fc receptors to bind antibody molecules and trigger killing of target cell)

endogenous pathway

the classical antigen presentation pathway by which cytosolic antigens are processed and presented on MHC I to CD8 T cells; can happen on any cell

exogenous pathway

the classical antigen presentation pathway by which extracellular antigens are processed and presented on MHC II to CD4 T cells; intravesicular pathogens in macrophages or extracellular/toxins in B cells

HLA-DM

an invariant MHC protein resembling MHC II in humans that is involved in loading peptides onto MHC II molecules; facilitates exchange of CLIP peptide for other peptides; non-classical MHC class II that binds to MHC class II and kicks off invatriant peptides; not polymorphic and does not bind peptides; a homologous protein in mice is called H-2M or sometimes H2-DM

CLIP

acidification cleaves invariant chain which leaves behind small peptide

invariant chain

prevents endogenous peptides from being loaded onto MHC class II; binds to MHC class II in the ER; signals in the cytoplasmic tail lead to proper sorting of MHC II

immunoproteasome

a form of proteasome found in cells exposed to interferons; contains three subunits that are different from the normal proteasome

proteasome

endogenous pathway; unfolds proteins, cleaves into peptides/amino acids

LMP2/LMP7

endogenous pathway; induced by interferons, increase production of peptides with preferred sequence for MHC class I; immunoproteasome subunits

RMA-S cells

a mutant cell line that has a defect in MHC class I assembly; used in the discovery of TAP1/2

interferons

several related families of cytokines originally named for their interference of viral replication; IFN-a and IFN-B are antiviral in their effects, IFN-y has other roles in the immune system

cross-priming

activation of CD8 T cells by dendritic cells in which the antigenic peptide presented by MHC I molecules is derived from an exogenous protein (i.e. by cross-presentation) rather than produced within the dendritic cells directly; loading antigenic peptides derived from exogenous proteins onto MHC class I molecules

eating yourself

cytosolic proteins engulfed by membrane and delivered to lysosome; induced by cellular stress, nutrient deprivation, or infection; happens in thymic epithelial cells

cross-presentation

the process by which extracellular proteins taken up by DCs (CD11c+) can give rise to peptides presented by MHC I molecules; enables antigens from extracellular sources to be presented by MHC I molecules and activate CD8 T cells; occurs when exogenous antigen is taken up by a CD8a+ or CD103+ dendritic cell and presented on MHC I to CD8 T cells - at some point the exogenous antigen is moved from the phagosome to the cytosol where it undergoes proteolysis and transport into the ER just like class I peptides; allows uninfected DCs to activate a CD8 T cell response which may happen because there are some cytosolic pathogens that do not infect DCs and since DCs are the key APC required for activating T cells it allows for "cross priming" of CD8 T cells so that the CD8 T cells may carry out their killing of the truly infected cells

direct presentation

the process by which proteins produced within a given cell give rise to peptides presented by MHC I molecules

autophagy

the digestion and breakdown by a cell of its own organelles and proteins in lysosomes; may be one route by which cytosolic proteins can be processed for presentation on MHC II molecules; can deliver cytosolic proteins to the lysosome for loading onto MHC class II; allows endogenous peptides to be presented on MHC class II in cTECs and mTECs (important for T cell selections)

B7.1/B7.2

cell-surface proteins on specialized APCs such as dendritic cells that are major co-stimulatory molecules for T cells; both bind to the CD28 and CTLA-4 proteins on T cells

CD28

an activating receptor on T cells that binds to the B7 co-stimulatory molecules present on specialized APCs such as DCs; the major co-stimulator receptor on naive T cells

peptide-binding groove/cleft

the longitudinal cleft in the top surface of an MHC molecule into which the antigenic peptide is bound

CDR (complementarity-determining region)

parts of the V domains of immunoglobulins and TCRs that determine their antigen specificity and make contact with the specific ligand; the most variable part of the antigen receptor and contribute to the diversity of these proteins; three such regions in each V domain

CD3 complex

the invariant proteins (gamma, delta, and epsilon) and the dimeric zeta chains which form the signaling complex of the TCR; each of them contains one or more ITAM signaling motifs in their cytoplasmic tails; longer cytoplasmic tails with ITAMS; associates with TCR; oppositely charged transmembrane regions; analagous to the Iga/IgB proteins for BCR

ITAM (immunoreceptor tyrosine-based activation motif)

sequence motifs in the signaling chains of receptors, such as antigen receptors on lymphocytes, that are the site of tyrosine phosphorylation after receptor activation leading to recruitment of other signaling proteins; when tyrosine is phosphorylated it can bind to things

SH2 domain

a member of the Src-family protein tyrosine kinases; these receptor-associated protein tyrosine kinases are involved in relaying signals from the antigen receptor in T and B cells; bind specific phosphotyrosines within ITAMs

Lck

a Src-family tyrosine kinase that associates with the cytoplasmic tails of CD4 and CD8 and phosphorylates the cytoplasmic tails of the TCRs signaling chains, thus helping to activate signaling from the TCR once antigen has bound

initial TCR signaling steps

Lck binds to tails of CD4/CD8; MHC:peptide binds TCR and CD4/CD8 bind MHC; Lck binds ITAMS (when CD4/CD8 bind MHC) and phosphorylates; Zap70 binds phosphorylated ITAMS on CD3 zeta chains; Lck also phosphorylates Zap70 which activates it

Zap70

a Syk-family tyrosine kinase that binds phosphorylated ITAMs on CD3 zeta chains and is activated when phosphorylated by Lck; phosphorylates SLP-76 and LAT which activates 3 pathways - Ca2+ mediated, PKC-mediated, and small G protein-mediated (RAS, Rac) - that all result in changes in gene expression, functional changes, differentiation and activation

Ca2+ mediated signaling pathway

PLC-y cleaves PIP2 into DAG and IP3; IP3 opens Ca2+ channels to allow extracellular calcium to enter cytoplasm; Ca2+ activates calmodulin (and PKC with DAG); when calmodulin binds Ca2+ it is activated by conformational change; Ca2+-calmodulin complex activates phoshpatase calcineurin; calcineurin dephosphorylates NFAT-p; NFAT (now activated) enters nucleus and activates transcription (IL-2/IL-2R)

cyclosporin (and FK506)

inhibits calcineurin which blocks NFAT activation; essential drug to prevent transplant rejection; immunosuppresive drug that blocks activation of NFAT by binding cyclophilin A (normally plays role in protein folding) and preventing interaction between inactive calcineurin and activated calmodulin so that the phosphatase is never activated and NFAT remains in its phosphorylated and inactive state in the cytosol

PKC (protein kinase C) mediated signaling pathway

PLC-y activates PKC along with DAG (from PIP2 cleavage into DAG and IP3 that opens Ca2+ channels); activates IkB kinase which phosphorylates IkB releasing it from NFkB; this allows NFkB to be translocated into the nucleus and activate transcription (IL-2/IL-2R)

Ras (small G protein) mediated pathway

Ras bound to GDP is inactive form; GEF exchanges GDP for GTP which activates Ras (forms Ras-GTP complex); GAP is a phosphatase that removes a phosphate group from Ras-GTP to reform Ras-GDP therefore inactivating Ras; active Ras activates the MAP kinase pathway (TCR activation - Ras:GDP to Ras:GTP - Raf (MAPKKK) - MEK (MAPKK) - MAP kinase - AP1)

AP-1

transcription factor that activates transcription/alters gene expression through the IL-2 gene promoter downstream of Ras and the MAP kinase cascade

Csk

kinase that inhibits PTKs (like Lck) by phosphorylating inhibitory tyrosine which binds to internal SH2 domain

CD45

phosphatase that activates PTKs (like Lck) by dephosphorylating inhibitory phospho-tyrosine that is bound to internal SH2 domain; a transmembrane tyrosine phosphatase found on all leukocytes; also called leukocyte common antigen; generic marker for hematopoietically-derived cells with the exception of erythrocytes

LAT (linker for activation of T cells)

a cytoplasmic adaptor protein with several tyrosines that become phosphorylated by the tyrosine kinase ZAP-70; helps to coordinate downstream signaling events in T cell activation

PLCy (phospholipase C-gamma)

key enzyme in intracellular signaling pathways leading from many different receptors; activated by membrane recruitment and tyrosine phosphorylation following receptor ligation, and it cleaves membrane inositol phospholipids into inositol triphosphate (IP3) and diacylglycerol (DAG); IP3 binds to Ca2+ channels and opens them allowing Ca2+ entry; fully activated by TCR signaling and CD28 signaling

NFAT (nuclear factor of activated T cells)

a family of transcription factors that are activated in response to increased cytoplasmic calcium following antigen receptor signaling in lymphocytes

IL-2

a key cytokine that is produced downstream of TCR signaling; helps activate T and B cells and also plays a role in lymphocytes development; promotes T cell survival and proliferation during activation; made by T cells

PD-1 (programmed death 1)

a receptor on T cells that, when bound by its ligands, inhibits signaling from the antigen receptor; contains an ITIM motif in its cytoplasmic tail; inhibits PI3K and activates PTEN (converts PIP3 to PIP2 so no increased glycolysis/GLUT1 expression) inhibiting signal 2 between CD28 and B7; normal role is to bind PD-L on APC when T cell is exhausted due to chronic infection or persistent antigen stimulation; creates a blockade that downregulates proliferation, cytokine production, and cytotoxicity so T cell can become reinvigorated

CTLA-4

a high-affinity inhibitory receptor on T cells for B7 molecules; its binding inhibits T cell activation by activating PP2A which inhibits Akt (dephosphorylates?)

CAR (chimeric antigen receptor) T cells

engineered fusion proteins composed of extracellular antigen-specific receptors (e.g. single-chain antibody) and intracellular signaling domains that activate and co-stimulate; expressed in T cells for use in cancer immunotherapy; manipulate patient's cells to recognize cancer; every T cell expresses gene of interest because injected with retrovirus (patient's T cells - plate with T cell mitogens and cytokines - add retroviral vector - CAR T cell production - put back in patient)

chimeric antigen receptor (CAR)

can activate T cells without going through APCs; ectodomain recognizes antigen and endodomain stimulates signaling

scFv (single chain variable fragment)

a simple way to represent antibody Vh and Vl as one protein; want it to bind to antigen on cancer cell...we know variable regions of antibody recognize antigen so all we need are those Fab fragments; link Vh and Vl chains together with linker to form one protein (ectodomain); can add another linker to fuse it to a transmembrane region and the endodomain for stimulation

T cells

precursors born in bone marrow, "educated" in the thymus; progenitors develop in the bone marrow and migrate to the thymus; precursor rearranges its receptor genes in the thymus; immature cells that recognize self MHC receive signals for survival (positive selection) and those that interact strongly with self antigen are removed from the repertoire (negative selection)

Ipilimumab

blocks negative signaling from CTLA-4; targets inhibitory receptor as immunotherapy to increase T cell activation

chimera

a single organism composed of different cells with distinct genotypes

immunological synapse

a highly organized interface that develops between a T cell and the target cell it is in contact with; formed by T cell receptors binding to antigen and cell-adhesion molecules binding to their counter parts on the two cells; clustering of TCR, MHC, and adhesion molecules at interface between T cell and APC

CD25

also known as IL-2 receptor alpha; high-affinity component of the IL-2 receptor; up-regulated by activated T cells and is constitutively expressed by Tregs to confer responsiveness to IL-2

CD44

a cell-surface glycoprotein expressed by naive lymphocytes and up-regulated on activated T cells; high expression is used as a marker for effector and memory T cells

double positive thymocyte

immature T cells in the thymus that are characterized by expression of both CD4 and CD8 and represent the progenitors to the remaining T cells developing in the thymus; in a normal thymus these represent about 5% of thymocytes

single positive thymocyte

a mature T cell that expresses either the CD4 or CD8 co-receptor, but not both

Th-POK

a zinc finger transcription factor that plays a crucial role in CD4 T-cell development and CD4/CD8 lineage decision; in deficient mice, developing T cells expressing MHC class II-restricted T-cell receptors are redirected into the CD8 T-cell lineage; TCR binding to MHC class II (moderate/prolonged signal) triggers expression which represses CD8 and transcribes CD4 (MHC class I signaling is weak/transient)

anergized in periphery

result if T cell sees self antigen without costimulation; signal 1 without signal 2; cells unresponsive forever even if interact with pathogen/signal 2 later; ensures tolerance to peripheral self antigens not expressed by mTECs/AIRE in the thymus

positive selection

a process occurring in the thymic in which only those developing T cells whose receptors can recognize antigens presented by self MHC molecules can mature; mediated by cTECs so developing T cells will be restricted by recipient genotype

negative selection

the process by which self-reactive thymocytes are deleted from the repertoire during T cell development in the thymus; T cells cannot mature to the single positive stage and exit the thymus if they strongly react against self MHC; autoreactive B cells undergo a similar process in the bone marrow; mediated by mTECs and APCs so cells will be deleted if they are auto-reactive to donor or recipient

bone marrow chimeras

mice whose original immune system has been wiped out by irradiation and replaced with that from another mouse through bone marrow transplantation (bone marrow from the donor mouse in injected intravenously into the recipient mouse)

thymic cortex

the outer region of each thymic lobule in which thymocytes proliferate, rearrange their TCR, and undergo thymic selection; especially positive selection on thymic cortical epithelial cells

thymic medulla

the central areas of each thymic lobe rich in bone-marrow derived APCs and the cells of a distinctive medullary epithelium

TCR transgenic mice

mice whose genome has been altered by the transfer of a specific TCR gene so that all of their T cells will express the same, specific TCR; these mice are often used to study T cell development; tools to observe positive and negative selection directly

AIRE

gene encoding a protein (autoimmune regulator) that is involved in the expression of numerous genes by thymic medullary epithelial cells (mTECs) enabling developing T cells to be exposed to self-proteins characteristic of other tissues, thereby promoting tolerance of these self proteins; allows expression of tissue-specific antigens in mTECs - if T cells recognize those antigens in the medulla with high affinity they undergo negative selection resulting in tolerance against peripheral organs; negative selection at the immature SP stage (instead of the DP stage like cortical negative selection) deficiency leads to an autoimmune disease called APECED (often including Type 1 diabetes)

ovalbumin (ova)

a classical model antigen derived from egg whites; specific peptides have been used to make TCR transgenic mice (OT-Is and OT-IIs)

OT-I and OT-II

Ova-specific TCR recognized by MHC I or MHC II

superantigen

a class of antigens that cause non-specific activation of T-cells resulting in polyclonal T cell activation and massive cytokine release; produced by some pathogenic viruses and bacteria most likely as a defense mechanism against the immune system; activate so many CD4 T cells by cross-linking MHC to the TCR-beta chain (V segment) so they will activate any T cells using that particular TCR VB

H-Y antigen

a male histocompatibility antigen that causes rejection of male skin grafts by female recipients of the same inbred strain of rodents; also detected by cytotoxic T cells and antibodies; male-specific antigen

spleen

mature T cells enter this organ from the bloodstream; referred to as a secondary lymphoid organ; antigen presenting cells (macrophages, DCs, B cells) interact with T cells; assuming these are naive T cells they are scanning DCs for peptide:MHC complexes that bind to their TCR ("cognate peptide"); if the T cell interacts with a DC that is presenting the cognate peptide in the presence of co-stimulation (B7) that T cell will become activated (proliferate extensively and differentiate) and become part of an adaptive immune response

thymus

referred to as a primary lymphoid organ; structure can be divided into the cortex where positive selection occurs and the medulla where negative selection (mostly) occurs

bone marrow

referred to as a primary lymphoid organ; where common lymphoid progenitor stem cells are made and maintained, these cells then migrate to the thymus to become thymocytes

lymph nodes

mature T cells enter this organ from the bloodstream/lymphatics; T cells need to cross the high endothelial venules (HEVs) to enter; T cell interact with antigen presenting cells (macrophages, DCs, B cells) and, assuming these are naive T cells, they are scanning DCs for peptide:MHC complexes that bind to their TCR; if the T cell interacts with a DC that is presenting the cognate peptide in the presence of co-stimulation (B7) that T cell will become activated (proliferate extensively and differentiate) and become part of an adaptive immune response

recognition phase

first phase of T cell activation; naive T cells encounter their cognate (peptide:MHC for which that T cell's TCR is specific) antigen presented on an activated DC with costimulation (so CD28 on the T cell binds to B7 on the DC) in a secondary lymphoid organ

activation phase

second phase of T cell activation; while in the same secondary lymphoid organ the now activated T cell undergoes differentiation and proliferation (clonal expansion) to generate a large pool of activated T cells that are specific for that same peptide:MHC complex; CD8 T cells become cytotoxic T lymphocytes and CD4 T cells can become Th1, Th2, or Th17; production of IL-2 and up-regulation of the IL-2 receptor help the activated T cell undergo clonal expansion; newly activated/differentiated T cells also begin making their other effector cytokines such as interferon gamma (IFN-y)

effector phase

third phase of T cell activation; the T cell clones leave the secondary lymphoid organs to home to the site(s) of infection where they use their TCRs and cytokine production to carry out tasks specific to their cell type; ex. CTLs use their TCR to recognize and kill infected cells presenting their cognate peptide on MHC I, CD4 T cells are able to activate macrophages and B cells and otherwise aid in inflammation

chromium release assay (aka killing assay)

ex. put memory CD8 T cells in a dish with cells that infected with CMV (CMV can infect macrophages, epithelial cells, etc. so we can easily use an epithelial or macrophage cell line); these infected cells must first be labeled with radioactive chromium; after combining the memory CD8 T cells with the infected cells we can use the release of radioactivity as a read-out for cell killing/lysis; more radioactivity \= more killing; as a control we can use uninfected 51-Cr labeled cells

FasL

as an infection is cleared, effector T cells will need to start turning off the immune response; expressed by T cells; interacts with Fas to activate the caspase-8 and caspase-3 dependent death of the T cells (apoptosis); also upregulated on CTLs when TCR signaled during CD8 activation so these CTLs interact with Fas expressed on the target cell surface and induce apoptosis; without it a person would be unable to efficiently turn off T cell responses and this would result in many potentially life-threatening issues such as autoimmunity and/or uncontrolled T cell proliferation

Fas/FasL

both upregulated on activated T cells; signaling leads to activation of caspases and programmed cell death (apoptosis); mutations lead to autoimmune disorders and lymphoproliferative disorders

CAD

when activated it enters the nucleus and cleaves DNA which leads to apoptosis; inhibitor is activated by caspase 3 which is activated/cleaved by caspase 8 downstream of FasL binding Fas

CTLA-4

as an infection is cleared, effector T cells will need to start turning off the immune response; expressed by T cells; will "steal" B7 away from CD28 because it has much higher affinity for B7 than does CD28 so it out competes for binding thus removing the co-stimulatory signal and causing the T cell to eventually die; TCR and CD28 signaling leads to upregulation; without it a person would be unable to efficiently turn off T cell responses and this would result in many potentially life-threatening issues such as autoimmunity and/or uncontrolled T cell proliferation

Treg suppression mechanisms

likely able to "steal" IL-2 away from effector T cells through their own IL-2 receptor (IL-2 plays a crucial role in ongoing positive feedback for active effector T cells); produce multiple suppressive cytokines such as IL-10 which acts to down-regulate MHC II and co-stimulatory signals on some APCs (among other roles); express CTLA-4 which has a higher affinity for the B7 co-stimulatory signal than CD28 and can therefore "steal" the co-stimulation away from effector T cells; can make perforin and granzyme B (like CTLs) to induce apoptosis in effector T cells

conjugate formation

first step of CTL killing; CTLs use adhesion molecules to "grab on" to target cells and then initiate TCR binding to the peptide:MHC; if the target cell is presenting the CTL's cognate peptide, the CTL will polarize toward the target cell (so bring important receptors and molecules toward the part of the CTL that is contacting the target cell)

granzyme B

most active granzyme released by granules of CTLs; enters through perforin pores and cells are equipped to die if exposed

membrane attack

second step of CTL killing; initiates the killing of the target cell and involves the release of cytotoxic granules at the interface between the CTL and the target cell; these granules contain perforin, which forms large pores in the target cell membrane, and granzymes, which are serine proteases that cleave and activate various caspases to initiate apoptosis; CTLs can also kill through interaction of FasL on their surface with Fas on the surface of the target cell

CTL dissociation

third step of CTL killing; not actually much happening here aside from the CTL "releasing" its target cell and moving on to kill other infected cells

target cell destruction

fourth step of CTL killing; perforin and granzymes kill the target cell by forming pores in its membrane and inducing apoptosis (respectively); granzymes cleave and activate caspase 8 which cleaves and activates caspase 3 which (through a few more steps) results in apoptosis; Fas/FasL killing follows a similar cell death pathway

cathepsin B

expressed by CTLs inside their granules; cleaves perforin and prevents it from forming pores in the membrane of the CTL; protease which cleaves perforin so when TCR is signaled at interface between target cell and CTL it will degrade perforin so it is not released onto target cell

Spi-6

serine protease that inhibits granzyme B-mediated apoptosis; upregulated in CTLs following activation