Antigen Presentation

Antigen Presentation

Antigen presentation is the fundamental process by which cells display peptide fragments on their surface using Major Histocompatibility Complex (MHC) molecules. This mechanism enables T cells to survey the body’s cells for signs of infection, malignancy, or damage, forming the basis for all T cell-mediated adaptive immunity.

Overview

T cells, unlike antibodies, cannot recognize free-floating antigens. They can only “see” peptide fragments bound to MHC molecules on the surface of other cells. This requirement for antigen presentation ensures that T cell responses are directed at cells that are either infected, abnormal, or have encountered pathogens—rather than at harmless extracellular proteins.

The Discovery of MHC Restriction

The principle that T cells recognize peptides only in the context of MHC molecules—known as MHC restriction—was discovered by Rolf Zinkernagel and Peter Doherty in 1974, earning them the 1996 Nobel Prize in Physiology or Medicine. Their work revealed that cytotoxic T cells could only kill virus-infected cells if both shared the same MHC alleles.

Two Pathways, Two Purposes

The immune system has evolved two distinct antigen presentation pathways, each designed to sample different cellular compartments:

MHC Class I Pathway: Endogenous Antigen Presentation

The Class I pathway monitors the intracellular protein environment, alerting the immune system to infections or cellular transformation.

Expression Pattern

MHC Class I molecules (HLA-A, -B, -C in humans) are expressed on virtually all nucleated cells. This ubiquitous expression ensures that any cell in the body can be surveyed by CD8+ T cells.

Exceptions with reduced/absent Class I:

• Red blood cells (anucleate)
• Neurons (reduced expression)
• Trophoblast cells (express non-classical HLA-G instead)
• Some tumor cells (immune evasion)

The Class I Processing Pathway

Step 1: Protein Degradation by the Proteasome

Cytosolic proteins (including viral proteins in infected cells) are degraded by the proteasome:

• 26S Proteasome: Multi-subunit protease complex
• Immunoproteasome: Variant with alternative catalytic subunits (LMP2, LMP7, MECL-1) induced by IFN-γ
• Generates peptides of 3-22 amino acids; optimal for Class I binding is 8-10 amino acids
• Immunoproteasome generates peptides with preferred C-terminal residues for MHC binding

Step 2: Peptide Transport into the ER

Peptides are transported from the cytosol into the endoplasmic reticulum by TAP (Transporter associated with Antigen Processing):

• TAP1/TAP2 heterodimer forms the transport channel
• ATP-dependent transport
• Preference for peptides of 8-16 amino acids with hydrophobic or basic C-termini
• TAP deficiency causes Bare Lymphocyte Syndrome Type I

Step 3: Peptide Loading onto MHC Class I

In the ER, peptides are loaded onto MHC Class I molecules with help from the peptide-loading complex (PLC):

Peptide Editing: Tapasin ensures that only MHC molecules loaded with high-affinity peptides are released. Suboptimally loaded MHC molecules are recycled.

Step 4: Surface Expression

Stable peptide-MHC Class I complexes:

• Exit the ER via Golgi
• Travel to the cell surface
• Display peptides for CD8+ T cell surveillance
• Half-life at surface: hours to days (depends on peptide affinity)

Clinical Significance of Class I Presentation

Viral Immune Evasion: Many viruses have evolved mechanisms to block Class I presentation:

• Herpes simplex virus (ICP47): Blocks TAP
• Cytomegalovirus (US2, US11): Targets MHC-I for degradation
• Adenovirus (E3): Retains MHC-I in ER

Cancer Immune Escape: Tumor cells frequently downregulate Class I presentation:

• Loss of MHC-I expression
• Defects in TAP, tapasin, or proteasome components
• Goal: Evade CD8+ T cell killing
• Checkpoint blockade may restore recognition

Deficiency Syndromes:

• TAP deficiency: Bare Lymphocyte Syndrome Type I; recurrent bacterial infections, bronchiectasis

MHC Class II Pathway: Exogenous Antigen Presentation

The Class II pathway samples the extracellular environment, enabling T cell responses against pathogens that don’t directly infect antigen-presenting cells.

Expression Pattern

MHC Class II molecules (HLA-DR, -DQ, -DP) are expressed primarily on professional antigen-presenting cells (APCs):

• Dendritic cells
• Macrophages
• B cells

Class II expression can be induced on other cell types by IFN-γ:

• Endothelial cells
• Epithelial cells
• Fibroblasts

This inducible expression is important in inflammatory conditions.

The Class II Processing Pathway

Step 1: Antigen Uptake

Professional APCs capture extracellular antigens through various mechanisms:

Step 2: Processing in Endosomal/Lysosomal Compartments

Internalized proteins are degraded in acidic compartments:

• Early endosomes (pH ~6.5): Initial acidification
• Late endosomes (pH ~5.5): Active processing
• Lysosomes (pH ~4.5-5.0): Extensive degradation

Proteases involved:

• Cathepsins (B, D, L, S)
• Asparagine endopeptidase (AEP)
• Generate peptides of 12-25 amino acids

Step 3: MHC Class II Assembly and Trafficking

In the ER, MHC Class II molecules are assembled with the invariant chain (Ii, CD74):

Invariant Chain Functions:

1. Blocks the peptide-binding groove (prevents premature peptide binding)
2. Trimerizes MHC Class II αβ dimers
3. Contains sorting signals for endosomal targeting
4. Protects MHC-II from degradation

Step 4: CLIP Exchange and Peptide Loading

MHC Class II-Ii complexes travel from the ER through the Golgi to endosomal compartments:

1. Ii degradation: Cathepsins progressively cleave Ii, leaving CLIP (Class II-associated Invariant chain Peptide) in the groove
2. HLA-DM function: This non-classical Class II molecule catalyzes exchange of CLIP for antigenic peptide
3. Peptide selection: HLA-DM also edits peptides, favoring high-affinity, stable complexes
4. HLA-DO modulation: In B cells and thymic epithelium, HLA-DO inhibits HLA-DM, affecting peptide selection

Step 5: Surface Expression

Peptide-loaded MHC Class II molecules:

• Travel to the cell surface
• Present peptides to CD4+ T cells
• Half-life at surface depends on peptide affinity
• Recycling occurs through endosomal pathway

Clinical Significance of Class II Presentation

Autoimmune Disease Associations: MHC Class II alleles show the strongest genetic associations with autoimmune diseases:

Deficiency Syndromes:

• Bare Lymphocyte Syndrome Type II: Defects in Class II transcription factors (CIITA, RFX complex); absence of CD4+ T cells, severe immunodeficiency

Professional Antigen-Presenting Cells

Three cell types are considered “professional” APCs due to their constitutive Class II expression and specialized antigen presentation capabilities:

Dendritic Cells (DCs)

The most potent APCs for initiating primary immune responses.

Immature DCs (in tissues):

• High endocytic/phagocytic capacity
• Low surface MHC and costimulatory molecules
• Constantly sampling the environment

Mature DCs (after antigen encounter):

• Reduced antigen uptake
• High surface MHC-II and costimulatory molecules (CD80, CD86)
• Migrate to lymph nodes via lymphatics
• Highly effective at activating naive T cells

DC Subsets:

Macrophages

Tissue-resident professional phagocytes.

• Efficient at antigen uptake and processing
• Present antigens to effector/memory T cells
• Less efficient at priming naive T cells than DCs
• Important for sustaining local immune responses
• Polarize into M1 (inflammatory) or M2 (regulatory) phenotypes

B Cells

Present antigens captured by their BCR.

• Highly efficient at presenting their cognate antigen (via BCR)
• Important for germinal center reactions (receiving T cell help)
• Can present to naive T cells under some conditions
• Unique: present the same antigen that activates them

Cross-Presentation

Cross-presentation is the ability to present exogenous antigens on MHC Class I molecules—a specialized function that bridges the two classical pathways.

Why Cross-Presentation Matters

Classical pathways create a problem:

• Intracellular pathogens that don’t infect APCs wouldn’t activate CD8+ T cells
• Tumor antigens might not reach APCs

Cross-presentation solves this by allowing DCs to:

• Take up exogenous antigens (dead cells, secreted proteins)
• Present them on Class I
• Prime CD8+ T cell responses against targets they never directly “infected”

Cross-Presenting Cells

cDC1 subset is most efficient at cross-presentation:

• Express DNGR-1 (CLEC9A) for dead cell recognition
• Have specialized endosomal machinery
• Critical for anti-tumor immunity
• Required for CD8+ T cell responses to many pathogens

Mechanisms of Cross-Presentation

Cytosolic Pathway:

1. Antigens escape from endosomes to cytosol
2. Degraded by proteasome
3. Peptides transported by TAP
4. Loaded onto MHC-I in ER (conventional pathway)

Vacuolar Pathway:

1. Processing occurs entirely within endosomal compartments
2. Class I molecules recruited to endosomes
3. Peptide loading occurs in endosomes
4. TAP-independent

Clinical Applications

Cross-presentation is a key target for:

• Cancer vaccines (deliver tumor antigens to cDC1s)
• Viral vaccines (induce CD8+ T cell responses)
• Immunotherapy strategies

The Immunological Synapse

When a T cell recognizes its cognate peptide-MHC complex, an immunological synapse forms—a highly organized interface between the T cell and APC.

Synapse Structure

The mature immunological synapse has a “bull’s-eye” organization:

Three Signals for T Cell Activation

Full T cell activation requires integration of three signals:

Signal 1: TCR Recognition

• TCR binds peptide-MHC
• CD4 or CD8 coreceptor stabilizes interaction
• Provides specificity

Signal 2: Costimulation

• CD28 on T cell binds CD80/CD86 on APC
• Provides “go” signal
• Without Signal 2, T cells become anergic (tolerant)

Signal 3: Cytokine Polarization

• Cytokines from APC direct T cell differentiation
• IL-12 → Th1
• IL-4 → Th2
• TGF-β + IL-6 → Th17
• TGF-β + IL-2 → Treg

Costimulatory and Coinhibitory Molecules

Costimulatory Molecules (Activating)

Coinhibitory Molecules (Checkpoints)

Immune Checkpoint Blockade

Antibodies blocking CTLA-4 or PD-1/PD-L1 are revolutionary cancer immunotherapies:

• Anti-CTLA-4 (ipilimumab): Enhances initial T cell activation
• Anti-PD-1 (nivolumab, pembrolizumab): Releases exhausted T cells
• Anti-PD-L1 (atezolizumab): Similar to anti-PD-1

These therapies work by “releasing the brakes” on T cell responses against tumors.

Key Concepts

1. Antigen presentation is required for T cell recognition—T cells cannot see free antigens

2. MHC Class I presents endogenous (intracellular) peptides to CD8+ T cells; expressed on all nucleated cells

3. MHC Class II presents exogenous (extracellular) peptides to CD4+ T cells; primarily on professional APCs

4. Cross-presentation allows exogenous antigens to be presented on Class I, enabling CD8+ responses to extracellular pathogens and tumors

5. Dendritic cells are the most potent APCs for initiating primary immune responses

6. Three signals (TCR recognition, costimulation, cytokines) are required for full T cell activation

7. Checkpoint molecules regulate T cell responses; their blockade is a powerful cancer therapy

Related Articles

• HLA System — Detailed coverage of human MHC genes
• T Cell Receptor Structure — How TCRs recognize peptide-MHC
• T Cell Development — How T cells learn MHC restriction
• Immune Tolerance — Preventing responses to self
• Immune Memory — Long-term protection

References

1. Blum JS, et al. (2013). Pathways of antigen processing. Annual Review of Immunology, 31:443-473.

2. Neefjes J, et al. (2011). Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nature Reviews Immunology, 11:823-836.

3. Joffre OP, et al. (2012). Cross-presentation by dendritic cells. Nature Reviews Immunology, 12:557-569.

4. Chen L, Flies DB. (2013). Molecular mechanisms of T cell co-stimulation and co-inhibition. Nature Reviews Immunology, 13:227-242.