T cell tutorial exam

AIRE

expressed by cortical epithelial cells in the thymus medulla and cortex to allow expression of proteins and presentation of antigens from peripheral tissue to promote tolerance to self-antigens

mTECs

express class I and class II in the thymus and are in the medulla and are responsible for the negative selection of T cells, eliminating autoreactive ones by expressing AIRE.

cTECs

they are similar in function to mTECs but are found in the cortex and are responsible for the positive selection of T cells ensuring that the T cell can signal at all.

DN2-DN3 stage

-          stage in T cell development where the TCRb or TCRyd rearrange.

DN4-DP stage

stage when TCRa rearranges

B-selection

stage in T cell development that ensures that the Beta chain of the TCR is functional before progressing. This is done by signaling through the pre-TCR.

death by neglect

-          this occurs when a T cell makes a fully rearranged TCR at the DP stage that cannot bind to pMHC complexes in the thymus and dies due to lack of signaling.

clonal deletion

-          this occurs when the TCR that is generated by the T cell reacts too strongly to a peptide MHC complex in the thymus and undergoes programmed cell death.

DP-SP stage

T cells are selected to be CD4 or CD8 based on their ability of their rearranged TCR to interact with a specific MHC I or MHC II.

thymic medulla

-          this is where the SP T cells accumulate and undergo another round of negative selection interacting with mTECs. This stage can also generate Tregs from the CD4 SP pool

cortical medullary junction

-          entrance location of the thymus for T cell progenitors in the blood

PSGL1

-          this ligand binds to T cell progenitors in the blood and allows entrance into the thymus.

CCR7 and CCR9

-          the receptors for the ligands CCL21, CCL25, and CCL19. These chemokines are secreted by thymic epithelial cells and induce T cell progenitors to enter the thymus.

notch signaling

-          this signaling pathway induces T cell progenitors that just entered the thymus to commit to the T lineage.

CXCR4

-          this receptor is expressed by DN thymocytes which recognize CCL12 on cTECs retaining the DN thymocytes in the cortex.

CCR4

-          expressed by SP thymocytes to induce trafficking to the medulla of the thymus

mimetic cells

-          cells that actively express and imitate other cells in the periphery to further improve tolerance in the T cell repertoire.S1PR

S1PR

-          receptor upregulated by the SP thymocytes that survive selection to allow re-entry into the blood.

ThPOK

transcription factor upregulated when CD4 TCR interact with MHC II

RUNX3

-          transcription factor upregulated when CD8 TCR interact with MHC I

iNKT cells

-          Invariant natural killer T (iNKT) cells are a subset of T lymphocytes that co-express T-cell and NK-cell markers and use a semi-invariant αβ TCR to recognize glycolipid antigens presented by the non-polymorphic MHC-I–like molecule CD1d.

MAIT cells

an innate‑like subset of αβ T cells whose semi‑invariant TCR recognizes small microbial vitamin B–derived metabolites presented by the non‑classical MHC‑I–like molecule MR1. The TCR of these cells is somewhat invariant as its required to recognize MR1

CD1d

-          non-classical MHC molecule that presents lipid like peptides and generates iNKT cells.

MR1

-          non-classical MHC that presents peptide metabolites and generates MAIT cells.

CD8aa IEL development

-          selected from DP thymocytes on self-peptide–MHC-I molecules in the absence of costimulatory molecules.

agonist selection

-          T cells surviving in the thymus even with high TCR affinity. Usually generates small T cell subsets

CD5

-          type I transmembrane receptor expressed on most thymocytes from the DP stage onward and on the majority of mature peripheral T cells, as well as a subset of B cells (B‑1a). Its surface level on individual T cells correlates with the strength/avidity of TCR interactions with self‑peptide–MHC during thymic selection, so CD5^hi T cells generally carry more self‑reactive TCRs.

Post-aire expressing mTEC compartment

mTECs that can be mimetic cells

gating for mTECs

EpCAM⁺CD45⁻MHCII^loPDPN⁻CD104⁻

Disruption of agonist signaling of CD4 T cells

induces the CD4+ CD25+ T cell precursors to become Tregs through foxp3, and persistent agonist signaling induces T effector cells to become IL-2+ T effector cells

TGFb

can promote foxp3 induction by disrupting agonist signaling in CD4 T cells

when clonal deletion occurs

stage 3 of CD4 T cell development

time of Treg induction

stage 4-5

primary Treg pathway

-          late stage agonist signaling disruption by TGFb generates pre Tregs which interact with IL-2 to induce mature Tregs

alternative Treg pathway

-          late agonist signaling in the presence of excessive IL-2 generates mature Tregs

RAG-GFP mice

mice that express GFP at different levels depending on RAG expression, allows to identify different stages of development in the thymus

OT-II transfer into OVA+ mice

-          allows us to study the induction of Tregs and clonal deletion in the thymus

RIP-OVA

-          OVA expression by pancreatic beta cells as a model of T1D

make Tregs in vitro

Culture CD4s on day 1 with TCR/CD28 and then put fresh media on day 2

Intra thymic transfer

-          allows the study of different cells in different environments in vivo

DN2a-DN2b stage

when T cell commitment occurs

CD25 and cKit

-          allow flow gating to identify DN1-DN4 in thymus flow gating

PU.1

blocks ILC genes in T cell development

notch signaling role

downregulation of non-lymphoid genes

TCF-1

one of the first factors induced when hematopoietic progenitors enter the thymus and receive Notch signals, and it is required for progression beyond the early thymic progenitor/DN1 stage into the T‑cell program

GATA-3

needed for efficient generation and maintenance of early T‑lineage progenitors (ETPs) and progression through DN2/DN3; hypomorphic or deleted Gata3 causes a marked reduction or block at these stages and impaired β‑selection. Also marker for Th2 differentiation

increased runx leads to…

PU.1 mediated runx depletion, increased bcl11b, increased, GATA-3, increased TCF-1, and increased development speed of thymocytes

bcl11b

zinc‑finger transcription factor that is essential for T‑cell lineage commitment and for maintaining T‑cell identity throughout thymic development. Its expression is first induced at the DN2a stage and peaks around DN2b, where it shuts down stem/multipotent and alternative lineage (NK/myeloid) programs. also supports survival and β‑selection of DN3 thymocytes and then is required in DP cells for proper TCR signaling and positive selection into both CD4 and CD8 SP thymocytes

OP9-DII1:

-          TEC culture to allow culture of thymocytes and differentiation

DN3-like Scid.adh.2C2

cells that are a clonal mouse pro‑T cell line that transcriptionally and phenotypically resemble committed DN2b/DN3 thymocytes and are widely used as a fixed, culture‑adapted model of this early T‑cell stage.

Mixed chimeric artificial thymic organoid

-          allows for in culture thymus study of multiple different thymocyte types such as one with and one without a gene KO’d

pTa

-          pre-alpha chain that binds to the beta chain of the TCR to test if the beta chain of the TCR can signal properly. The pre-TCR is also invariant

absence of pTa signaling

leads to dedifferentiation of thymocytes

unusual DN4 and SP thymocytes

these populations occur when thymocytes are cultured in the absence of MHC. this subset looks more cancerous, proliferative, and dedifferentiated by upregulating myeloid programs

PreTCR/self MHC engagement

essential to coordinate phenotype with the correct transcriptional program and TCRb repertoire during early T cell development

yd T cells

-          innate-like tissue resident sentinel effector T cells with TCRs that recognize non-classical ligands (non-peptide) in an MHC or non MHC manner. These cells populate barrier sites and develop in the thymus as normal and are restricted in their Vy and Vd TCR genes used.

SLAM

-          ligand on T cells that if interact at the same time as CD1d on a CD1d APC will induce NKT cell differentiation.

E box proteins

-          E2A, HEB, can be positive and negative regulators. They drive expression of T lineage genes such as bcl11b, notch targets, rag and can promote the generation of multiple T cell subsets and lineages

id3

these proteins block E box proteins by forming inactive heterodimers, transiently reducing their DNA binding post-TCR signaling (pre-TCR for αβ, γδTCR for γδ); this "pauses" E targets for chromatin remodeling and stage advancement. Activation of this reduces TCR for ydNK T cells and allows the generation in collaboration with HEB and TCR signaling the generation of ydT17 cells

PLZF

transcription factor that drives the innate-like effector program in specific γδ T cell subsets during thymic development

Vy1vd6.3

invariant TCR expressed by NKyd T cells

trav15

-          TCR gene segment that encodes the Vd6.3

id3 role

-          regulates E2A and HEB and promotes the generation of ab and normal yd T cells by not allowing the E2A and HEB to bind to the NKyd TCR gene trav15. When the id3 is lost, increased NKyd T cells are present.

ydT17 cells

express low CD27 and low CD24, produce IL-17 and are CD44 positive

ydT1 cells

are CD73 positive, CD24 negative, produce IFNy, are CD27 positive

HEB KO

-          results in more yd T cell production and alters the TCR usage landscape and significantly reduces IL-17 positive yd T cells and diverges towards ab T cell lineage programs

MAF

-          a transcription factor essential for the differentiation and maintenance of IL-17-producing γδ T cells (Tγδ17), particularly Vγ4⁺ and Vγ6⁺ subsets, acting as a commitment factor during thymic maturation.

IELs

-          these cells are mostly CD8 T cells that are easy to activate, produce cytokines, are CD8aa+, and can be ab or yd TCR+.

Unconventional TCRyd IEL

-          these cells are CD4- CD8- and CD8aa+ and are usually TCRy7+ and express NK cell receptors. They interact with BTNLs and non-classical MHCs. These are generated in the thymus through tgfb signaling during yd TCR selection

MICA and MICB

non classical MHC that is upregulated during cellular stress

Conventional ab IEL

-          these cells are CD4 or CD8+ with the CD8aa and have diverse TCRs and are restricted to pMHC

CD8 ab IEL

-          these are type A IELs that are conventional CD8ab T cells that kill infected cells through MHC I in the epithelium in the gut. These IELs are peripherally induced.

Type b IELs

-          nonconventional CD8αα cytotoxic αβ or γδT cells and kill stressed epithelial cells. They may be activated by classical or non-classical MHC, such as MIC-A, MIC-B, and TL (Thymic leukemia antigen). They are induced in the periphery by RA and TGFb

Butyrophilin

this is a chemical released by microbes in the gut that are passed through epithelial cells and interact with yd IELs resulting in yd TCR activation

ulcerative colitis

-          chronic inflammation in the gut. It is thought to be caused by inappropriate chronic immune responses directed against mucosal antigens

inflammatory and memory like TCF1+ PD1+ yd T cells

yd T cell subset associated with ulcerative colitis

enterocyte

-          Enterocytes are specialized epithelial cells lining the small and large intestines, primarily responsible for nutrient absorption and maintaining intestinal barrier function

BTNLs

ligands expressed by epithelial cells in the gut that differer in their version of this ligand in UC vs healthy

ThPOK

master regulator of CD4⁺ T cell lineage commitment during thymic development.

ThPOK downregulation in gut CD4 T cells

this results in foxp3 downregulation and upregulation of runx3 and induces IEL phenotype

ThPOK deletion

this results in a loss of Tregs and an increase in IELs

Foxp3-cre-gfp:tdtomato mice

-          allows GFP to be expressed in a cell that ever expressed foxp3 but after tamoxifen it labels cells that are currently foxp3 to allow fate mapping of cells that once were positive or negative for foxp3

CD4 cre thpok flox

mouse to KO thpok from CD4s

OT-II cre runx3 flox

cells that cant become IELs

feed mice OVA to…

induce a gut response by transferring OT-2 cells

LCMV

infection model that can be used to study acute infection that is normally cleared or chronic infection that cant be cleared.

TOX

-          involved in the formation of exhausted T cells and during the effector differentiation response

chronic antigen exposure

this results in different states of terminal exhaustion and terminal effector cells and is a result of chronic infection or tumor

T exhausted precursor cells

these cells are TCF1+, TOX+, PD-1+ and form early during infection and regardless of if it is going to be chronic or acute infection

day 4

time point that Tpex cells develop

high affinity TCR engagement promotes…

-          generation of the tpex cells in chronic and acute infection

TCR transgenic P14 cells

-          cells with a transgenic TCR that recognizes a high affinity gp33 and low affinity gp296 antigen in LCMV

transfer of chronic ptex into acute infection

these cells downregulated canonical markers of the chronic stem-like CD8+ T cells and expressed markers (CD127 and CD62L) associated with central memory CD8+ T cells

transfer of acute ptex into chronic infection

these CD8+ T cells functioned like chronic resource cells and responded effectively to PD-1 therapy

CD28

costimulatory molecule on T cells that binds to CD80/CD86 on APCs as co-stimulation. can trogocytose its ligand as well

CTLA-4

molecule expressed by some cells to inhibit CD28 signaling generating inactivated T cells or anergic T cells by binding to B7 inhibiting CD28 binding. Method used by tumor cells to escape immune surveillance. This molecule is high on tregs and activated T cells. can trogocytose its ligand as well during TCR activation. outcompetes CD28.

trogocytosis

the ability of a cell to remove a ligand/receptor from one cell to another

method to analyze trogocytosis

-          Co-culture of jurkat T cells with fluorescent reports for ctla4 mixed with raji B cells that have a CD80 or CD86 GFP reporter to look for trogocytosis

ipiluminab

anti-CTLA-4 blocking antibody

CD28.3scFv

antibody that blocks CD28 without activating it