History of Vaccination

• Thucydides (430 BC): Recognized that plague survivors could care for the sick without reinfection, an early observation of immunity.
• Variolation (15th Century): Introduced dried smallpox scabs into the skin or nose to induce a mild infection and immunity; practiced in China, India, and the Ottoman Empire.
• Lady Montague: Brought variolation from the Ottoman Empire to England and tested it on prisoners and her children.
• Edward Jenner (1796): Demonstrated cowpox inoculation protected against smallpox and coined the term "vaccination".
• Louis Pasteur (1800s): Pioneered live-attenuated vaccines for rabies, anthrax, and cholera and advanced the germ theory of disease.
• Von Behring: Won the 1901 Nobel Prize for identifying antibodies in serum that could transfer immunity, laying the foundation for humoral immunity.
• Metchnikoff: Won the 1908 Nobel Prize for discovering phagocytic cells that ingest pathogens, forming the basis of cell-mediated immunity.

Smallpox Eradication

• Causative Agents: Variola major caused 30% mortality, and Variola minor caused ~1% mortality.
• Symptoms: High fever, rash, pustules, scarring, and complications, including blindness.
• Eradicated: In 1980, due to WHO-led vaccination campaigns.
• Key Reasons for Eradication Success: No animal reservoir, no chronic carrier state, only one virus serotype, an effective and durable vaccine, high global cooperation, and surveillance.

Innate Immunity

• Definition: The first line of defense that is immediate, non-specific, and does not improve with repeated exposure.
• Features: Present from birth, rapid response (minutes to hours), and no immunological memory.
• Humoral Components: Lysozyme breaks down bacterial cell walls, the complement system (alternative pathway) promotes inflammation, cell lysis, and phagocytosis, and cytokines & interferons signal and regulate immune responses.
• Cellular Components: Neutrophils are first responders, phagocytosing pathogens; macrophages engulf pathogens, present antigens, and release cytokines; NK cells kill virus-infected and abnormal cells, and mast cells release histamine to promote inflammation.
• Receptors: Pattern Recognition Receptors (PRRs), like Toll-like receptors, detect PAMPs (pathogen-associated molecular patterns).

Adaptive Immunity

• Definition: An antigen-specific immune response that develops after exposure.
• Features: Slow initial response (days), highly specific, and develops immunological memory.
• Humoral Components: B lymphocytes become plasma cells, producing antibodies (IgM, IgG); the complement system (classical pathway) and cytokines play a role.
• Cellular Components: T helper cells (CD4+) activate B cells and cytotoxic T cells; T cytotoxic cells (CD8+) destroy infected or cancerous cells; memory T and B cells provide faster, stronger responses upon re-exposure.
• Receptors: B cell and T cell receptors (BCRs & TCRs) are highly specific, generated via gene rearrangement.

Humoral Immunity

• Definition: Immunity mediated by soluble molecules in body fluids.
• Innate Humoral Components: Lysozyme hydrolyses peptidoglycan in bacterial cell walls, the complement system (Alternative Pathway) enhances opsonisation and directly lyses pathogens, and cytokines regulate inflammation and immune signalling.
• Adaptive Humoral Components: Antibodies (Immunoglobulins) are produced by B cells/plasma cells in response to antigens; IgM is the first antibody produced and is effective in early infection; IgG is the most abundant in serum, crosses the placenta, and provides a strong secondary response; the complement system (Classical Pathway) is activated by antigen-antibody complexes to support inflammation, opsonisation, and cell lysis and cytokines promote B cell differentiation, isotype switching, and immune memory.

Cellular Immunity

• Innate Cellular Components: Neutrophils respond rapidly to bacteria; macrophages are longer-lasting phagocytes that present antigens via MHC II to CD4+ T cells; NK Cells recognise and kill cells lacking MHC I, and mast cells initiate inflammatory responses by releasing histamine and cytokines.
• Adaptive Cellular Components: T Helper Cells (CD4+) recognise antigen-MHC II complexes, secreting cytokines to activate B cells and macrophages; T Cytotoxic Cells (CD8+) recognise antigen-MHC I complexes and release perforin and granzymes to induce apoptosis in infected cells.
• B Cells: They can act as APCs, undergo clonal expansion, and differentiate into plasma or memory B cells

Primary and Secondary Immune Response

• Initiated by: Primary response involves naive lymphocytes, and the secondary response involves memory lymphocytes.
• Lag Phase: Primary response lag is 4–7 days, while the secondary response is 1–2 days.
• Peak Antibody Level: Primary response peaks at 7–14 days, and the secondary response peaks at 3–5 days.
• Dominant Antibody Class: IgM dominates the primary response, while IgG dominates the secondary response.
• Response Strength: The primary response is low to moderate, and the secondary response is high, rapid, and prolonged.
• Immunological Memory: Absent in the primary response but present in the secondary response.

Clonal Selection Theory

• Only lymphocytes with receptors matching the antigen proliferate and differentiate, forming the foundation for immune specificity and memory.

Glossary

• Antigen (Ag): Any substance triggering an immune response.
• Epitope: The specific region of an antigen recognized by an antibody or TCR.
• Antibody (Ab): A Y-shaped protein that binds antigens.
• Cytokines: Small proteins for cell signalling.
• Phagocytosis: A process by which cells ingest particles or microbes.
• Complement System: Proteins assisting antibodies and phagocytes in pathogen destruction.
• Major Histocompatibility Complex (MHC) Class I: Present on all nucleated cells, presents to CD8+ T cells.
• Major Histocompatibility Complex (MHC) Class II: Present on APCs, presents to CD4+ T cells.
• Clonal Selection: Antigen exposure activates specific lymphocyte clones.
• Memory Cells: Long-lived B and T cells respond more rapidly upon re-exposure.

Haematopoiesis

• Definition: The process that generates all blood cells from a common pluripotent stem cell (HSC).
• Developmental Timeline: Embryonic begins in the yolk sac, foetal shifts to the liver and spleen, and postnatal takes place primarily in the bone marrow.
• Differentiation Pathways: The lymphoid lineage produces B lymphocytes, T lymphocytes, and natural killer (NK) cells, while the myeloid lineage produces granulocytes, monocytes (→ macrophages and dendritic cells), megakaryocytes (→ platelets), and erythrocytes.

Cluster of Differentiation (CD Markers)

• CD markers are surface molecules used to identify and classify immune cells based on functions, stages of development, or activation state.
• CD3: A pan T cell marker associated with the T cell receptor (TCR).
• CD4: Present on T helper cells; binds to MHC class II.
• CD8: Present on cytotoxic T cells; binds to MHC class I.
• CD19/CD21: Present on B cells and involved in signal transduction.
• CD56: Present on Natural Killer cells and used for target cell recognition.

B Lymphocytes (B cells)

• Origin: Bone marrow
• Key Surface Molecules: CD19, CD21, CD40, CD72, BCR (IgM and IgD)
• Functions: They recognise antigens via BCR, act as antigen-presenting cells to helper T cells, differentiate into plasma cells to secrete antibodies, and contribute to long-term immunity via memory B cells.

T Lymphocytes (T cells)

• Origin: Bone marrow, mature in thymus
• T Helper Cells (CD4+): Recognise antigen presented by MHC class II molecules on APCs and secrete cytokines to help activate B cells and cytotoxic T cells.
• T Cytotoxic Cells (CD8+): Recognise antigen presented by MHC class I on infected or abnormal self-cells and release perforin and granzyme to induce apoptosis in target cells.
• Core Markers: CD3, CD4 or CD8, and CD28 (for costimulation with B7 on APCs).

MHC Molecules

• MHC Class I: Present on all nucleated cells, present endogenous antigens, and recognised by CD8+ cytotoxic T cells.
• MHC Class II: Found only on professional APCs, present exogenous antigens, and recognised by CD4+ helper T cells.
• Antigen presentation requires processing and loading onto MHC molecules.

Phagocytosis Mechanism

• Chemotaxis & Adherence: Phagocytes are attracted to infection sites via chemical signals and bind pathogens via receptors.
• Engulfment: Formation of a phagosome by membrane extension around the pathogen.
• Digestion: Phagosome fuses with lysosome to form a phagolysosome, where enzymes degrade the microbe.
• Exocytosis: Digested materials are expelled or presented on MHC molecules to T cells.

Frustrated Phagocytosis

• Occurs when phagocytes cannot engulf a target, leading to extracellular release of enzymes which causes tissue damage.

Granulocytes Overview

• All are derived from the myeloid lineage and contain cytoplasmic granules filled with enzymes and mediators.

Neutrophils

• Abundance: Most common granulocyte (40–75% of WBCs)
• Function: First to arrive at infection and are efficient phagocytes.
• Granules: Primary contain lysosomal enzymes, and secondary contain collagenase and lactoferrin.

Eosinophils

• Abundance: 1–6% of WBCs
• Functions: Defence against parasitic infections and they play a key role in allergic responses.
• Effector Molecules: Major Basic Protein (MBP), and Eosinophil Cationic Protein (ECP).
• Express Fc receptors for IgE, enabling Antibody-Dependent Cellular Cytotoxicity (ADCC).

Basophils and Mast Cells

• Basophils: Mature in bone marrow and circulate in the blood.
• Mast Cells: Migrate to tissues and complete maturation there.
• Function: Mediate Type I hypersensitivity
• Granule Contents: Histamine, serotonin, heparin, leukotrienes, and cytokines.
• Receptors: FcεRI binds IgE.

Primary (Central) Lymphoid Organs

• Bone Marrow: Site of haematopoiesis and B cell development.
• Thymus: Site where T cell maturation and education occur.
• Cortex: Site of positive selection where cells recognise self-MHC.
• Medulla: Site of negative selection where autoreactive cells are removed.

Secondary (Peripheral) Lymphoid Organs

• Lymph Nodes: Distributed throughout the body, filter lymphatic fluid.
• Cortex: Contains B cell zones.
• Paracortex: Contains T cell zones.
• Medulla: Contains plasma cells.
• Spleen: Filters blood, not lymph.
• White pulp: Site of immune functions.
• Red pulp: Site of RBC clearance.
• MALT (Mucosa-Associated Lymphoid Tissue): Defends mucosal surfaces.
• Peyer’s Patches: Located in the ileum, contain B cell follicles and M cells.
• Tonsils: First-line defence in the oral and nasal cavities.
• Appendix: A GALT component involved in antigen sampling in the gut.

Lymphocyte Recirculation

• Lymphocytes circulate between blood, lymph, and secondary lymphoid tissues to maximise the chances of encountering specific antigens, completing one full recirculation circuit every 12–24 hours.

Innate Immunity

• Definition: Refers to the non-specific, first line of defence against pathogens, present at birth, functions immediately or within hours.
• Key Characteristics: Rapid Response, Non-Specific, No Memory
• Bridges to Adaptive Immunity: Initiates inflammation and recruits adaptive immune cells.

Physical & Mechanical Barriers

• Skin: Multi-layered keratinised epithelium that prevents entry of pathogens.
• Mucous Membranes: Line respiratory, GI, and genitourinary tracts and trap microbes.
• Cilia: Move mucus and trapped pathogens out of the respiratory tract.
• Mechanical Actions: Blinking, sneezing, coughing, vomiting, diarrhoea, and urination help expel pathogens.

Chemical & Biochemical Barriers

• Lysozyme: Present in tears and saliva to break peptidoglycan bonds in bacterial walls.
• Fatty Acids & Lactic Acid: On skin and lower pH to inhibit microbial growth.
• Stomach Acid (HCl): Kills most ingested microbes.
• Bile Salts: Disrupt microbial membranes.
• Defensins: Small peptides that insert into membranes and cause microbial cell lysis.
• Lactoferrin: Binds free iron, restricting bacterial growth.

PRRs & Immune Surveillance

• Purpose: Detect conserved microbial structures (PAMPs) and DAMPs.
• Expression: Found on innate immune cells and some epithelial cells.

PRR Families

• TLRs (Toll-like receptors): Located on plasma membranes or endosomes, recognise LPS (TLR4), flagellin (TLR5), viral dsRNA (TLR3), and ssRNA (TLR7/8).
• CLRs (C-type lectin receptors): Detect fungal carbohydrates.
• NLRs (NOD-like receptors): Detect intracellular bacterial molecules and activate inflammasomes.
• RLRs (RIG-I-like receptors): Detect viral RNA.

Viral Recognition

• Viral PAMPs: Uncapped ssRNA, dsRNA, and viral envelope proteins.
• Cytosolic DNA Sensors: IFI16 and cGAS detect viral DNA → activate STING pathway → IFN release.
• Response: Secretion of Type I interferons (IFN-α, IFN-β), cytokines (IL-1, IL-6, TNF-α).

Inflammation Overview

• Eliminate pathogens, prevent spread, initiate repair.
• Cardinal Signs: Calor (heat), Rubor (redness), Tumor (swelling), Dolor (pain), and Functio laesa (loss of function).

Acute Inflammation

• Vasodilation: Increased blood flow.
• Vascular Permeability: Fluid/proteins leak into tissues.
• Leukocyte Extravasation: Rolling, adhesion, and diapedesis.
• Phagocytosis & Killing: Mainly by neutrophils, followed by macrophages.

Key Mediators

• Histamine, Bradykinin, Prostaglandins: Cause vasodilation and permeability.
• Cytokines: IL-1, IL-6, TNF-α induce fever and acute-phase response.
• Chemokines: CXCL8 recruits neutrophils, and CCL2 recruits monocytes.

Inflammasomes

• Components: NLR proteins, adaptor proteins, and pro-caspase-1
• Function: Activate caspase-1, which cleaves pro-IL-1β & pro-IL-18.

Acute Phase Response

• Triggered by: Cytokines IL-1, IL-6, TNF-α.
• Results in: Fever, hormonal changes, and a liver response where CRP, serum amyloid A, and fibrinogen are produced.
• CRP binds microbes, activating the classical complement pathway.

Chronic Inflammation

• Persistent Inflammation: Due to unresolved infection or autoimmunity
• Features: Accumulation of macrophages and lymphocytes.
• Tissue damage is from ROS and enzymes, fibrosis, and granulomas.

Primary Cell Types

• Neutrophils: First responders, phagocytose and kill pathogens, granules contain myeloperoxidase, defensins, and elastase.
• Macrophages: Present antigen to T cells via MHC II and secrete cytokines.
• Dendritic Cells: Key APCs, capture antigen in the periphery, migrate to lymph nodes, and activate naive T cells.
• Mast Cells: Release histamine and serotonin causing vasodilation and recruitment.
• Eosinophils & Basophils: Important in parasitic infections and allergies.

NK Cells

• Type: Large granular lymphocytes; innate lymphocytes.
• Function: Kill virus-infected or tumour cells lacking MHC I
• Mechanism: They release perforin to forms pores and granzymes to induce apoptosis.
• Regulation: Inhibitory receptors detect MHC I (normal cells), and activating receptors detect stress ligands.

Steps of Phagocytosis

• Chemotaxis: Movement of phagocytes toward infection.
• Adherence: Binding via receptors.
• Ingestion: Formation of phagosome.
• Fusion: Phagosome + lysosome → phagolysosome.
• Digestion: O₂-independent and O₂-dependent mechanisms occur.
• Exocytosis: Expulsion of digested material.

O₂-independent mechanisms

• Lysozyme: degrades cell wall
• Defensins: disrupt membranes
• Lactoferrin: sequesters iron
• Enzymes (e.g. proteases)

O₂-dependent mechanisms

• ROS: superoxide, hydrogen peroxide, hydroxyl radicals
• RNS: nitric oxide, nitrogen dioxide

Complement System

• Definition: A cascade of plasma proteins that aid in pathogen destruction, inflammation, and immune complex clearance.
• Pathways of Activation: Classical is triggered by antigen-antibody complexes, lectin is triggered by mannose-binding lectin binding microbial surfaces, and alternative is triggered directly by microbial surfaces.
• Functions of Complement: C3b opsonises, C5a is a chemoattractant for neutrophils and promotes inflammation, C3a/C5a increase vascular permeability and smooth muscle contraction, and MAC forms pores in microbial membranes causing cell lysis.

Antigens

• Antigen (Ag): Any substance capable of being recognised by the immune system.
• Immunogen: An antigen capable of inducing an adaptive immune response.
• Immunogenicity Factors: Foreignness, molecular size, chemical complexity, and degradability.
• Epitopes: The specific part of the antigen recognised by the immune system.
• B Cell Epitopes: Often conformational and are located on the surface of proteins.
• T Cell Epitopes: Always linear peptides presented on MHC molecules.

Antibodies (Immunoglobulins)

• Produced by: Activated B cells (plasma cells)
• Contain 2 Heavy (H) chains and 2 Light (L) chains
• Chains have Variable (V) and Constant (C) regions
• Variable region: Contains hypervariable (complementarity determining regions – CDRs) that form the antigen-binding site
• Constant region: Defines isotype and determines effector functions
• Functions: Neutralisation, opsonisation, complement activation, Antibody-dependent cell-mediated cytotoxicity (ADCC), and degranulation of mast cells.

Immunoglobulin Isotypes

• IgG: 80% of serum antibodies and the only class that crosses the placenta.
• IgM: First antibody produced during primary immune response.
• IgA: Major antibody in mucosal secretions.
• IgE: Lowest serum concentration and important in allergy and defence against helminths.
• IgD: Found in low levels in serum and co-expressed with IgM on naive B cells.

Antibody Epitope Recognition

• Isotype Epitope: Defined by constant region and is the same within species.
• Allotype Epitope: Allelic variation in the constant region and varies between individuals.
• Idiotype Epitope: Located in the variable region, unique to a specific antibody, and determines antigen specificity.

Haptens

• Molecules antigenic but too small to be immunogenic.
• Cannot activate T cells or induce B cell responses alone
• Haptens can become immunogenic when bound to a larger carrier protein

Antigen-Antibody Binding Site

• Interaction occurs between the epitope on the antigen and the CDRs in the variable region of antibody H and L chains
• Binding Forces: Hydrogen bonds, Van der Waals forces, electrostatic interactions, and hydrophobic interactions
• Binding Properties: Affinity, Avidity, and Specificity

B Cell Development

• Occurs in the bone marrow
• Undergoes V(D)J recombination to create unique BCRs
• Plasma Cells: Secrete antibodies
• Memory B Cells: Persist long-term, respond rapidly on re-exposure

Consequences of Antigen-Antibody Binding

• Neutralisation: Blocks pathogen binding to host receptors or inactivates toxins
• Opsonisation: Enhances phagocytosis via Fc receptors
• Complement Activation: Especially via IgM and IgG
• ADCC: NK cells recognise and kill antibody-tagged cells
• Degranulation: Binding of IgE on mast cells triggers histamine release

B Cell Development Summary

• Antigen-independent phase (in bone marrow):
  • Begins with a pluripotent haematopoietic stem cell (HSC)
  • Progresses through stages:
    • Pro-B cell
    • Pre-B cell
    • Immature B cell
  • Negative selection ensures self-reactive B cells are eliminated or undergo receptor editing
• Antigen-dependent phase (in secondary lymphoid tissues):
  • Mature B cell
  • The B cell undergoes:
    • Activation
    • Clonal expansion
    • Class switching (isotype switching)
    • Differentiation into: Plasma cells and Memory B cells

Clonal Selection Hypothesis

• Each B cell expresses a single, unique BCR specific for one antigenic epitope
• Antigen engagement selectively activates that B cell
• Activated B cell proliferates, generating a clone of identical daughter cells producing the same antibody

B Cell Receptor (BCR) Complex

• Composed of: Membrane-bound Immunoglobulin (mIg) and Igα/Igβ heterodimer
• Igα/Igβ heterodimer: Intracellular signalling component

B Cell Co-receptor Complex

• Enhances sensitivity and response to antigen
• Components: CD19, CD21 (CR2), and CD81 Summary of Surface Markers at Each Stage
• Pro-B Cell: CD45R, CD19, CD43, CD24
• Pre-B Cell: CD45R, CD19, CD24, CD25
• Immature B: CD25, surface IgM , CD19, MHC Class I
• Mature B: Surface IgM + IgD, CD19, CD21, MHC Class II, CD40

Production of a Humoral Immune Response

• Plasma Cells:
  • Derived from activated B cells
  • Produce large quantities of antibodies
  • Limited lifespan (days to weeks)
• Memory B Cells:
  • Long-lived cells
  • Retain BCR of original specificity
  • Respond rapidly upon re-exposure to antigen with robust antibody production Primary vs Secondary Humoral Responses
• Primary Response: Involves Naive B cells
• Secondary Response: Involves Memory B cells
• Lag Phase: Longer in primary response and short in secondary response
• Peak Ab Level: Higher in the secondary response and lower in the primary response
• Dominant Ab: IgM dominates primary and IgG (predominantly), also IgA, & IgE in secondary response
• Affinity: Higher in secondary and lower in primary
• Magnitude: Up to 1000x stronger in secondary

T-dependent (TD) B Cell Activation

• Required for most protein antigens
• B cell undergoes proliferation, class switching, and differentiation
• CD40–CD40L: Essential for CSR and germinal centre formation
• B7–CD28: Co-stimulation required for T cell activation
• Cytokines: Direct class switching and B cell fate

Germinal Centre Reaction

• B cell proliferation
• Somatic hypermutation (SHM) → antibody affinity maturation
• Class switch recombination (CSR)
• Generation of memory B cells and long-lived plasma cells

T-independent (TI) Antigens

• Activate B cells without T cell help
• Generally non-protein, often repetitive structures
• Responses primarily involve IgM production; no memory
• TI-1 Antigens: Polyclonal B cell activators
• TI-2 Antigens: Highly repetitive epitopes
• Comparison Table: Shows the basic differences between T-dependent and T-independent Antigens

Isotype (Class) Switching

• Definition: Changing the antibody class without changing specificity
• CD40–CD40L and specific cytokines are required signals.
• IL-4 → IgE, IFN-γ → IgG1, and TGF-β → IgA

Negative Regulation of B Cell Activation

• CD22: Inhibitory receptor; recruits phosphatases.
• ITIMs: Block downstream signalling.
• Necessary to maintain peripheral tolerance

MHC

• MHC (Major Histocompatibility Complex): Encodes cell-surface glycoproteins that present antigenic peptides to T cells, facilitating immune surveillance.
• Immune Roles: Identifies infected or abnormal self-cells, critical in transplant rejection and autoimmunity, and dictates adaptive immune response specificity.
• Human MHC – HLA System: Located on chromosome 6, Class I Genes are HLA-A, HLA-B, and HLA-C, Class II Genes are HLA-DP, HLA-DQ, and HLA-DR, while Class III Genes encode non-presenting proteins

MHC Class I Structure and Function

• MHC Class I Structure and Function: Composed of α chain (α1, α2, α3) + β2-microglobulin (non-MHC encoded), α1 + α2 bind peptides, and α3 interacts with CD8.
• Expression: On all nucleated cells
• Function: Presents endogenous peptides to CD8+ cytotoxic T cells.

MHC Class II Structure and Function

• Composed of α (α1, α2) and β (β1, β2) chains
• α1 + β1 = peptide-binding groove
• β2 domain binds CD4
• Expression: Restricted to professional APCs (dendritic cells, macrophages, B cells)
• Function: Presents extracellular-derived peptides to CD4+ helper T cells

MHC Polymorphism

• Extremely polymorphic: Each locus has many alleles across population
• Co-dominant expression: Both maternal and paternal alleles expressed
• Individual Expression:
• Expression: Up to 6 different MHC I molecules and 12 MHC II combinations.
• Significance: Ensures population-level diversity in antigen presentation, affecting vaccine responses and disease susceptibility

Antigen Processing and Presentation

• Antigen Processing: Proteins (self or non-self) are degraded into peptides within cells
• Antigen Presentation: Processed peptides are loaded onto MHC molecules and displayed on the cell surface
• Self-MHC Restriction: TCRs recognise peptide-MHC complexes only if MHC is self-derived

Cytosolic (Endogenous) Pathway

• Ubiquitination: Proteins targeted for degradation.
• Proteasome Degradation: Generates short peptide fragments.
• Transporter (TAP) transports peptide into RER.
• Peptide Loading: Occurs as MHC class I components are assembled
• Presented to: CD8+ cytotoxic T lymphocytes

Endocytic (Exogenous) Pathway

• Antigen Uptake: Phagocytosis, receptor-mediated endocytosis, pinocytosis
• Processing: Enzymatic degradation in acidified endosomal compartments
• Peptides associated with MHC II
• Presented to: CD4+ T cells

Cross-Presentation

• Definition: Loading of exogenous antigens onto MHC Class I
• CD4+ T cell engagement enhances APC cross-presentation capacity

Non-Peptide Antigen Presentation

• CD1 Molecules: Present lipid/glycolipid antigens, are recognised by NKT cells, and have 5 isoforms.
• MR1 Presents vitamin B derivatives Recognized by MAIT cells.