2. Pattern Recognition Receptors (PRRs) and Toll-like Receptors (TLRs)

The innate immune system identifies pathogens using germline-encoded Pattern Recognition Receptors (PRRs) that detect highly conserved molecular structures.

2.1 Molecular Targets: PAMPs vs. DAMPs

• Exogenous
  PAMPs

  Pathogen-Associated Molecular Patterns: highly conserved, pathogen-specific molecular signatures essential for microbial survival. Examples include double-stranded RNA (dsRNA) of viruses, unmethylated CpG DNA sequences in bacteria, bacterial pilin and flagellin, lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, and lipoteichoic acid in Gram-positive cell walls.

• Endogenous
  DAMPs

  Damage-Associated Molecular Patterns: endogenous molecules released from damaged, stressed, or dying host cells, signaling tissue damage.

2.2 Mammalian PRR Classes

Mammals possess several distinct classes of cellular and soluble PRRs:

2.3 Toll-Like Receptor (TLR) Architecture and Ligands

TLRs were originally identified for their role in the embryonic development of Drosophila melanogaster (controlling dorso-ventral polarity) and adult fly fungal resistance. They are Type I integral transmembrane glycoproteins ranging from 700 to 1100 amino acids.

• N-terminal
  Extracellular Domain

  Contains 16 to 28 leucine-rich repeats (LRRs) arranged in a horseshoe shape, responsible for PAMP/DAMP ligand binding.

• C-terminal
  Intracellular Domain

  Contains a conserved Toll/IL-1 receptor (TIR) domain that initiates downstream signaling cascades.

TLRs are categorised by their subcellular localisation, which correlates with their ligand specificity:

2.4 TLR Signaling Pathways

Ligand binding induces the dimerisation of TLRs (either as homodimers or heterodimers). This conformational change recruits specific cytoplasmic adaptor proteins to the TIR domain, initiating two primary signaling pathways.

Figure: TLR Signaling Pathways. TLR dimerisation recruits one of two adaptor proteins to the TIR domain. All TLRs except TLR3 signal through MyD88, driving a kinase cascade that activates NF-κB and the transcription of pro-inflammatory cytokines (IL-1, IL-6, TNF-α). TLR3 and endosomal TLR4 signal through TRIF, activating Interferon Regulatory Factors (IRF3/IRF7) to drive transcription of Type I interferons (IFN-α, IFN-β) and promote dendritic cell maturation.

3. The Inflammatory Response and Cytokine Biology

Inflammation is a coordinated response designed to deliver host defence cells and molecules from the blood directly to the site of infection or tissue damage.

3.1 Clinical Hallmarks of Inflammation

Historically described by five Latin terms:

• Sign 1
  Calor & Rubor
  (heat & redness)

  Result from increased vascular diameter (vasodilation) and increased local blood flow.

• Sign 2
  Tumor
  (swelling / edema)

  Caused by increased vascular permeability leading to the leakage of fluids and plasma proteins into tissue spaces.

• Sign 3
  Dolor
  (pain)

  Caused by chemical mediators stimulating local nerve endings.

• Sign 4
  Functio Laesa
  (loss of function)

  Results from the combined tissue swelling and pain.

3.2 Cytokine Characteristics and Mechanics

Cytokines are low molecular weight (typically less than 30 kDa), non-immunoglobulin soluble proteins secreted by immune cells to coordinate cellular communication. Unlike hormones, which are produced by specialised glands and act endocrine-style on restricted targets, cytokines are secreted by many widely distributed cells in response to specific stimuli, acting locally or systemically.

Cytokines exhibit four hallmark regulatory properties:

• Property 1
  Pleiotropy

  A single cytokine exerts distinct biological activities on different target cells.

• Property 2
  Redundancy

  Multiple different cytokines mediate the same functional outcome.

• Property 3
  Synergy

  The combined effect of two cytokines is significantly greater than the sum of their individual effects.

• Property 4
  Antagonism

  One cytokine directly inhibits or counteracts the biological effect of another.

Figure: Pleiotropy vs. Redundancy. Pleiotropy occurs when a single cytokine (Cytokine X) produces distinct effects on different target cells (A, B, C). Redundancy is the converse: multiple distinct cytokines (Cytokine Y, Cytokine Z) converge on the same target cell (D) to produce the same functional outcome (Effect 4).

3.3 Major Cytokine Families

• Family
  Interleukins (ILs)

  Secreted primarily by leukocytes to regulate other leukocytes.

• Family
  Chemokines

  Chemoattractant cytokines defined by four conserved cysteine residues, signaling through G-protein coupled receptors (GPCRs) to direct cell migration.

• Family
  Interferons (IFNs)

  Critical mediators of antiviral defence, cell growth inhibition, and immune activation. Grouped into Type I (IFN-α, IFN-β), Type II (IFN-γ), and Type III.

• Family
  TNF Family

  A group of 19 structurally related proteins (including TNF-α and TNF-β) regulating cell survival, differentiation, and apoptosis.

• Family
  Hematopoietins

  Cytokines that drive hematopoietic stem cell differentiation, including Colony-Stimulating Factors (CSF: G-CSF, M-CSF, GM-CSF) and Erythropoietin (Epo).

Primary Innate Cytokines

4. Adaptive Immunity

Adaptive (acquired) immunity is an evolutionary feature restricted to jawed vertebrates.

4.1 Key Characteristics of Adaptive Immunity

Adaptive immunity displays four key characteristics:

• Feature 1
  Antigenic Specificity

  The capacity to distinguish subtle differences among distinct antigens.

• Feature 2
  Diversity

  The ability to recognise and respond to billions of unique antigenic configurations.

• Feature 3
  Immunologic Memory

  The capacity to recall previous encounters with an antigen, resulting in a primary response that transitions into a much faster, larger, and more effective secondary response.

• Feature 4
  Self/Non-Self Recognition

  The ability to respond only to foreign molecules while remaining tolerant to self-antigens (self-tolerance).

4.2 Innate vs. Adaptive Immunity: A Comparative Analysis

4.3 Classifications of Acquired Immunity

Adaptive immunity can be acquired naturally or artificially, and is divided into active or passive forms.

Figure: Classification of Acquired Immunity. Adaptive immunity splits into active immunity, where the host's own immune system is activated and undergoes clonal expansion to create memory, and passive immunity, where the host receives preformed antibodies or cells for immediate but temporary protection without memory formation. Each branch further divides into a naturally-acquired and an artificially-acquired route.

5. Cells of the Immune System: Lineage and Differentiation

All mature blood cells develop from self-renewing, pluripotential Hematopoietic Stem Cells (HSCs) in the bone marrow. This developmental process, called hematopoiesis (or haemopoiesis), branches early into two main lineages: the Common Myeloid Progenitor (CMP) and the Common Lymphoid Progenitor (CLP).

Figure: Hematopoiesis. The HSC gives rise to a Multipotent Progenitor, which branches into the myeloid lineage (CMP, in rust) and the lymphoid lineage (CLP, in purple). The CMP further differentiates through the MEP and GMP into red blood cells, platelets, granulocytes, and monocyte-derived macrophages/dendritic cells; the CLP differentiates directly into B cells, T cells, and NK cells.

5.1 The Lymphoid Lineage (CLP Derivatives)

Lymphocytes constitute 20% to 40% of circulating white blood cells; however, 99% reside in lymphoid tissues and organs.

1. B Lymphocytes (B Cells)

• Maturation
  Site

  Arise and mature within the bone marrow of mammals (or the Bursa of Fabricius in birds).

• Receptor
  Antigen Receptor

  Express membrane-bound immunoglobulins (antibodies) that directly bind free, unprocessed extracellular antigens.

• Function
  Effector Function

  Upon activation and helper T cell signaling, naive B cells proliferate and differentiate into antibody-secreting plasma cells and long-lived memory B cells. B cells also act as professional Antigen-Presenting Cells (APCs).

2. T Lymphocytes (T Cells)

• Maturation
  Site

  Arise in the bone marrow but migrate to the thymus to undergo maturation, TCR gene rearrangement, and positive/negative selection.

• Receptor
  Antigen Receptor

  Express a membrane-bound T-cell receptor (TCR), a heterodimer composed of either αβ or γδ chains. The TCR can only recognise processed peptide fragments presented on Major Histocompatibility Complex (MHC) molecules of APCs.

3. Natural Killer (NK) Cells

• Class
  Classification

  Large, granular lymphocytes belonging to the Innate Lymphoid Cell (ILC) family. Unlike B and T cells, they do not express antigen-specific receptors and do not display immunological memory.

• Maturation
  Site

  Mature in the bone marrow; thymus maturation is not required.

• Mechanism
  Mode of Action

  Kill infected, stressed, or malignant host cells in an antigen-non-specific manner by releasing perforin and granzymes.

• Regulation
  NK Receptors

  Regulated by a balance of activating and inhibiting receptors (NKRs). Inhibiting receptors recognise self-MHC Class I molecules on healthy host cells. Because viral infection or malignant transformation often downregulates MHC Class I ("missing self"), the inhibitory signal is lost, triggering NK cell degranulation.

4. Natural Killer T (NKT) Cells

• Class
  Classification

  A distinct lymphocyte subset sharing properties of both T cells and NK cells.

• Receptor
  Antigen Receptor

  Express a semi-invariant TCR alongside NK cell markers. Unlike classical T cells, their TCR does not recognise MHC-peptide complexes; instead, it recognises foreign and self glycolipid antigens presented by the MHC Class I-like molecule CD1d.

5.2 The Myeloid Lineage (CMP Derivatives)

1. Granulocytes

Characterised by irregularly shaped, multilobed nuclei (polymorphonuclear) and prominent cytoplasmic granules:

• Cell
  Neutrophils (PMNs)
  • Make up 50% to 70% of circulating WBCs.
  • Their granules stain with both acidic and basic dyes.
  • Short-lived phagocytes (circulating 7–10 hours before migrating to tissues, where they live only a few days).
  • Extravasation Cascade: (1) adhesion to endothelial cells, (2) penetration through endothelial cell junctions, (3) penetration of the vascular basement membrane, (4) migration towards chemotactic signals.
• Cell
  Eosinophils
  • Make up 2% to 5% of WBCs.
  • Stain brightly with the acidic dye eosin and possess a bilobed nucleus.
  • Active in host defence against protozoan and helminth parasites by releasing highly toxic cationic proteins and ROS into the extracellular environment.
• Cell
  Basophils
  • Make up less than 1% of circulating WBCs.
  • Stain with the basic dye methylene blue and possess a lobed nucleus.
  • Non-phagocytic; express high-affinity IgE Fc receptors (FcεR). Antigen binding cross-links IgE, triggering degranulation and release of vasoactive amines (histamine, serotonin), prostaglandins, and leukotrienes to initiate allergic responses.
• Cell
  Mast Cells
  • Arise from pluripotent stem cells in the bone marrow but enter circulation in an immature state. They migrate to tissues (mucosal surfaces, skin) where they mature under the influence of c-kit ligand and Stem Cell Factor (SCF).
  • Like basophils, contain large amounts of histamine-rich granules and express high-affinity IgE receptors, playing a critical role in allergies and anaphylaxis.

2. Monocytes and Macrophages

Macrophages are highly phagocytic cells present in almost all healthy tissues, divided into two distinct developmental origins:

• Origin 1
  Inflammatory Macrophages

  Differentiate from recruited blood monocytes during infection or tissue inflammation.

• Origin 2
  Tissue-Resident Macrophages

  Originate from embryonic progenitor cells during fetal development. They do not circulate and are self-renewing, performing tissue-specific physiological and homeostatic functions.

3. Dendritic Cells (DCs)

Dendritic cells arise from both myeloid and lymphoid lineages, exhibiting long, membrane-like extensions resembling dendrites.

• Type
  Classical Antigen-Presenting DCs

  Capture antigen in peripheral tissues (by phagocytosis or macropinocytosis), process it, and migrate to secondary lymphoid organs. There, they upregulate co-stimulatory molecules and constitutively express exceptionally high levels of MHC Class II molecules, acting as professional APCs to activate naive T_H cells.

• Subtypes
  Four Major DC Subtypes

  Langerhans cells, interstitial dendritic cells, myeloid dendritic cells, and lymphoid dendritic cells.

6. Lymphoid Organs: Architecture and Function

The lymphatic system is organized into primary (central) lymphoid organs, where lymphocytes mature, and secondary (peripheral) lymphoid organs, where mature lymphocytes encounter antigens and initiate immune responses.

Figure: Classification of Lymphoid Organs. Primary lymphoid organs (Bone Marrow, Thymus) provide the microenvironment for antigen-independent lymphocyte maturation. Secondary lymphoid organs (Spleen, Lymph Nodes, MALT) capture antigens and support antigen-dependent activation of mature lymphocytes.

6.1 Primary Lymphoid Organs

These organs provide the microenvironment necessary for B-cell and T-cell precursors to mature and acquire their antigen-specific receptors.

Thymus

A flat, bilobed organ situated above the heart, surrounded by a capsule and divided into lobules by connective tissue strands called trabeculae. Each lobule consists of:

• Zone
  Outer Cortex

  Packed with immature, rapidly proliferating T-cell precursors (thymocytes) undergoing positive selection.

• Zone
  Inner Medulla

  Contains more mature thymocytes undergoing negative selection (to eliminate self-reactive T cells).

After thymic selection, functional, self-tolerant T cells enter the bloodstream and home to secondary lymphoid organs.

6.2 Secondary Lymphoid Organs

These organs are anatomically designed to trap and concentrate foreign antigens, bringing them into contact with migrating, mature lymphocytes.

1. Spleen

The largest secondary lymphoid organ, located in the abdominal cavity. It specializes in trapping blood-borne antigens and is the main site of systemic antibody production. The spleen parenchyma is divided into two distinct regions:

• Region 1
  Red Pulp

  Composed of venous sinusoids and splenic cords (Billroth's cords) containing erythrocytes, macrophages, lymphocytes, and granulocytes.

  • Macrophages destroy blood-borne pathogens
  • Removes worn-out, ruptured, or defective red blood cells and platelets
  • Stores up to one-third of the body's platelets
  • Serves as a site of hematopoiesis during fetal development
• Region 2
  White Pulp

  Organized lymphoid tissue arranged around central arteries, forming the Periarterial Lymphatic Sheath (PALS):

  • The PALS is dominated by T cells.
  • Surrounding lymph follicles contain B cells. Upon antigen stimulation, these follicles develop germinal centres where B cells undergo rapid clonal expansion and differentiation into plasma cells.

Figure: Spleen Parenchyma. Red pulp clears defective blood cells, stores platelets, and supports fetal hematopoiesis. White pulp is organized around central arteries into the T-cell-dominated PALS and B-cell-containing follicles; antigen stimulation drives follicles to develop germinal centres, the site of B-cell clonal expansion and plasma cell differentiation.

2. Lymph Nodes

Small, encapsulated, bean-shaped structures (typically less than 1 cm in diameter) distributed along lymphatic vessels throughout the body. They act as filters for lymph to trap tissue-derived antigens:

3. Mucosa-Associated Lymphoid Tissue (MALT)

Organized lymphoid structures situated at mucosal surfaces of the respiratory, digestive, and genitourinary tracts, which are major entry ports for pathogens. Key components include:

• Component
  BALT

  Bronchus-Associated Lymphoid Tissue.

• Component
  GALT

  Gut-Associated Lymphoid Tissue. GALT includes the tonsils and adenoids, and Peyer's patches.

7. Innate and Adaptive Immunity Are Interdependent

Innate and adaptive immune systems do not function in isolation. They are highly cooperative and interdependent.

Figure: Innate-Adaptive Feedback Loop. The innate system instructs the adaptive response through antigen presentation and co-stimulatory signals, while the adaptive system, once activated, enhances innate effector mechanisms through cytokines and antibody-mediated targeting.