---

Histology of the Thymus

Overview

---

Gross/Architectural Organization

• The thymus is bilobed, with each lobe encased in a vascularized connective tissue capsule
• Capsular extensions (septa) penetrate the parenchyma, dividing each lobe into many incomplete lobules
• Each lobule has two distinct zones: an outer cortex and a central medulla
• The medullae of adjacent lobules are continuous with each other (hence "incompletely separated")

---

Staining Characteristics

---

Cortex

Thymocytes (T Lymphoblasts)

Thymic Epithelial Cells (TECs) of the Cortex

1. Squamous TECs — form a continuous layer (joined by desmosomes and occluding junctions) lining the capsule, septa, and microvasculature. This creates the blood-thymus barrier (along with vascular endothelium and pericytes), preventing unregulated antigen exposure of thymocytes.
2. Stellate TECs — extend long cytoplasmic processes bound together by desmosomes to form the cytoreticulum — the structural scaffold for lymphoblasts. These are also APCs that express MHC I and II molecules and present antigens to developing T cells. Some also secrete cytokines that promote T-cell maturation.
3. Squamous TECs at the corticomedullary junction — express MHC class II molecules and form a sheetlike corticomedullary barrier.

Also in the cortex:

• Macrophages — remove apoptotic thymocytes (up to ~80% of cells are deleted by positive selection)

---

Medulla

Medullary TECs form:

• A second boundary layer at the corticomedullary junction
• A cytoreticulum supporting lymphocytes, dendritic cells, and macrophages (less densely packed than in the cortex)
• Hassall's (thymic) corpuscles — the hallmark of the thymic medulla

Hassall's Corpuscles

• Concentric, lamellated whorls of eosinophilic epithelioreticular cells (type VI TECs), often with a keratinized/hyalinized core
• Up to 100 µm in diameter
• Unique to the thymic medulla — their presence confirms thymic tissue on microscopy
• Secrete cytokines (including TSLP) that regulate local dendritic cell activity, particularly promoting development of regulatory T cells (Tregs) for peripheral immune tolerance

---

T-Cell Selection (Two-Stage Process)

Positive Selection (in the cortex)

• TECs present peptides on MHC I and II to developing thymocytes
• Cells whose TCRs can recognize MHC molecules with appropriate affinity → survive and move to medulla
• Cells with faulty/nonfunctional TCRs → apoptosis (~80% of all thymocytes)
• Selects for CD4+ (MHC II-restricted) or CD8+ (MHC I-restricted) single-positive cells

Negative Selection (in the medulla)

• Medullary TECs express tissue-specific peripheral antigens via the Aire (Autoimmune Regulator) gene, mimicking thousands of organ-specific proteins
• These proteins are transferred to dendritic cells, which present them to thymocytes
• T cells whose TCRs strongly bind self-antigens → apoptosis (clonal deletion)
• Surviving cells have self-tolerant TCRs → exported as naïve T cells

---

Blood-Thymus Barrier

1. Continuous capillary endothelium with tight junctions
2. Endothelial basal lamina
3. Pericytes
4. Squamous TECs with their basal lamina

---

Thymic Involution

• Lymphoid tissue mass and cellularity decrease
• Replaced by adipose tissue
• Remnant lobules still retain cortex and medulla architecture
• Reduced output of naïve T cells, potentially contributing to declining immune function in the elderly

---

Clinical Correlates

---

---

The Immune Response — Comprehensive Notes

---

Overview: Two Lines of Defence

---

PART I: INNATE IMMUNITY

1. Physical & Chemical Barriers (First Line)

• Skin — keratinized epithelium blocks penetration
• Mucous membranes — mucus traps organisms; cilia sweep them out
• Secretions — lysozyme (tears, saliva), low pH (stomach), defensins (gut epithelium)

2. Pattern Recognition Receptors (PRRs)

3. Key Cells of Innate Immunity

Neutrophils

• First responders to infection; recruited by chemokines (IL-8/CXCL8)
• Kill by: phagocytosis, oxidative burst (ROS, HOCl), degranulation, NETs
• Short-lived (~6–12 hours at tissue site)

Macrophages

• Derived from monocytes; resident in all tissues (Kupffer cells, microglia, alveolar macrophages, etc.)
• M1 (classical activation): stimulated by IFN-γ + LPS → microbicidal, pro-inflammatory (TNF, IL-1, IL-12, ROS)
• M2 (alternative activation): stimulated by IL-4, IL-13 → anti-inflammatory, tissue repair (IL-10, TGF-β)
• Functions: phagocytosis, antigen presentation, cytokine secretion

Dendritic Cells (DCs)

• Professional APCs — the critical link between innate and adaptive immunity
• Capture antigens at epithelial surfaces → process → migrate to lymph nodes
• During maturation: upregulate MHC II, CD80/CD86 (costimulators), and CCR7 (lymph node homing)
• Plasmacytoid DCs: major producers of type I interferons (IFN-α/β) in viral infections

Natural Killer (NK) Cells

• Lymphoid cells that do not require prior sensitization
• Kill virus-infected cells and tumor cells via perforin/granzyme pathway
• Governed by balance of activating (NKG2D) and inhibitory (KIR, CD94/NKG2A) receptors
• Kill target cells that downregulate MHC I (a viral evasion strategy) — "missing-self" recognition
• Produce IFN-γ → activates macrophages

Mast Cells & Basophils

• Located at mucosal surfaces and skin
• Express FcεRI (binds IgE); also activated by complement (C3a, C5a)
• Release: histamine (vasodilation, permeability), leukotrienes, prostaglandins, cytokines
• Defend against parasites; central mediators of type I hypersensitivity

Eosinophils

• Key in defence against helminths; release major basic protein (MBP), ECP
• Also contribute to allergic inflammation

4. The Inflammatory Response

• Histamine (mast cells, platelets) → vasodilation, increased permeability
• Serotonin (platelets) → vasoconstriction at high doses

• COX pathway → Prostaglandins (PGE₂, PGI₂): vasodilation, pain, fever; TXA₂: platelet aggregation, vasoconstriction
• Lipoxygenase pathway → Leukotrienes: LTB₄ (neutrophil chemotaxis); LTC₄/D₄/E₄ (bronchoconstriction, permeability)
• Lipoxins/Resolvins → anti-inflammatory, resolve inflammation

5. Complement System

Classical pathway  ──→ C3 convertase
Alternative pathway ──→  (C4b2a or C3bBb)  ──→ C3b + C3a
Lectin pathway     ──→                      ──→ C5 convertase → MAC (C5b-9)

• Classical: triggered by antibody (IgM or IgG) bound to antigen → C1 activation
• Alternative: triggered by microbial surfaces (LPS, fungal cell walls) — no antibody required; spontaneous C3 hydrolysis
• Lectin: MBL (mannose-binding lectin) binds microbial carbohydrates → activates C1-like proteases (MASPs)

Clinical note: Inherited MAC deficiency (C5–C9) → recurrent Neisseria (meningococcal/gonococcal) infections

---

PART II: ADAPTIVE IMMUNITY

1. Cardinal Properties

• Specificity: Each lymphocyte clone recognises one epitope (via BCR or TCR) — clonal selection (Burnet, 1957)
• Diversity: 10⁷–10⁹ distinct specificities generated by V(D)J recombination
• Memory: Long-lived memory cells respond faster and more vigorously on re-exposure (basis of vaccination)
• Contraction: After pathogen elimination, >90% of effector cells die by apoptosis; memory cells persist
• Self-tolerance: Failure of self-reactive lymphocytes to respond (central + peripheral tolerance)

2. Antigen Presentation & MHC

• Expressed on all nucleated cells
• Presents endogenous (cytosolic/viral) peptides (8–10 aa) processed by the proteasome → TAP → ER
• Recognised by CD8+ T cells

• Expressed on professional APCs (DCs, macrophages, B cells)
• Presents exogenous (phagocytosed) peptides (13–25 aa) processed in endolysosomes
• Recognised by CD4+ T cells

3. T Lymphocytes

1. Signal 1: TCR binds peptide–MHC complex on APC
2. Signal 2 (costimulation): CD28 on T cell binds CD80/CD86 (B7) on APC
   • Without Signal 2 → anergy (functional unresponsiveness)
   • This is exploited therapeutically (CTLA-4-Ig / abatacept blocks costimulation)

• Kill virus-infected cells and tumour cells via:
  • Perforin/granzyme pathway → granzyme B enters cell via perforin pores → caspase activation → apoptosis
  • Fas–FasL interaction → apoptosis

4. B Lymphocytes & Humoral Immunity

B Cell Activation

• T-independent antigens: Polysaccharides, LPS directly cross-link BCR → mostly IgM, no memory
• T-dependent antigens: Protein antigens require CD4+ Tfh cell help (CD40L–CD40 + IL-21) → full response

Germinal Centre Reaction (Secondary Lymphoid Organs)

1. Somatic hypermutation — BCR variable regions mutated to refine specificity
2. Affinity maturation — B cells with highest affinity for antigen preferentially survive (selected by FDCs)
3. Class switch recombination — IgM → IgG, IgA, IgE (driven by T cell cytokines)

Immunoglobulin Classes & Functions

• Neutralisation — blocks binding of virus/toxin to host receptors
• Opsonisation — IgG Fc region bound by FcγR on phagocytes → enhanced phagocytosis
• Complement activation — IgM/IgG activate classical pathway → opsonisation + MAC
• ADCC — IgG-coated target cell killed by NK cells via FcγRIII (CD16)

5. The Adaptive Response — Step by Step

ANTIGEN ENTRY
      ↓
Captured by DENDRITIC CELLS at epithelial surfaces
      ↓
DCs mature → migrate to draining LYMPH NODE
      ↓
Present peptide-MHC to NAÏVE T CELLS (Signal 1 + Signal 2)
      ↓
CLONAL EXPANSION (IL-2 autocrine proliferation)
      ↓
DIFFERENTIATION
   ├── CD4+ Th cells → cytokine secretion → help B cells and macrophages
   ├── CD8+ CTLs → kill infected cells
   └── Memory T cells (long-lived)
      ↓
B CELL ACTIVATION (T-dependent)
   CD40L–CD40 contact + cytokines from Tfh cells
      ↓
GERMINAL CENTRE REACTION
   Somatic hypermutation → affinity maturation → class switching
      ↓
PLASMA CELLS (antibody secretion) + MEMORY B CELLS
      ↓
ANTIGEN ELIMINATED
      ↓
CONTRACTION: effector cells die by apoptosis (~90%)
MEMORY CELLS PERSIST (rapid recall on re-exposure)

---

PART III: Innate–Adaptive Interface

---

PART IV: Immunologic Memory & Vaccination

• After primary infection/immunisation, memory B and T cells accumulate
• Memory cells:
  • Are more numerous than naïve precursors
  • Have lower activation thresholds
  • Respond faster and more vigorously (secondary response)
• Vaccination exploits memory: a safe antigen (attenuated pathogen, subunit, mRNA) generates memory without disease
• Plasma cells in bone marrow can produce low-level protective antibodies for years to decades

---