immuno lect 6 revised

What is the limitation of innate recognition?

Innate cells only recognize surface molecules that are common to many pathogens and conserved over evolution. Microbes evolve faster than hosts and often evade innate cells.

What advantage does the adaptive immune system add?

It can recognize an almost infinite array of antigens, so each pathogen can be targeted specifically

What happens when a BCR or TCR binds its specific antigen?

The cell is activated, proliferates, and differentiates

How many antigen specificities does each lymphocyte have, and how many different TCRs do humans have?

One specificity per lymphocyte; more than 10⁸ different TCRs in humans

Give examples of tailored lymphocyte functions.

Different types of T helper effector cells, cytotoxic T cells, different types of antibodies

What is the structure of the TCR?

A transmembrane heterodimer of α + β chains (αβ T cells) or γ + δ chains (γδ T cells). The extracellular variable regions contain the antigen-binding site.

What is CD3, and what does it do?

Four transmembrane polypeptides (γ, δ, ε, ζ chains) complexed with the TCR. It doesn’t bind ligand, but it’s essential for intracellular signaling to activate the T cell.

Which co-receptors associate with the TCR?

CD4 or CD8 (except in γδ T cells)

What do CD4 and CD8 bind?

CD4 binds MHC class II. CD8 binds MHC class I.

In which cells does antigen receptor gene rearrangement occur?

Only in T and B lymphocytes during their development

Which enzymes are required for V(D)J rearrangement?

RAG1 and RAG2 (recombination activating genes)

Is gene rearrangement driven by antigen?

No. It happens independently of antigen, so receptors aren’t generated in response to antigen.

What gene segments make up the germline TCR genes?

V (variable), D (diversity), J (joining), C (constant). Each species has its own number of each.

What does a functional rearranged TCR gene contain?

One of each segment: VJC or VDJC

How is the β chain rearranged?

D joins J, then the DJ joins a V, giving a new VDJ segment

How is the α chain rearranged?

V joins J directly, giving a new VJ segment

Define combinatorial diversity and junctional diversity.

Combinatorial: random joining of different V, (D), J segments. Junctional: random nucleotides added or removed between segments during joining.

What process repairs the V(D)J junctions, and why is it “intentionally sloppy”?

Non-homologous DNA end joining. Random additions, annealing, and repair make thousands of possible sequences per junction.

What does defective V(D)J recombination cause?

Severe combined immunodeficiency (SCID), from DNA-PKcs defects or RAG deficiency

Which animals get SCID, and from which defect?

Jack Russell Terriers (DNA-PKcs), Arabian horses (DNA-PKcs), various knockout/mutant mice, and humans (DNA-PKcs, RAG defects, and others)

What happens first in a double-negative (CD25⁺) thymocyte?

TCRβ gene rearrangement (up to four tries). The β chain pairs with pre-Tα (a surrogate α chain) and is expressed with CD3.

What happens after a successful pre-TCR is expressed?

β rearrangement stops, the cells proliferate, CD4 and CD8 are expressed (double positive), and TCRα rearranges (multiple tries)

When is a thymocyte ready for selection?

When a functional α chain pairs efficiently with the β chain, giving a CD3-low CD4⁺CD8⁺ thymocyte

What four outcomes can random TCR rearrangement produce?

Nonsense (no receptor), non-functional TCRs (useless), self-reactive TCRs (dangerous), non-self-reactive TCRs (good)

What does a double-positive T cell express?

TCR with CD3, plus both CD4 and CD8

Where does positive selection happen, and with which cells?

In the thymic cortex, with cortical thymic epithelial cells that express MHC I and MHC II

What happens to DP thymocytes that do or don’t interact with MHC–peptide in the cortex?

Those that interact get survival signals. Those that don’t die by apoptosis (up to 96%).

How does positive selection determine CD4 vs. CD8?

Cells that bind MHC I lose CD4 and become CD8⁺. Cells that bind MHC II lose CD8 and become CD4⁺.

What two things does positive selection accomplish?

It determines CD4 or CD8 expression and eliminates non-functional TCRs

Where does negative selection happen, and what makes it possible?

In the thymic medulla. Medullary thymic epithelial cells express many proteins normally found in other tissues, and medullary APCs present those peptides.

What happens to a thymocyte that binds self-peptide too strongly?

It’s negatively selected and dies

What is central tolerance?

Destruction of self-reactive thymocytes in the thymus (negative selection)

What is the outcome of very high affinity for self-peptide–MHC?

Apoptosis, i.e., negative selection (removal of self-reactive T cells)

What is the outcome of higher (but not very high) affinity?

Positive selection with activation of IL-2Rα (CD25) and FOXP3, leading to differentiation into Tregs

What is the outcome of lower affinity?

Positive selection and differentiation into effector T cells (Teff)

What is the outcome of very low affinity?

No survival signal, so apoptosis (“death by neglect”)

Why are Tregs still needed after thymic selection?

Some Teff cells keep self-reactivity and can cause autoimmunity or alloreactive responses (pregnancy, organ or stem cell transplant). Tregs limit these responses.

Where do Tregs come from?

A subset of self-reactive thymocytes that survive and differentiate into Tregs

What do Tregs do?

They’re immunosuppressive T cells that help prevent autoimmune responses in the periphery

Define peripheral tolerance.

Mechanisms outside the primary lymphoid organs that prevent immune responses against self or harmless material (food, commensals). Tregs are one example.

How common are γδ T cells?

A small fraction of T cells in most mammals, but the majority in ruminants and chickens

Do γδ T cells express CD4 or CD8?

no

What determines whether a double-negative thymocyte becomes a γδ T cell?

Whether γ and δ rearrange before TCRβ. A cell can’t express both: TCRδ is deleted when TCRα rearranges.

How does antigen recognition by γδ T cells differ from αβ T cells?

They don’t require MHC–antigen and can recognize unprocessed antigen without MHC

What are the other features of γδ T cells?

Often mucosa-associated; less diverse repertoire (few V gene segments); cytotoxic function similar to CD8⁺ T cells

What three signals does T cell activation and differentiation require?

Signal 1: antigen. Signal 2: co-stimulation. Signal 3: cytokines.

Where do naïve T cells go after leaving the thymus, and what can activate them?

They migrate to lymph nodes. Only an APC (almost always a DC) presenting their specific antigen can activate them.

What is signal 1, and is it enough on its own?

TCR binding MHC–antigen. It’s not sufficient by itself.

Where do antigens for signal 1 come from?

Microbial proteins (bacteria, parasites, viruses) and tumor antigens (ectopic expression)

How are antigens presented to CD4 vs. CD8 T cells?

CD4: extracellular antigen is endocytosed and presented on MHC II. CD8: cytosolic antigen is presented on MHC I. DCs can also cross-present extracellular antigen to CD8 T cells, which is important for tumors and viruses.

What is signal 2?

Co-stimulation: CD80/86 (B7) on the APC binding CD28 on the T cell

When do APCs express high levels of CD80/86?

Only when activated by cytokines, pathogens, or T cells (“danger signals”). Otherwise expression is low.

What happens if a naïve T cell gets signal 1 without signal 2?

Apoptosis or anergy (non-responsiveness). This is a check against self-reactivity that helps maintain peripheral tolerance.

What provides signal 3, and what does it determine?

Cytokines in the environment or from the APC. They provide context and determine the T cell phenotype (Th1, Th2, etc.).

How does IL-2 receptor expression change on activation?

Naïve T cells express a low-affinity IL-2R. After signals 1 and 2 they express a high-affinity IL-2R and start secreting IL-2.

What does IL-2 binding to the high-affinity receptor do?

Induces T cell proliferation

Which cell delivers all three signals to prime naïve T cells?

The activated dendritic cell (antigen on MHC, co-stimulation, cytokines)

What happens in the lymph node during T cell activation?

The DC presents specific peptide and provides co-stimulation, triggering naïve T cell proliferation and differentiation. T cell IL-2 drives autocrine proliferation.

What do activated CD8 and CD4 T cells do in the periphery?

Local immune responses direct them to the infection site. CD8: recognize peptide on MHC I on infected cells and kill them. CD4: recognize peptide on MHC II on macrophages and other APCs and provide help through cytokines and co-stimulatory molecules.

Define clonal expansion.

Preferential proliferation of antigen-specific lymphocytes

Why is there little bystander proliferation?

Antigen-specific T cells both produce IL-2 and preferentially respond to it

How much do CD8⁺ T cells expand after antigen?

From 1 in 10⁵–10⁶ to 1 in 3–10, about 50,000-fold

How much do CD4⁺ T cells expand after antigen?

From 1 in 10⁵–10⁶ to 1 in 10³–10⁴, about 100-fold

What do antigen-specific T cells do after clonal expansion?

They leave the lymph node and go to the tissues to fight

What is a Th0 cell?

A naïve helper T cell

What determines which type of Th cell a naïve CD4 T cell becomes?

Cytokines released by APCs (signal 3). The nature of the innate response determines which cytokines are secreted.

What are the most common Th subsets?

Th1, Th2, Th17, Tfh (T follicular helper), Treg

Which cytokines drive Th1 differentiation? What is the Th1 master transcription factor, what does it produce, and what does it defend against?

Driven by IFN-γ and IL-12. Master factor T-bet. Produces IFN-γ and TNF. Defends against intracellular pathogens.

Which cytokine drives Th2 differentiation? What is its master transcription factor, what does it produce, and what does it handle?

Driven by IL-4. Master factor GATA3. Produces IL-4, IL-5, IL-6, IL-13. Involved in allergy and asthma, and controls parasites and extracellular pathogens.

Which cytokines drive Th17 differentiation? What is its master transcription factor, and what does it produce?

Driven by TGF-β plus IL-6. Master factor RORγt. Produces IL-17A, IL-17F, IL-21, IL-22. Involved in pathogen defense, autoimmunity, transplant rejection, and cancer.

Which cytokine drives Treg differentiation? What is its master transcription factor, and what does it produce?

Driven by TGF-β. Master factor Foxp3. Produces TGF-β and IL-10. Maintains immune homeostasis and tolerance.

Which cytokines drive Tfh differentiation, what is its master transcription factor, and what does it do?

Driven by IL-6 and IL-21. Master factor Bcl6. Expresses CXCR5. Helps germinal center B cells make antibody (affinity maturation, class switching).

Which cytokines do Th1 cells produce, and which pathogens do they target?

IFN-γ and TNF-β; intracellular pathogens

What does IFN-γ from Th1 cells do?

Activates macrophages for enhanced microbial killing, and enhances B cell proliferation and differentiation (opsonizing antibodies)

What does TNF-β from Th1 cells do?

Activates macrophages for enhanced microbial killing, and enhances B cell proliferation and differentiation (opsonizing antibodies)

What does TNF-β from Th1 cells do?

Helps kill chronically infected cells, releasing bacteria for macrophages to destroy; can induce macrophages to leave blood vessels at the infection site

What do Th2 cells target?

Parasites and extracellular pathogens. They’re also involved in allergy and asthma.

What does IL-4 from Th2 cells do?

Induces B cell differentiation into neutralizing IgG and IgE (IgE induces mast cell degranulation)

What does IL-5 from Th2 cells do?

Stimulates eosinophil activation

What do Th17 cells do?

Drive inflammation against bacteria, fungi, and parasites. IL-17 attracts neutrophils and macrophages and synergizes with other cytokines to augment inflammation. Different Th17 subsets have different functions, and some can be immunosuppressive.

How do Tregs use IL-2 to suppress responses?

They constitutively express CD25 (high-affinity IL-2R) and bind and deplete IL-2, so less is available to effector T cells

How do Tregs use CTLA-4?

CTLA-4 binds CD80/86 on APCs, transmitting suppressive signals and sequestering co-stimulatory molecules, which disrupts Teff priming and activation

Which immunosuppressive cytokines do Tregs produce?

IL-10, IL-35, and TGF-β, which downregulate APCs and Teff cells

How do Tregs use ATP to suppress responses?

They release ATP, which is converted to adenosine. Adenosine sends suppressive signals to Teff cells and APCs through the A2A receptor.

What do Tfh cells do, and where do they work?

They’re associated with germinal center reactions in lymph nodes. They help B cells become plasma cells and provide signals for affinity maturation and class switching.

How do CD8 T cells differ from CD4 T cells in activation requirements?

Naïve CD8 cells need more co-stimulation (a higher activation threshold). DCs with high co-stimulatory molecule levels are sometimes enough; otherwise they need CD4 help.

Where can IL-2 for CD8 activation come from?

The APC, CD4⁺ T cells, or CD8⁺ T cells

Do activated CD8 T cells kill the APC that primed them?

No. The priming APC is not killed.

How do CD8 T cells kill using cytotoxic granules?

Perforin forms a pore, and granzyme enters and induces apoptosis

How do CD8 T cells kill using Fas/FasL?

Activated CTLs express FasL, which binds the death receptor Fas on the target cell. Fas ligation activates caspases, causing apoptosis.

What fraction of effector T cells become memory cells, and how long do they last?

5–10%. They can persist for years or a lifetime, giving long-lasting protection.

Why do vaccines aim to generate memory, and what is required for it?

Memory gives long-lasting protection against previously encountered microbes. Generating memory requires CD4 T cell help.

Why does the T cell response contract after antigen is cleared?

The innate response abates, co-stimulation and IL-2 decrease, and anti-apoptotic proteins drop. Most activated cells die and new activation declines.

Define homeostasis.

Literally “standing still”: the mechanisms by which biological systems maintain stability

How do T cells die during contraction?

By apoptosis: through neglect (lack of antigen stimulation) or negative signaling (e.g., CTLA-4, PD-1)

How much of the expanded T cell population is deleted during contraction, and what remains?

About 95% is deleted. About 1/10 of CD8⁺ and 1/100–1/1000 of CD4⁺ T cells remain as memory.