MHC & Antigen Presentation – Comprehensive Notes

Page 1

• Topic & Source: “MHC and Antigen Presentation,” based on Abbas et al., Chapter 6 (pp. 123-149) & Chapter 16 (pp. 370-371)
• Course Placement: Immunology Block 1, Class 11, 08 Apr 2024
• Instructor: Kaushlendra Tripathi, MS PhD, VCOM-Carolinas (ktripathi@carolinas.vcom.edu)
• Time Stamp of Slides: 08 May 2025

Page 2 – Learning Objectives

1. Define both minor & major histocompatibility complexes (MHC/HLA).

2. Differentiate types, localization, structures, functions of MHC.

3. Explain MHC restriction & its significance in immunity.

4. Identify cell types expressing MHC-I vs MHC-II.

5. Relate codominant expression & gene polymorphism to population survival.

6. Trace exogenous (extracellular) pathway ⇒ MHC-II presentation.

7. Trace endogenous (intracellular) pathway ⇒ MHC-I presentation.

8. Compare alternative routes: cross-alignment, cross-presentation, cross-dressing, CD1 (lipid) & glycoprotein pathways.

9. Show why MHC-I & MHC-II presentation is critical for adaptive activation.

10. Define superantigens & clinical impact.

Page 3 – Immune Overview & What to Know

• Innate mechanisms: phagocytosis (neutrophils, macrophages, DCs), complement MAC, Ab-mediated neutralization.
• Adaptive roles: Helper T (cytokine release), Cytotoxic T (CTL), Regulatory T.
• Keys for exam:
– HLA/MHC structure & properties
– Antigen processing/presentation (classic & alternative)
– Clinical relevance: MHC in health/disease
• Essential question: How do T cells identify microbes/foreign proteins? Answer = via peptide–MHC complexes on APCs.

Page 4 – Dendritic Cell (DC) Lifecycle & Specialization

A. Sequence in peripheral tissues → lymph node:

1. Antigen capture by skin/tissue DCs (e.g., Langerhans).

2. DC activation (↑B7, ICAM-1, IL-12, class II MHC).

3. Migration via afferent lymphatics to T-cell zone.

4. Antigen presentation to naïve T cells.
   B. Phenotypic shifts:
   – Resting DC: many Fc & mannose receptors, low class II, short half-life ≈ $10\text{ h}$, ≈$10^6$ surface molecules.
   – Activated DC: ↓FcR, ↑co-stims/B7/ICAM-1, high class II, long half-life > $100\text{ h}$, ≈$7\times10^6$ surface molecules.

Page 5 – T-Cell Peptide Recognition Pipeline

• Microbe → innate uptake (macrophage/B/ DC).
• DC degrades proteins → pathogen-specific peptides delivered to surface.
• APC decides MHC-I or MHC-II route → Presents to CD8 vs CD4 T cells, respectively.

Page 6 – Definitions: MHC vs HLA, Major vs Minor

• Major Histocompatibility Complex (MHC): self-identifier proteins, dominant in transplant compatibility.
• Human Leukocyte Antigen (HLA): human version of MHC first found on leukocytes.
• Two protein sets:
– Major: highly immunogenic, rapid graft rejection.
– Minor: weakly immunogenic, subtle self/non-self cues.

Page 7 – Functional Cartoon

• Internal (cytosolic) vs external (phagocytic) Ag sources.
• Vesicular loading: peptide binds MHC, traffics to membrane.
• End result = APC displaying MHC–peptide for T-cell receptor (TCR) binding.

Page 8 – Recap of Definitions (HLA = MHC)

• MHC present in all vertebrates; “HLA” reserved for humans.
• Dominant transplant factors.
• Discussion continues focusing on Major complexes only.

Page 9 – Core Functions of MHC

I. Lymphocyte development (thymic selection): ensure TCR can recognize self-MHC and delete strongly self-reactive cells.
II. Immune response phase: display processed peptides after endocytosis/phagocytosis/infection.

Page 10 – MHC Loci on Chromosome 6

1. Class I locus:
   • Classical: HLA-A, ‑B, ‑C
   • Non-classical: HLA-E, ‑F, ‑G

2. Class II locus: HLA-DP, ‑DQ, ‑DR

3. Class III locus: assorted secreted immune proteins (e.g., complement C2/C4, TNF-α/β).

Page 11 – Diversity & Genetics

• ≈300 alleles per classical gene → unique profile per person.
• Haplotype: one set of alleles on each chromosome 6.
• Codominant expression: both parental haplotypes expressed simultaneously.
• Population benefit: broad coverage against pathogens.

Page 12 – Expression Patterns & Targets

• Classical MHC-I: all nucleated cells + platelets → ligand for CD8 T.
• Non-classical MHC-I: restricted; HLA-G = immunosuppressive (placenta).
• MHC-II: DCs, macrophages, B cells → ligand for CD4 T.
• MHC-III: soluble complement/cytokines (single-chain).

Page 13 – Shared Structural Blueprint

• Both classes = heterodimers with Ig-like domains & a peptide-binding groove.
• Peptide MUST be lodged in groove for correct folding.
• Function: bind self & non-self peptides for
– selection,
– activation of T/B cells,
– detection of “altered self” (infection/tumor).

Page 14 – Peptide Groove Mechanics

• Anchor residues of peptide fit pockets on groove floor → high-affinity attachment.
• One MHC binds many peptides (promiscuity) but only one at a time.
• Peptide ends protrude to contact TCR.
• Population polymorphism amplifies peptide universe.

Page 15 – Clinical Angle: Polymorphism

• Transplant matching challenge → graft rejection if mismatched.
• Disease correlations (e.g., HLA-B27 & ankylosing spondylitis OR HLA-DR3 & SLE).

Page 16 – Concept of MHC Restriction

• A given TCR recognizes peptide only when bound to a particular self-MHC allele.
• Classic mouse strain experiment: virus-specific CTLs kill only infected targets sharing same class I allele.

Page 17 – (Duplicate of Page 12) Re-emphasize expression rules.

Page 18 – MHC-I Structural Detail

• Components:
– α-chain (α1-α3) encoded in locus.
– β2-microglobulin (non-MHC).
• α1/α2 form groove; peptide length $8!\text{–}!11$ AA.
• Universally expressed; presents to CD8.
• Memory aid: “1 × 8 = 8.”

Page 19 – MHC-II Structural Detail

• α + β chains (both encoded in MHC); α1/β1 = groove.
• Peptides $14!\text{–}!20$ AA; may overhang groove.
• Expressed only on APCs; present to CD4.
• Memory aid: “2 × 4 = 8.”

Page 20 – Quick Table

• MHC-I → CD8 T (1×8).
• MHC-II → CD4 T (2×4).

Page 21 – Up-Regulation of Presentation

• DC/mac activation ↑MHC & cytokines.
• IFN-γ from NK or T cells boosts both MHC-I and II (even induces II on non-APCs like endothelium).

Page 22 – “Power in Numbers”

• Infected non-APC = only MHC-I; APC = both I & II → stimulates all arms (CD4, CD8, B).

Page 23 – Two Historic Pathways

1. Endogenous/Class I (cytosolic).

2. Exogenous/Class II (vesicular).
   • Exceptions: cross-presentation (Class I of exogenous).

Page 24 – Schematic of Both Pathways

• Class I: cytosolic protein → proteasome → peptide ↦ TAP → ER → MHC-I.
• Class II: endosome protein → lysosome → peptide ↦ MHC-II.

Page 25 – Endogenous/Class I Steps

1. Cytosolic protein (self/viral).

2. Ubiquitination → proteasome digestion.

3. Peptide ↦ TAP in ER.

4. Load onto HLA-A/B/C → Golgi → surface.

Page 26 – Exogenous/Class II Steps

1. External Ag internalized.

2. Invariant chain (Ii) keeps groove occupied (CLiP) en route to MIIC.

3. Fusion of MIIC with endosome; HLA-DM swaps CLiP for peptide.

4. Complex traffics to surface.

Page 27 – Comparing Pathways

1. Only APCs have Class II.

2. Location of Ag origin: vesicle vs cytosol.

3. Outcome: CD4 vs CD8 activation.

Page 28 – Alternative I: Cross-Presentation

• DC phagocytoses infected cell.
• Escaped peptide/protein → TAP/ER → MHC-I → CD8.

Page 29 – Efficiency & DC Specificity

• Only DCs robustly perform cross-presentation owing to specialized machinery.

Page 30 – Why Cross-Presentation Matters

• Allows CTL responses to viruses/tumors when DC itself isn’t infected.
• Solves “extrinsic” antigen dilemma for MHC-I.

Page 31 – Alternative II: CD1 & Lipid Antigen

• CD1 resembles MHC but presents lipid/glycolipid (e.g., mycobacterial cell wall) to NKT cells.
• Needs β2-microglobulin; loads in endosomal compartments.

Page 32 – Alternative III: Glycopeptide Presentation

• Glycoprotein endocytosed by B cell/DC → degraded → glycopeptide.
• Peptide portion seats in MHC-II groove; carbohydrate protrudes for CD4 recognition.

Page 33 – Immunodominant Epitopes

• Within a protein, multiple peptides compete; highest-affinity one wins = immunodominant.
• Important for vaccine design.

Page 34 – Stability & Timing

• Each MHC molecule displays one peptide but holds it stably, giving time for rare cognate T cell to engage.

Page 35 – MHC & B-Cell Interplay

1. BCR-mediated uptake → exogenous Class II pathway → present to CD4.

2. In return, CD4 T delivers cytokines & CD40L signals for isotype switch & plasma cell differentiation.

Page 36 – Three-Way Interface for T-Cell Activation

• Anchor residues ←→ MHC pockets.
• Peptide side chains ←→ TCR CDR loops.
• Invariant MHC ridge ←→ TCR framework → ensures specificity & MHC restriction.

Page 37 – Role of Co-Receptors

• CD4 binds MHC-II α2; CD8 binds MHC-I α3.
• Co-receptor engagement crucial for signaling.

Page 38 – Overall Specialization

1. Structural differences

2. Distinct processing pathways

3. Cell-type expression

4. CD4 vs CD8 targeting → tailored effector functions (e.g., macrophage activation vs cytotoxicity).

Page 39 – Superantigens

• Bind external surfaces of MHC-II & TCR-β (outside groove).
• Commonly bacterial exotoxins:
– Staph aureus enterotoxin B → food poisoning/TSS.
– Strep pyogenes exotoxin A → scarlet fever.

Page 40 – Cytokine Storm Mechanism

• Normal peptide activation: ≤$0.001\%$ T cells.
• SuperAg: up to $20\%$ T cell activation.
• Massive TNF-α, IL-1, IL-2 → fever, vascular leak, shock, MODS.

Page 41 – Roles of HLA Across Biology

• Thymic selection (negative & positive).
• Transplantation matching.
• Pathogen & tumor defense.
• Immune tolerance (e.g., HLA-G in placenta).

Page 42 – Principle of Specialization + Diversity

Different APCs × different MHC molecules × different effector T subsets = broad protective repertoire vs PAMPs/DAMPs.

Page 43 – Integrated Summary

• Codominance + polymorphism + cell-specific expression → coordinated, non-autoimmune responses.
• Self & antigenic restriction protects host while eliminating invaders.

Page 44 – Summary I (Structure & Rules)

• MHC-I: α-chain + β2m, groove = α1/α2, CD8 contact α3.
• MHC-II: α + β, groove = α1/β1, CD4 contact α2.
• MHC-III: soluble mediators (C2/C4/TNF/HSP-70).
• Key properties: peptide-only binding, codominance, polymorphism, restriction, one-peptide-at-a-time.

Page 45 – Summary II (Pathways & Alternatives)

• Classic Endogenous (Class I) & Exogenous (Class II).
• Alternatives: cross-presentation, glycopeptide, lipid/CD1.

Page 46 – Summary III (B-Cell Roles & SuperAgs)

• B cells present via Class II and receive CD4 help (CD40-CD40L).
• Superantigens bypass groove → massive, dysregulated activation.

Page 47 – COMBANK Question 1 (Clinical Correlation)

• Answer: “Present antigenic fragments to T helper lymphocytes” (i.e., MHC-II function).

Page 48 – COMBANK Question 2

• Failure to acidify phagolysosome → defective pathogen processing for MHC-II → impaired CD4 activation.

Page 49 – Next Topic Teaser

• “Antigen Receptors and Lymphocyte Development” (builds on MHC-TCR interaction principles).

Page 50–60 (Supplemental Highlights)

• Videos linked for visualizing MHC gene location & pathways.
• “Ultimate Goals”:
– Endogenous proteins → MHC-I → CD8.
– Exogenous proteins → MHC-II → CD4.
• Exogenous pathway recap: endocytosis → lysosome → MIIC → surface.
• Endogenous recap: proteasome → TAP/ER → Golgi → surface.
• Transplantation categories: autograft, isograft, allograft, xenograft; mismatch grows with genetic distance.
• Disease-associated HLA table (FYI, not testable).
• Two-level restriction diagram: self vs antigenic.

Page 61 – Big-Picture Take-Away

MHC diversity underlies species-level protection, while restriction ensures properly tailored individual immune responses without autoimmunity.

Cross-Lecture/Real-World Connections

• Previous Lectures: Pattern recognition (PRR/PAMP) signals drive IFN-γ that up-regulates MHC expression, linking innate cues with adaptive activation.
• Clinical: HLA typing essential for bone-marrow & organ transplantation; HLA-B*57:01 testing before prescribing abacavir (drug hypersensitivity).
• Tumor Immunology: Checkpoint blockade (e.g., anti-PD-1) efficacy partly depends on intact MHC-I presentation in tumor cells.
• Autoimmunity: HLA-DR/DQ alleles confer susceptibility via faulty peptide selection in thymus.
• Pregnancy: HLA-G expression protects fetus (semi-allograft) by inducing tolerance.

Ethical/Philosophical Notes

• Balancing diversity vs transplant compatibility raises questions of donor selection equity and genomic privacy.
• Superantigen-induced cytokine storms illustrate dangers of microbial “short-cuts” around immune checks, paralleling issues in therapeutic T-cell engineering (CAR-T toxicity).

Equations / Numeric Highlights

• Peptide lengths: Class I = $8!\text{–}!11\ \text{AA}$; Class II = $14!\text{–}!20\ \text{AA}$.
• Endogenous activation ratio: $\le0.001\%$ of total T cells.
• Superantigen activation: $\approx20\%$ of T cells.
• Surface molecule numbers on DCs: resting $\sim10^6$ vs activated $\sim7\times10^6$.

Quick Mnemonics

• “1×8 = 8” → MHC-I ↔ CD8.
• “2×4 = 8” → MHC-II ↔ CD4.

Key Vocabulary

• MIIC = MHC-II compartment.
• CLiP = Class-II-associated invariant chain peptide.
• TAP = Transporter associated with Antigen Processing.
• HLA-DM/HLA-DO = catalysts/regulators of CLiP exchange.
• Cross-dressing = intercellular transfer of intact peptide–MHC complexes (mentioned under “alternative methods”).

Practical Take-Home

Master the classic and alternative pathways plus expression patterns; these dictate which subset of T cells becomes activated, guiding clinical expectations in infections, vaccines, transplant rejection, cancer, and immunopathology.