Immune Tolerance

Immune Tolerance

Immune tolerance encompasses the mechanisms by which the adaptive immune system avoids mounting destructive responses against the body’s own tissues. Failure of tolerance results in autoimmune disease—conditions where T cells and/or antibodies attack self-antigens, causing chronic inflammation and tissue damage.

Overview

The adaptive immune system faces a fundamental paradox: it must generate enormous receptor diversity to recognize any possible pathogen, yet this same diversity inevitably produces receptors capable of recognizing self-tissues. Evolution has addressed this challenge through multiple overlapping tolerance mechanisms that eliminate or control potentially dangerous autoreactive lymphocytes.

Two Levels of Tolerance

These complementary systems provide multiple checkpoints to ensure self-tolerance while preserving the ability to respond to foreign antigens.

Central Tolerance

T Cell Central Tolerance in the Thymus

The thymus is where developing T cells learn the critical distinction between self and non-self—a process that eliminates most thymocytes before they ever reach the periphery.

Positive Selection (Thymic Cortex)

Purpose: Ensure T cells can functionally interact with self-MHC molecules

Process:

1. Double-positive (CD4+CD8+) thymocytes express newly rearranged TCRs
2. TCRs are tested against self-peptide-MHC on cortical thymic epithelial cells (cTECs)
3. Low-to-moderate affinity binding → survival signal
4. No binding → death by neglect (fail to receive survival signal)

Outcome: ~95% of thymocytes die at this stage because their randomly generated TCRs cannot productively engage self-MHC

Result: Surviving T cells are MHC-restricted—they can only recognize antigens presented by self-MHC molecules

Negative Selection (Thymic Medulla)

Purpose: Eliminate T cells that react too strongly to self-antigens

Process:

1. Single-positive thymocytes migrate to the medulla
2. TCRs are tested against diverse self-peptides presented by:
   • Medullary thymic epithelial cells (mTECs)
   • Thymic dendritic cells
   • B cells
3. High-affinity binding → clonal deletion (apoptosis)
4. Moderate affinity → potential Treg development
5. Low affinity → survival and export

The Affinity Model:

TCR Signal Strength:
None ────────────────────────────────────────── Very Strong
  │                    │                    │
Death by           Survival             Clonal
neglect         (positive selection)   deletion
                     │
              [Regulatory T cell
               development window]

AIRE and Tissue-Restricted Antigens

A critical problem: How can the thymus test T cells against antigens normally expressed only in specific peripheral tissues (like insulin in the pancreas or thyroglobulin in the thyroid)?

The Solution: AIRE (Autoimmune Regulator)

AIRE allows mTECs to express a remarkable sampling of tissue-specific proteins—effectively creating a “mirror” of peripheral self within the thymus.

AIRE Deficiency: APECED

• Autoimmune PolyEndocrinopathy-Candidiasis-Ectodermal Dystrophy
• Also called APS-1 (Autoimmune Polyglandular Syndrome Type 1)
• Mutations in AIRE gene
• Patients develop multiple autoimmune conditions: hypoparathyroidism, adrenal insufficiency, mucocutaneous candidiasis
• Demonstrates the essential role of central tolerance

Regulatory T Cell Development

Not all self-reactive thymocytes are deleted. Some with intermediate TCR signaling are diverted into the regulatory T cell (Treg) lineage:

Development Requirements:

• TCR signal strength between that causing survival and deletion
• CD28 costimulation
• IL-2 signaling
• Upregulation of FOXP3 (master Treg transcription factor)

Thymic Tregs (tTregs or nTregs):

• Exit thymus as CD4+ CD25+ FOXP3+ cells
• Self-reactive TCR repertoire
• Suppress autoreactive responses in periphery
• Essential for maintaining tolerance throughout life

B Cell Central Tolerance in the Bone Marrow

Developing B cells are tested against self-antigens in the bone marrow microenvironment.

Outcomes Based on Self-Antigen Encounter

Receptor Editing

A remarkable salvage mechanism unique to B cells:

1. Autoreactive immature B cell receives strong BCR signal
2. RAG genes are reactivated
3. New light chain V-J rearrangement occurs
4. Replaces the original autoreactive light chain
5. If new BCR is no longer autoreactive → survival
6. If still autoreactive → further editing attempts or deletion

Significance: An estimated 25-50% of mature B cells show evidence of receptor editing, indicating how common autoreactive initial rearrangements are

Comparison: T Cell vs. B Cell Central Tolerance

Peripheral Tolerance

Despite central tolerance, some autoreactive lymphocytes escape to the periphery. Multiple backup mechanisms provide additional protection.

Immunological Ignorance

Definition: Autoreactive cells exist but never encounter their cognate antigen

Conditions Enabling Ignorance:

• Antigen in immunologically privileged sites (eye, brain, testes)
• Antigen expressed at very low levels
• Antigen sequestered behind physical barriers
• Antigen not drained to lymphoid organs

Breaking Ignorance:

• Tissue damage releases sequestered antigens
• Inflammation increases antigen presentation
• Breakdown of blood-tissue barriers
• Can trigger autoimmune responses (e.g., sympathetic ophthalmia after eye injury)

Anergy

Definition: Functional unresponsiveness despite antigen recognition—lymphocytes are present but cannot respond effectively.

T Cell Anergy

Induction: Occurs when T cells receive Signal 1 (TCR engagement) without Signal 2 (costimulation)

TCR signal + CD28 costimulation → Full activation
TCR signal alone → Anergy

Mechanisms:

• Failure to produce IL-2
• Upregulation of inhibitory receptors (CTLA-4, PD-1)
• Altered signaling pathways
• Epigenetic modifications

Characteristics of Anergic T Cells:

• Do not proliferate upon restimulation
• Cannot provide help
• Upregulate E3 ubiquitin ligases (GRAIL, Cbl-b)
• May persist but are functionally silenced

B Cell Anergy

Induction: Chronic exposure to soluble self-antigen

Characteristics:

• Reduced surface IgM expression (IgD may be retained)
• Short lifespan
• Excluded from lymphoid follicles
• Cannot respond to T cell help
• Compete poorly with normal B cells

Regulatory T Cells (Tregs)

The most active mechanism of peripheral tolerance.

Tregs continuously suppress potentially autoreactive lymphocytes in the periphery.

Treg Types

Treg Phenotype

Core markers:

• CD4+ CD25high FOXP3+
• CD127 (IL-7Rα) low
• High CTLA-4 expression
• High GITR expression
• CD45RA (naive) or CD45RO (memory) subsets

FOXP3: The master transcription factor that defines and maintains Treg identity

Treg Suppression Mechanisms

IPEX Syndrome

Immune dysregulation, Polyendocrinopathy, Enteropathy, X-linked

IPEX dramatically demonstrates the essential role of Tregs in maintaining tolerance.

Peripheral Deletion

Chronically stimulated autoreactive T cells can undergo activation-induced cell death (AICD):

Mechanism:

• Repeated TCR stimulation
• Upregulation of FasL (CD95L)
• Fas-FasL interaction triggers apoptosis
• Also involves Bim (BH3-only protein)

Purpose:

• Limits duration of immune responses
• Eliminates chronically activated (potentially autoreactive) cells
• Contributes to contraction phase after infection

Immune Privilege

Certain tissues actively suppress immune responses to protect critical structures from inflammatory damage:

Tolerance vs. Autoimmunity

Factors Maintaining Tolerance

Factors Breaking Tolerance

The Danger Hypothesis

Proposed by Polly Matzinger: The immune system responds not simply to “non-self” but to danger signals indicating tissue damage or pathogen presence:

• Damaged cells release DAMPs (damage-associated molecular patterns)
• DAMPs activate APCs and promote costimulation
• This may explain why self-antigen exposure during inflammation can break tolerance
• Complements classical self/non-self model

Therapeutic Implications

Enhancing Tolerance (Autoimmunity Treatment)

Breaking Tolerance (Cancer Immunotherapy)

The Tolerance-Cancer Trade-off: Cancer immunotherapy deliberately breaks tolerance to tumor antigens. The consequence: immune-related adverse events (irAEs)—essentially iatrogenic autoimmunity affecting:

• Skin (dermatitis)
• Gut (colitis)
• Liver (hepatitis)
• Endocrine organs (thyroiditis, hypophysitis)
• Rarely: myocarditis, nephritis, neurological events

Measuring Tolerance

Clinical Assessments

Research Tools

• Tetramers: Detect self-antigen-specific T cells by frequency
• TCR sequencing: Identify autoreactive clonotypes
• Single-cell analysis: Characterize autoreactive cells
• Mouse models: Transgenic TCR, tolerance induction protocols

Key Concepts

1. Central tolerance eliminates or converts autoreactive lymphocytes during development in thymus (T cells) and bone marrow (B cells)

2. AIRE enables thymic expression of tissue-restricted antigens, allowing deletion of autoreactive T cells; its absence causes multi-organ autoimmunity

3. Peripheral tolerance provides backup through ignorance, anergy, Treg suppression, and deletion

4. Regulatory T cells are essential for maintaining tolerance; FOXP3 mutations (IPEX) cause fatal autoimmunity

5. Multiple overlapping mechanisms ensure tolerance is robust, but genetic and environmental factors can break it

6. Cancer immunotherapy deliberately breaks tolerance to tumors, but immune-related adverse events reflect the cost of this approach

Related Articles

• T Cell Development — Thymic selection and tolerance
• B Cell Development — Bone marrow tolerance checkpoints
• HLA System — MHC and autoimmune disease associations
• Immune Repertoire — Repertoire composition and autoreactivity
• Germinal Centers — Where SHM can generate autoreactivity

References

1. Klein L, et al. (2014). Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nature Reviews Immunology, 14:377-391.

2. Sakaguchi S, et al. (2020). Regulatory T cells: how do they suppress immune responses? International Immunology, 21:1105-1111.

3. Nemazee D. (2017). Mechanisms of central tolerance for B cells. Nature Reviews Immunology, 17:281-294.

4. Anderson MS, et al. (2002). Projection of an immunological self shadow within the thymus by the Aire protein. Science, 298:1395-1401.