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Comprehensive Pathology Notes

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1. Hypersensitivity Reactions

Definition

Classification (Gell and Coombs)

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Summary Chart

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Type I - Immediate Hypersensitivity (IgE-mediated)

Pathogenesis

1. Sensitization phase: First exposure to antigen (allergen) drives Th2 differentiation, which produces IL-4 and IL-13, promoting isotype switching of B cells to produce IgE.
2. IgE binding: IgE binds via its Fc region to FcεRI (high-affinity Fc receptor) on mast cells and basophils, "arming" them.
3. Re-exposure and cross-linking: Second exposure to the same allergen cross-links adjacent surface IgE molecules, triggering mast cell activation.
4. Two-phase response:
   • Immediate phase (within minutes): Degranulation releases preformed mediators - histamine, tryptase, heparin, chymase. These cause vasodilation, increased vascular permeability, smooth muscle contraction, and mucus secretion.
   • Late phase (4-12 hours): Newly synthesized mediators include leukotrienes (LTC4, LTD4), prostaglandins, PAF, and cytokines (IL-3, IL-5, GM-CSF, TNF-α). These recruit eosinophils and basophils, causing sustained inflammation and tissue damage.

Mediators and Their Effects

Examples

• Anaphylaxis: Systemic, life-threatening - bee sting, peanut allergy
• Asthma: Airway bronchoconstriction
• Allergic rhinitis (hay fever): Nasal congestion, sneezing
• Urticaria/angioedema: Skin wheal-and-flare
• Atopic dermatitis: Chronic skin inflammation

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Type II - Cytotoxic/Antibody-Mediated Hypersensitivity

Pathogenesis

1. Complement-mediated lysis: Antibody binds to cell surface → activates classical complement pathway → formation of membrane attack complex (MAC) → cell lysis. Example: Transfusion reactions (ABO mismatch), Rh hemolytic disease of the newborn.
2. Antibody-dependent cell-mediated cytotoxicity (ADCC): IgG-coated target cells are killed by NK cells, eosinophils, or macrophages via Fc receptors.
3. Complement/Fc receptor-mediated phagocytosis (opsonization): Antibody-coated cells are recognized by macrophages in spleen/liver → phagocytosis and destruction. Example: Autoimmune hemolytic anemia, idiopathic thrombocytopenic purpura (ITP).
4. Functional alteration without cell destruction: Antibodies against receptors block or mimic receptor function.
   • Blocking: Myasthenia gravis (anti-ACh receptor antibodies block neuromuscular transmission)
   • Stimulating: Graves' disease (anti-TSH receptor antibodies stimulate thyroid)

Examples

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Type III - Immune Complex-Mediated Hypersensitivity

Pathogenesis

1. Immune complex formation: Antibodies (IgG) bind to circulating soluble antigens, forming antigen-antibody complexes. Under normal circumstances, these are cleared by the mononuclear phagocyte system.
2. Deposition: When complexes are formed in excess antigen, they become small and soluble, evading clearance, and deposit in vessel walls, glomeruli, joint spaces, and skin.
3. Complement activation: Deposited complexes activate the complement cascade → C3a and C5a anaphylatoxins → mast cell degranulation (increases vascular permeability) → C5a also acts as a potent neutrophil chemoattractant.
4. Neutrophil-mediated injury: Neutrophils attempt to phagocytose fixed complexes but cannot; they instead release lysosomal enzymes, reactive oxygen species → fibrinoid necrosis of vessel walls (vasculitis) and tissue damage.

Histological Features

• Fibrinoid necrosis: Pale pink amorphous material replacing vessel walls
• Neutrophilic infiltrate
• Immune complex deposits visible by immunofluorescence (granular/lumpy-bumpy pattern)

Examples

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Type IV - Delayed-Type/Cell-Mediated Hypersensitivity

Pathogenesis

1. Antigen is presented by APC (macrophage) to CD4+ Th1 cells via MHC II.
2. Sensitized Th1 cells, on re-exposure, secrete cytokines: IFN-γ (activates macrophages), TNF (promotes inflammation), IL-2 (T cell proliferation).
3. Activated macrophages become "angry macrophages" - release more TNF, IL-12, reactive oxygen species.
4. Result: granuloma formation and tissue destruction.

1. CD8+ T cells recognize antigen presented by MHC class I on target cells.
2. Direct killing via perforin/granzyme pathway or Fas-FasL interaction.
3. Example: viral infections, transplant rejection, killing of tumor cells.

Examples

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2. Amyloidosis

Definition

Chemical Composition of All Amyloids

1. Protein-derived amyloid fibers - the component that differs among subtypes
2. Amyloid P component (SAP) - a 25-kDa glycoprotein, a member of the pentraxin family, present in ALL forms
3. Ground substance - sulfated glycosaminoglycans (heparan sulfate) and proteoglycans

Staining Properties

• Congo red: Salmon-pink on light microscopy; apple-green birefringence under polarized light - the diagnostic gold standard
• Thioflavin T: Fluorescent staining
• PAS: Weakly positive, diastase resistant
• Crystal violet: Purple (metachromatic)
• Electron microscopy: Straight, non-branching, non-anastomosing fibrils 8-12 nm in diameter

Classification

Chart 1: Biochemical Classification of Major Amyloids

Chart 2: Clinical Classification

AMYLOIDOSIS
├── SYSTEMIC
│   ├── Primary (AL) - plasma cell disorder
│   ├── Secondary (AA) - chronic inflammation
│   ├── Dialysis-related (Aβ2M)
│   ├── Heredofamilial (ATTR, Afib, ApoA-I...)
│   └── Senile systemic (wild-type ATTR - cardiac)
│
└── LOCALIZED
    ├── Cutaneous (macular, lichen, nodular)
    ├── Cerebral (Alzheimer's - Aβ plaques)
    ├── Pancreatic (type 2 DM - AIAPP)
    └── Medullary thyroid carcinoma (calcitonin)

Pathogenesis

1. A predisposing condition leads to overproduction of an amyloidogenic precursor protein (e.g., plasma cell clone producing light chains in myeloma; elevated SAA in chronic inflammation).
2. The protein adopts an abnormal beta-pleated sheet conformation - cofactors such as SAP, glycosaminoglycans, and seeding by existing fibrils promote this misfolding.
3. Oligomeric intermediates (soluble, cytotoxic) form first, then polymerize into insoluble fibrils.
4. SAP binds to all amyloid fibrils - stabilizes deposits and protects them from proteolysis.
5. Fibrils accumulate extracellularly → compress and replace normal parenchyma → organ dysfunction.
6. Deposits exist in a dynamic state and can regress if the source is eliminated (demonstrated by SAP scintigraphy). - Brenner and Rector's The Kidney

Pathology in Specific Organs

Kidney (Most Common Clinically Significant Site)

• Gross: Enlarged, pale, waxy, firm kidneys
• Light microscopy (H&E): Amorphous eosinophilic material expanding the mesangium in glomeruli; may involve capillary walls, interstitium, and blood vessels
• Congo red: Apple-green birefringence under polarized light
• Immunofluorescence: Deposits labeled with anti-lambda or anti-kappa (AL); anti-SAA (AA)
• Electron microscopy: 8-12 nm non-branching fibrils in mesangium, GBM (subepithelial, intramembranous, subendothelial)
• Clinical: Nephrotic syndrome (massive proteinuria, hypoalbuminemia, edema) → progressive renal failure
• Predominantly AL (86%) and AA (7%) in renal biopsy series - Brenner and Rector's The Kidney

Spleen

1. Sago spleen: Deposits limited to follicles/white pulp → translucent sago grain-like nodules on cut section. Most common initially.
2. Lardaceous (diffuse) spleen: Diffuse involvement of red pulp → large, firm, pale-yellow, waxy appearance ("lard-like"). Seen in advanced disease.

Liver

• Gross: Hepatomegaly; pale, waxy cut surface
• Micro: Deposits in space of Disse (between sinusoidal lining cells and hepatocytes) → progressive hepatocyte atrophy
• May cause cholestasis, mildly elevated liver enzymes
• Rarely causes liver failure

Heart

• Gross: Firm, rubbery, enlarged heart
• Micro: Deposits between myocardial fibers
• Types: ATTR (senile/wild-type - most common cause of cardiac amyloid in elderly), AL
• Echocardiogram: "Sparkling" or "granular sparkling" appearance of myocardium; concentric hypertrophy
• Clinical: Restrictive cardiomyopathy, heart failure, arrhythmias, conduction defects. Cardiac involvement is the primary cause of death in amyloidosis.

Other Organs

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3. Systemic Lupus Erythematosus (SLE)

Definition

Autoantibodies in SLE

Etiopathogenesis

Genetic Factors

• HLA associations: HLA-DR2 or HLA-DR3 each confer odds ratio of 2-3; if both present, odds ratio ~5
• Complement deficiencies: C1q, C2, C4 deficiencies in ~5% of SLE patients → impaired clearance of immune complexes and apoptotic cells → failure of B-cell tolerance
• FcγRIIB polymorphism: Defective inhibitory Fc receptor → inadequate control of B-cell activation
• PTPN22 polymorphism: Phosphatase involved in lymphocyte signaling
• TREX1 mutations: DNase that degrades intracellular DNA; mutations lead to accumulation of nuclear material

Environmental Factors

• Ultraviolet (UV) light: Induces apoptosis of skin cells → release of nuclear antigens (nucleosomes, dsDNA, ribonucleoproteins) that normally remain intracellular
• Drugs: Procainamide, hydralazine, isoniazid → drug-induced lupus (anti-histone antibodies; usually ANA+ but anti-dsDNA-)
• Infections: Molecular mimicry, TLR activation by microbial nucleic acids
• Estrogen: Explains female predominance; estrogen enhances autoimmune responses

Pathogenesis Model (IFN-α Loop)

UV light / Apoptosis
        ↓
Release of nuclear antigens (dsDNA, nucleosomes)
        ↓
Inadequate clearance (complement deficiency, TREX1 mutation)
        ↓
Activation of plasmacytoid dendritic cells (pDCs) via TLR7/TLR9
        ↓
Massive IFN-α production ("interferon signature")
        ↓
Activation of autoreactive B cells and T cells
        ↓
Production of anti-dsDNA, anti-Smith autoantibodies
        ↓
Immune complex formation and deposition
        ↓
Complement activation → Inflammation → Tissue damage

Why Autoantibodies Cause Disease

• Immune complexes: Anti-dsDNA + dsDNA complexes deposit in glomeruli, skin, joints, choroid plexus → complement activation → neutrophil recruitment → tissue damage (Type III hypersensitivity)
• Direct cell targeting: Anti-RBC → hemolytic anemia; anti-platelet → thrombocytopenia (Type II hypersensitivity)

Classification Criteria (EULAR/ACR 2019)

Morphology (Pathological Findings)

Skin (Malar/Butterfly Rash)

• Acute cutaneous lupus: Butterfly (malar) rash - erythematous macular-papular eruption over cheeks and nasal bridge, sparing nasolabial folds; photosensitive
• Discoid lupus: Erythematous plaques with central scarring and follicular plugging; heals with scarring alopecia
• Histology: Vacuolar degeneration of basal layer, thickening of basement membrane, perivascular lymphocytic infiltrate
• Immunofluorescence: "Lupus band test" - granular deposits of IgG, IgM, C3 at DEJ (positive in both lesional and non-lesional skin in SLE, unlike in discoid lupus)

Kidney (Lupus Nephritis)

• Class I: Minimal mesangial (normal LM, deposits by IF/EM)
• Class II: Mesangial proliferative (mesangial deposits + hypercellularity)
• Class III: Focal proliferative (<50% glomeruli affected) - active lesions
• Class IV: Diffuse proliferative (≥50% glomeruli) - most common and most severe; "wire-loop" lesions (massive subendothelial deposits), hyaline thrombi
• Class V: Membranous (diffuse subepithelial deposits, resembles idiopathic MN)
• Class VI: Advanced sclerosing (≥90% global sclerosis)

Heart

• Libman-Sacks endocarditis: Non-bacterial verrucous endocarditis - small, irregular, sterile vegetations on both surfaces of the mitral valve (most commonly) and tricuspid valve. Distinctive because they occur on both sides of valve leaflets (unlike rheumatic fever, which is only on atrial surface of mitral valve).
• Pericarditis (fibrinous)
• Myocarditis (less common)

Blood Vessels

• Vasculitis: Immune-complex deposition in small vessels → leukocytoclastic vasculitis
• Libman-Sacks endocarditis (as above)
• Antiphospholipid syndrome in some: thrombosis (paradoxically) → increased risk of MI, stroke

Joints

• Non-erosive synovitis (in contrast to rheumatoid arthritis, which is erosive)
• Arthralgia and arthritis without joint deformity

Spleen

• Onion-skin lesion (periarteriolar fibrosis): Concentric fibrosis around splenic arterioles - characteristic of SLE on histology

CNS/Neuropsychiatric

• Small vessel vasculopathy (non-inflammatory), microthrombi (from antiphospholipid antibodies)
• Cognitive dysfunction, psychosis, seizures

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4. Graft Versus Host Disease (GVHD)

Definition

Prerequisites (Three Requirements)

1. The transplanted cells must be immunologically competent (contain mature T lymphocytes)
2. The recipient must express tissue antigens not present in the donor (HLA mismatch - either major or minor histocompatibility differences)
3. The recipient must be unable to reject the transplanted cells (immunosuppressed, as in HSCT recipients)

Pathogenesis

1. The preconditioning regimen (chemotherapy + total body irradiation) damages rapidly dividing tissues (gut, skin, liver) → activates host dendritic cells (APCs) → they upregulate HLA molecules and other minor histocompatibility antigens.
2. Host APCs present recipient alloantigens to donor T cells (both CD4+ and CD8+).
3. Donor T cells become activated and expand → produce cytokines, especially IL-2, TNF-α, and IFN-γ, which amplify the host-donor immune interaction.
4. Cytokine storm leads to inflammation and destruction of target organs: skin, liver, gastrointestinal tract (the classic triad).
5. Some degree of immunologic competence of transplanted cells is actually desired for the graft-versus-tumor (GVT) effect - donor cells attack residual malignancy.

Classification

Acute GVHD

• Classic: Within 100 days of transplant; can occur up to 1 year with tapering of immunosuppression
• Onset: Typically days 14-42 after HSCT, peak at day 30

• Skin: Erythematous morbiliform eruption of face and trunk → may become confluent → exfoliative erythroderma; bullae in severe cases. Starts with follicular/eccrine duct involvement (looks like keratosis pilaris). More monomorphous than drug eruption; involves upper back.
• Liver: Cholestatic jaundice (elevated bilirubin, alkaline phosphatase)
• GI tract: Profuse watery or bloody diarrhea, abdominal pain, nausea/vomiting

Chronic GVHD

• Occurs later (>100 days or with features distinct from acute GVHD)
• Resembles autoimmune/connective tissue diseases (Sjögren's, scleroderma, lichen planus, primary biliary cirrhosis)
• Skin: Lichenoid or sclerodermoid changes, dyspigmentation, scleroderma-like fibrosis
• Eyes: Sicca syndrome (dry eyes)
• Oral cavity: Lichenoid changes, xerostomia
• Lung: Bronchiolitis obliterans (obstructive lung disease)
• Liver: Chronic cholestatic disease

Target Organs

Treatment

• Prevention: HLA-matching, T-cell depletion of graft, calcineurin inhibitors (cyclosporine, tacrolimus) + methotrexate
• Acute GVHD: Systemic corticosteroids (first-line); refractory: ruxolitinib (JAK1/2 inhibitor), ibrutinib
• Chronic GVHD: Steroids + cyclosporine; photopheresis; rituximab

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5. Role of MHC in Disease

Background

MHC Classes

Mechanisms by Which MHC Alleles Confer Disease Susceptibility

1. Differential Peptide Binding (Molecular Mimicry)

• Different MHC alleles have different peptide-binding clefts with unique amino acid compositions.
• A particular allele may bind and present self-peptides that would not otherwise be presented → activates autoreactive T cells.
• Example: The DQβ chain polymorphism at a critical position in the peptide-binding groove correlates most strongly with susceptibility to type 1 diabetes.

2. Failure of Negative Selection

• If a self-peptide/MHC complex is not present in the thymus, self-reactive T cells specific for that combination are not deleted → escape into periphery as autoreactive cells.
• Some alleles may fail to present critical self-antigens in the thymus, allowing escape of potentially autoreactive clones.

3. Defective T-Regulatory Cell Function

• Certain HLA alleles may affect the efficiency of Treg generation or function, impairing peripheral tolerance.

4. Protective Alleles

• Some alleles are protective because they bind self-peptides so strongly that autoreactive T cells are deleted in thymus.
• Example: HLA-DQ6 (DQB1*0602) is strongly protective against type 1 diabetes (relative risk = 0.02).

HLA Disease Associations (Key Table)

How MHC Contributes: The Arthritis Example (HLA-B27)

• Ankylosing spondylitis is 87x more common in HLA-B27+ individuals.
• Proposed mechanisms include:
  1. Arthritogenic peptide hypothesis: HLA-B27 presents specific peptides (possibly from gut bacteria) that activate cytotoxic T cells attacking the spine/sacroiliac joints.
  2. Molecular mimicry: HLA-B27 resembles antigens of Klebsiella pneumoniae; anti-Klebsiella antibodies cross-react with HLA-B27.
  3. Misfolding: HLA-B27 tends to misfold in the ER → triggers ER stress and unfolded protein response → inflammatory cytokine production.

MHC Beyond Autoimmune Disease

• Transplantation: Degree of MHC mismatch determines the intensity of allograft rejection
• Susceptibility to infectious disease: Some HLA alleles affect ability to mount immune responses against pathogens (e.g., HLA-B57 is protective against HIV progression)
• Drug hypersensitivity: HLA-B5701 - abacavir hypersensitivity; HLA-B1502 - carbamazepine Stevens-Johnson syndrome in Han Chinese

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6. Protein Misfolding Diseases

Definition and Concept

The Prion Principle

• Rich in beta-sheet structure (vs. alpha-helix of PrP^C)
• Resistant to protease digestion (and harsh physical/chemical denaturing)
• Self-propagating: It acts as a template to convert newly synthesized PrP^C → PrP^Sc
• Transmissible (at least in classic prion diseases)

Classification of Protein Misfolding Diseases

Chart: Major Categories

Shared Molecular Mechanisms

1. Normal Protein Folding vs. Misfolding

• Proteins fold into their native 3D conformation aided by molecular chaperones (HSP70, HSP90, GRP78/BiP).
• Mutations, oxidative stress, aging, or overwhelming chaperone capacity can cause misfolding.
• Misfolded proteins expose hydrophobic regions normally buried → prone to aggregation.

2. Beta-Sheet Conversion and Fibrillization

• Many misfolded proteins convert from alpha-helical or random-coil to beta-sheet rich structures.
• These oligomerize → protofibrils → mature insoluble fibrils.
• Toxic species: Soluble oligomeric intermediates (NOT the end-stage fibrils) are generally more toxic to cells.

3. Seeding and Templated Misfolding (Prion-Like Spreading)

• Pre-existing misfolded aggregates act as seeds that catalyze the misfolding of normal protein.
• Evidence for cell-to-cell spreading in Alzheimer's (tau/Aβ), Parkinson's (α-synuclein transplantation studies), ALS (TDP-43).
• In PD: After dopaminergic transplantation (1990s), healthy fetal grafts showed Lewy bodies 11-16 years later, indicating transmission of α-synuclein pathology from host to graft. - Bradley and Daroff's Neurology in Clinical Practice

4. Cellular Toxicity Mechanisms

• Proteasome dysfunction: Misfolded proteins overwhelm the ubiquitin-proteasome system
• Mitochondrial dysfunction: Aggregates damage mitochondria → oxidative stress
• ER stress / Unfolded Protein Response (UPR): Accumulation of misfolded proteins in ER activates UPR; if prolonged → apoptosis
• Membrane disruption: Oligomeric intermediates can perforate membranes
• Synaptic dysfunction: In neurons, aggregates disrupt synaptic vesicle trafficking

5. Degradation Pathways

• Ubiquitin-proteasome system (UPS): Primary route for misfolded cytoplasmic proteins
• Autophagy-lysosomal pathway: Handles aggregates too large for proteasome
• Failure of either system leads to aggregate accumulation

Key Examples in Detail

Alzheimer's Disease

• Aβ amyloid: From amyloid precursor protein (APP) cleaved by β and γ-secretase → Aβ40/Aβ42 peptides → form senile plaques (extracellular)
• Tau: Hyperphosphorylated tau dissociates from microtubules → forms neurofibrillary tangles (intracellular)
• Both pathologies spread through the brain in a prion-like manner

Parkinson's Disease

• α-Synuclein misfolds → forms Lewy bodies (intracytoplasmic eosinophilic inclusions, halo appearance)
• Braak staging: pathology starts in olfactory bulb/gut enteric nervous system → ascends to substantia nigra → cortex
• Substantia nigra dopaminergic neuron loss → dopamine deficiency → motor symptoms

Prion Diseases

• CJD: Sporadic (most common, ~85%), Familial (PRNP mutations, ~15%), Acquired (iatrogenic via contaminated tissue/instruments, vCJD via BSE)
• Pathology: Spongiform encephalopathy - vacuolation of neuropil, neuronal loss, astrogliosis, NO inflammatory infiltrate
• vCJD: Florid (daisy-like) PrP plaques surrounded by vacuoles; tonsil biopsy positive for PrP^Sc

Therapeutic Implications

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