Comprehensive Study Guide: Organs of the Immune System and Innate and Infl and Nate and Innate and Path and Innate and Innate and

Overview of Lymphoid Organs

• Lymphoid organs are stationed throughout the entire body to ensure comprehensive immune surveillance.
• They are primarily concerned with the growth, development, and differentiation of lymphocytes.
• These organs are structurally and functionally diverse but are connected by blood and lymphatic vessels, which facilitate the circulation of lymphocytes.
• These organs facilitate both specific (adaptive) and non-specific (innate) immunity.

Classification of Lymphoid Organs

Lymphoid organs are classified based on the functional development of lymphatic cells into three groups:

1. Primary Lymphoid Organs (Central/Generative Organs): Sites where lymphocyte maturation takes place. They include the thymus and the bone marrow.
2. Secondary Lymphoid Organs (Peripheral): Sites that trap antigens (Ag) and provide the environment for mature lymphocytes to interact with those antigens. Examples include lymph nodes, spleen, mucosal-associated lymphoid tissues (MALT), and gut-associated lymphoid tissue (GALT).
3. Tertiary Lymphoid Organs: These normally contain fewer lymphoid cells than secondary organs. An example is cutaneous-associated lymphoid tissues (CALT).

Primary Lymphoid Organs: Bone Marrow and Thymus

• Role in Hematopoiesis: Immature lymphocytes are generated during hematopoiesis. They mature and become committed to a particular antigenic specificity within primary lymphoid organs.
• Immunocompetence: A lymphocyte is considered immunocompetent (capable of mounting an immune response) only after it has matured within a primary lymphoid organ.
• T-cell Development: T-cells arise in the bone marrow but develop and mature in the thymus.
• B-cell Development: In many mammals, including humans and mice, B-cells originate and mature in the bone marrow.
• Circulation: Once mature lymphocytes are generated, they circulate through the blood and lymphatic system to reach other tissues.

Detailed Structure and Function of the Thymus

• Site of T-cell Maturation: The thymus is the dedicated site for T-cell development and maturation.
• Location: It is a flat, lobed organ situated just above the heart.
• Morphology:
  • Each lobe is surrounded by a capsule.
  • Lobes are divided into lobules by strands of connective tissue called trabeculae.
• Internal Compartments:
  • Cortex: The outer compartment; densely packed with immature and proliferating thymocytes. Some mature cells migrate from here to the medulla.
  • Medulla: The inner compartment; sparsely populated with thymocytes. It is here that thymocytes learn to discriminate between self and non-self.
• Cellular Composition: Besides lymphoid cells, the thymus contains:
  • Epithelial cells (both cortical and medullary).
  • Macrophages ($M\Phi s$).
  • Dendritic cells (DCs).
  • Nurse cells.
  • Hassall’s corpuscles (found in the medulla).
• Fate of Thymocytes: More than $95\%$ of all thymocytes die by apoptosis within the thymus without reaching maturity. This process involves clonal selection:
  • Termination of T-cells that cannot recognize Ag-MHC complexes.
  • Termination of T-cells that react with self Ag-MHC to prevent autoimmune diseases.
• Post-Maturation: T-cells leave the medulla via peripheral blood circulation to populate secondary lymphoid organs.

Clinical and Experimental Roles of the Thymus

• Thymectomy: The surgical removal of the thymus. In mice, this leads to a decrease in circulating lymphocytes and an almost complete absence of cell-mediated immunity.
• DiGeorge’s Syndrome: A congenital birth defect in humans caused by a mutation on the $22^{nd}$ chromosome, resulting in the absence of the thymus and severe T-cell deficiency.
• Nude Mice: A specific laboratory strain with a genetic mutation resulting in an absent or deteriorated thymus. This causes an inhibited immune response due to a lack of T-cells. These mice also lack body hair (hence the name "nude").
• Aging (Involution):
  • The thymus attains its maximum size at puberty and then diminishes (involution).
  • Cortical and medullary cells decrease while total fat content increases.
  • Average weight in infants: $70\,g$.
  • Average weight in the elderly: $3\,g$.
  • Experimental evidence: Thymectomized adult mice implanted with a newborn thymus ($1-day$ old) showed significantly better immune function improvement than those receiving a thymus from a $33-month$ old mouse.

Secondary Lymphoid Organs: The Spleen

• General Characteristics: A large, ovoid organ located high in the left abdominal cavity. It is supplied by the splenic artery rather than lymphatic vessels.
• Function: Specializes in filtering blood and trapping blood-borne antigens, making it critical for responding to systemic infections.
• Recirculation: More recirculating lymphocytes pass through the spleen daily than through all lymph nodes combined.
• Structure: Surrounded by a capsule with trabeculae projecting inward to compartmentalize the organ. It has two main compartments separated by a diffuse marginal zone:
  • Red Pulp: Composed of reticular tissue and sinuses bathed in blood. It is populated by macrophages, numerous RBCs, and few lymphocytes. It is the site where old or defective RBCs are destroyed; macrophages here often contain engulfed RBCs or degraded iron pigments.
  • White Pulp: Arranged into the Periarteriolar Lymphoid Sheath (PALS), which surrounds branches of the splenic artery and is populated mainly by T-cells.
• Follicular Zones: Primary lymphoid follicles (rich in B-cells) are attached to the PALS. Upon antigenic challenge, these develop into secondary follicles containing germinal centers with rapidly dividing B-cells (centroblasts) and plasma cells.
• Blood Entry: Blood-borne Ags and lymphocytes enter through the splenic artery into the marginal zone. Ag is trapped by interdigitating DCs and carried to the PALS for presentation to $T_H$ cells using MHC II molecules.
• Splenectomy: Effects vary by age. In children, it may lead to increased bacterial sepsis, primarily caused by:
  • Streptococcus pneumoniae
  • Neisseria meningitidis
  • Haemophilus influenzae

Secondary Lymphoid Organs: Lymph Nodes

• Function: Sites where immune responses are mounted against antigens found in the lymph. They are the first organized lymphoid structures to encounter antigens entering tissue spaces.
• Morphology: Encapsulated, bean-shaped structures containing a reticular network packed with lymphocytes, macrophages, and dendritic cells.
• Architecture:
  • Cortex: Outermost layer containing lymphocytes (mostly B-cells), macrophages, and follicular DCs arranged in primary follicles. These enlarge into secondary follicles after antigenic challenge.
  • Paracortex: Located beneath the cortex; populated largely by T-lymphocytes and interdigitating DCs (iDCs) that migrated from tissues. This is a "thymus-dependent" area (depleted in neonatally thymectomized mice). iDCs here express high levels of MHC II.
  • Medulla: Innermost layer, sparsely populated with lymphoid cells, many of which are plasma cells.
• Lymph Flow: Lymph enters via incoming vessels, percolates through the node where Ag is trapped by phagocytes and DCs, and exits via outgoing vessels.

Mucosal-Associated Lymphoid Tissue (MALT)

• Definition: Organized lymphoid tissues defending the mucous membranes of the respiratory, digestive, and urogenital systems.
• Components: Includes tonsils, Peyer’s patches, the appendix, and the lamina propria of intestinal villi.
• Antibody Production: MALT contains a population of antibody-producing plasma cells that exceeds the number found in the spleen, lymph nodes, and bone marrow combined.
• Tonsils: found in three locations:
  • Lingual (base of tongue)
  • Palatine (sides of the back of the mouth)
  • Pharyngeal/Adenoids (roof of the nasopharynx)
  • Waldeyer’s Ring: A protective ring at the upper ends of the respiratory and alimentary tracts consisting of $2$ palatine tonsils, the pharyngeal tonsil, the lingual tonsil, and $2$ tubal tonsils.
  • Mechanism: Tonsils use specialized "M cells" on their surface to capture inhaled or ingested antigens and alert B and T cells.
• Peyer's Patches: Found in the submucosal layer of the intestinal lining (mainly ileum). They contain follicles rich in B-cells and use M cells to deliver small particles, viruses, and bacteria to submucosal macrophages for processing.

Cutaneous-Associated Lymphoid Tissue (CALT)

• Skin Barrier: The epidermal layer consists of keratinocytes which secrete cytokines and can express MHC II molecules to function as APCs.
• Langerhans Cells: Specialized dendritic cells in the epidermis that internalize antigens via phagocytosis or endocytosis.
• Migration: Langerhans cells migrate from the epidermis to regional lymph nodes, where they differentiate into interdigitating DCs (iDCs) to activate naïve $T_H$ cells.

The Innate Immune System

• Characteristics: Fast-acting, non-specific, generic response. It includes cells and molecules pre-deployed before infection.
• Response Time: Hours (compared to days for adaptive immunity).
• Specificity: Limited and fixed; recognizes broad classes of pathogens.
• Memory: Response to repeat infection is identical to the primary response.
• Barriers:
  • Anatomic: Skin (pH $3-5$; mechanical barrier) and Mucous membranes (flora competition, mucus entrapment, cilia propulsion).
  • Physiologic: Temperature (fever inhibits growth) and Low pH (stomach acidity).
  • Chemical Mediators: Lysozyme (cleaves bacterial walls), Interferon (antiviral state), Complement (lysis/phagocytosis), Toll-like receptors (signal cytokine secretion), and Collectins.
  • Phagocytic/Endocytic: Specialized cells like monocytes, neutrophils, and tissue macrophages.
  • Inflammatory: Vascular fluid leakage containing antibacterial serum proteins and influx of phagocytes.

Pattern Recognition Receptors (PRRs)

• Molecular Patterns: PRRs recognize broad structural motifs (Pattern-Associated Molecular Patterns - PAMPs) found on microbes but absent in hosts. Receptors are encoded in the host germline.
• PRR Families:
  • CLR (C-type Lectin Receptors): Transmembrane proteins recognizing glycans (e.g., Dectin-1 recognizes $\beta-1,3-glucans$ in fungi).
  • TLR (Toll-like Receptors): Located on plasma membranes or in endosomes; recognize proteins, nucleic acids, and glycans.
  • NLR (Nucleotide-binding oligomerization domain-like receptors): Cytoplasmic sensors. NOD1 and NOD2 recognize bacterial peptidoglycan. Form inflammasomes.
  • RLR (RIG-I like receptors): Cytoplasmic sensors of viral RNA (e.g., RIG-I and MDA5).
• PAMP Examples: LPS (gram-negative), Lipoteichoic acid (gram-positive), Flagellin, peptidoglycans, ssRNA, dsRNA, CpG DNA.
• DAMPs (Damage Associated Molecular Patterns): Molecules displayed on stressed or injured human cells (e.g., Heat Shock Proteins (HSPs), Uric acid, ATP, Histones). These signal "danger" and can lead to a "vicious cycle" of inflammation.

Detailed Analysis of Toll-like Receptors (TLRS)

• Structure:
  • LRR (Leucine-rich repeats): Repeating segments of $24-29$ amino acids (sequence: xLxxLxLxx) containing the ligand-binding site.
  • TIR Domain: Interacts with other members of the TLR signal transduction pathway; contains highly conserved sequences (Box 1, 2, and 3).
• Diversity: Humans express $11$ TLR genes; mice express $12$.
• Specific TLR Ligands:
  • TLR2: Peptidoglycan, Lipoproteins (Gram-positive).
  • TLR3: dsRNA (Viruses).
  • TLR4: Lipopolysaccharides (LPS - Gram-negative).
  • TLR5: Flagellin (Bacteria).
  • TLR7/8: ssRNA (Viruses).
  • TLR9: CpG DNA (Bacteria/Viruses).
• Pathogen Sabotage: Patterns for evading TLR discovery include camouflaging targets (e.g., P. aeruginosa), interfering with downstream signaling (e.g., Y. pestis), or "sneaking through the back door" via invasion proteins (e.g., Shigella and Listeria).

The Complement System

• Definition: A group of about $30$ soluble and cell-bound proteins that augment antibodies in killing bacteria, primarily synthesized in the liver as inactive precursors (zymogens).
• Properties: They are heat-labile (inactivated at $56^\circ C$ for $30\,minutes$) and constitute $5\%$ of normal serum.
• Main Effects:
  1. Lysis of cells, bacteria, and viruses.
  2. Opsonization (enhancing phagocytosis).
  3. Activation of inflammatory response.
  4. Clearance of immune complexes (deposition in spleen/liver).
• Nomenclature:
  • Classical components are designated C1 through C9 (order of discovery).
  • Reaction sequence: C1, C4, C2, C3, C5, C6, C7, C8, C9.
  • Cleaved fragments: 'a' is generally the smaller fragment (diffuses away), 'b' is the larger fragment (binds to target). Exception: $C2a$ is the large fragment and $C2b$ is the small fragment.
  • Activated complexes with enzymatic activity have a bar over them (e.g., $\overline{C4b2a}$).

Complement Pathways

1. Classical Pathway: Antibody-dependent. Triggered by Ag-Ab complexes binding to C1q.
2. Lectin Pathway: Antibody-independent. Initiated by Mannose-Binding Lectin (MBL) binding to mannose on pathogen surfaces, activating MASP-1 and MASP-2.
3. Alternative Pathway: Antibody-independent. Stimulated by pathogen surfaces directly (e.g., LPS). Uses Factors B, D, and C3b to form an amplification loop.

Stages of Complement Activation

• Formation of C3 Convertase:
  • Classical/Lectin: $\overline{C4b2a}$
  • Alternative: $\overline{C3bBb}$
• Function of C3b: The central molecule. Acts as an opsonin and binds to C3 convertase to form C5 convertase.
• Formation of C5 Convertase: Cleaves C5 into $C5a$ (pro-inflammatory) and $C5b$.
• Membrane Attack Complex (MAC): $C5b$ initiates late events, recruiting C6, C7, C8, and multiple C9 molecules to form a cytotoxic pore ($C5b-9$).
  • Leading to death by osmotic flux in Gram-negative bacteria like Neisseria meningitidis.
  • Deficiencies in MAC components lead to recurrent Neisseria infections.

Endocytosis and Inflammation

• Endocytosis Types: Includes Phagocytosis (solid particles), Pinocytosis (extracellular fluid), and Receptor-mediated endocytosis.
• Macropinocytosis: "Cell drinking"; nonspecific uptake used by macrophages and DCs to survey extracellular fluid for antigens.
• Inflammatory Response: A protective attempt to remove pathogens and repair tissue.
• Key Signs of Inflammation (PRISH / SRHPI):
  • Pain (Dolor): Release of chemicals like bradykinin/histamine.
  • Redness (Rubor): Vasodilation and increased blood volume.
  • Immobility/Loss of Function (Functio Laesa): The main pathologic feature.
  • Swelling (Tumor): Increased capillary permeability (oedema).
  • Heat (Calor): Cytokine expression and localized rise in temperature.