B and T cell tolerance

What are the two checkpoints of tolerance, and why are both needed?

• The first checkpoint is central tolerance, which happens where lymphocytes are generated: the thymus for T cells and the bone marrow for B cells. Here the goal is to eliminate self-reactive cells before they leave.

• The second checkpoint is peripheral tolerance, which happens in peripheral organs such as the spleen, lymph nodes and tissues. It is needed because the central checkpoint is not perfect: some self-reactive T or B cells slip through to the periphery, so further control mechanisms are required there.

How does the thymus use positive and negative selection to control self-reactive T cells?

During T cell development in the thymus, the TCR specificity is generated through many random rearrangements, so some T cells will recognize self-antigens. Positive selection happens in the thymic cortex, where T cells interact with cortical epithelial cells. T cells that bind self-peptide-MHC with adequate affinity receive survival signals and are "trained" and eligible for function, becoming CD4 or CD8 single-positive. Negative selection is the test that follows, where T cells are exposed to self-antigens (regulated by the transcription factor AIRE) presented via MHC. If they bind too strongly, they fail the exam and undergo deletion by apoptosis. A third outcome: cells that bind with medium strength can escape deletion and become thymic regulatory T cells (tTregs).

What are the four peripheral mechanisms that control self-reactive T cells that escaped the thymus?

Self-reactive conventional T cells that reach the periphery can be controlled in four ways.

(1) Ignorance: the self-antigen is present in too low an amount or with too low affinity to activate the TCR. T cells are separated from the antigens that can activate them (e.g., by the blood–brain barrier).

(2) Deletion:

1. Death by Neglect: T cells die when they are outcompeted for essential growth factors (like IL-2) by surrounding activated cells.

3. Chronic TCR Stimulation: Because self-antigens are never cleared, repetitive TCR signaling constantly upregulates Fas/FasL, driving AICD to remove persistent autoreactive T cells.

4. High-Affinity Deletion: Self-antigens that bind to the TCR too strongly directly trigger intracellular apoptotic pathways to eliminate dangerous clones.

AICD (Fas/FasL): Activated T cells express both Fas and FasL; their interaction triggers cell suicide (apoptosis). Thsi is how apoptosis works.

(3) Inhibition:

1. Lack of Co-stimulation (Signal 2 Deficiency) Anergy

When antigen presentation occurs without co-stimulatory signals, T cells enter a state of functional unresponsiveness termed anergy. In this state, the T cell cannot produce IL-2 and fails to achieve full activation.

2. Upregulation of Inhibitory Receptors

To actively block T cell activation, inhibitory co-stimulatory molecules such as CTLA-4 and PD-1 are expressed. CTLA-4 outcompetes CD28 for B7 binding, while PD-1 delivers inhibitory signals that shut down downstream TCR pathways.

Anergy and inhibition are commonly triggered by chronic antigenic stimulation (e.g., persistent exposure to self-antigens or high systemic doses of soluble protein antigens) or presentation by non-activated, resting antigen-presenting cells (APCs).

(4) Suppression: the cell is converted into a regulatory T cell by the cytokine environment. The overall aim is to keep the self-reactive T cell from becoming activated.

How are peripherally induced FoxP3+ Tregs generated, and how do they suppress the immune response?

When naive T cells in the body encounter self-antigens, the surrounding chemical environment can transform them into induced regulatory T cells (iTregs).

The main trigger for this change is TGF-$\beta$, a signaling protein made by surrounding tissue and epithelial cells. TGF-$\beta$ turns on the master gene FoxP3, which officially converts the cell into a regulatory T cell. At the same time, the T cell needs IL-2 to survive and multiply. Another signal, IL-10, plays a smaller supporting role during this conversion—its main job comes later, when the Treg uses it as a tool to calm down inflammation.

Once converted, these induced Tregs work to stop autoimmune attacks using four main suppression mechanisms:

(1) blocking costimulation (indirect suppression) through inhibitory molecules. Normally, T cell activation needs a second signal: CD28 on the T cell binds CD80/CD86 on the antigen-presenting cell. Induced Tregs disrupt this by using inhibitory molecules such as CTLA-4 (and PD-1 binding PD-L1) to take the place of CD28 binding. Because this activating signal is blocked, no IL-2 is produced, so the T cell cannot survive or proliferate. When this inhibitory interaction happens between the T cell and a dendritic cell, the dendritic cell also produces metabolites (IDO) that have an inhibitory effect on effector T cells. Together, these effects create a tolerogenic, anti-inflammatory environment.

(2) converting extracellular ATP into anti-inflammatory adenosine using their cell surface enzymes which then it binds receptors on other cells and induces anti-inflammatory reactions, which dampens inflammation.

(3) sequestering IL-2 with their high CD25 expression, so nearby T cells lack survival signals

(4) directly killing effector T cells through perforin and granzyme granules that trigger apoptosis.

What are Tr1 cells, and how do they suppress inflammation?

Tr1 cells are a type of regulatory T cells that are FoxP3⁻. They develop in the periphery during chronic antigen exposure, especially in an IL-10-rich environment, and their development is further promoted by IL-27. They mainly suppress immune responses by secreting high levels of IL-10, an anti-inflammatory cytokine. IL-10 inhibits APC function and reduces the activation, proliferation, and survival of pro-inflammatory effector cells, such as Th1 cells. This helps control the immune response and prevent excessive tissue inflammation.

How do B cells achieve central and peripheral tolerance?

B cells develop in the bone marrow, so central tolerance happens there, and peripheral tolerance happens in the spleen. In the bone marrow, a B cell that binds a self-antigen strongly first attempts receptor editing, changing its BCR to a non-self-reactive one. If receptor editing does not work, the cell undergoes deletion by apoptosis. Some B cells become anergic (unresponsive) when the antigen is present in low amounts. In the periphery, the same logic applies: strong self-antigen binding causes deletion; weak binding or low antigen leads to anergy or ignorance; and if naive B cells that recognize self-antigen require co-stimulation from helper T cells. If they encounter anergic T cells (or receive no T-cell help), they fail to receive survival signals (CD40/CD40L interaction and cytokines), inducing B-cell anergy and subsequent apoptosis due to growth factor starvation.