Autoimmunity

Autoimmunity is a condition that arises when the immune system loses its ability to distinguish between 'self' and 'non-self,' a critical failure of immunological tolerance. Consequently, the body's defense mechanisms mistakenly target and attack its own healthy cells, tissues, and organs as if they were foreign pathogens. This self-directed assault, often driven by autoantibodies and self-reactive T cells, leads to chronic inflammation, tissue damage, and the development of a wide spectrum of autoimmune diseases.

1. Fundamentals of the Immune System
   1. Core Principles of Immunity
      1. Innate Immunity
         1. Definition and Characteristics
         2. Physical Barriers
            1. Skin
            2. Mucous Membranes
            3. Epithelial Tight Junctions
         3. Chemical Barriers
            1. Antimicrobial Peptides
            2. Complement Components
            3. pH and Enzymatic Barriers
         4. Cellular Components
            1. Neutrophils
            2. Macrophages
            3. Dendritic Cells
            4. Natural Killer Cells
            5. Eosinophils
            6. Basophils
            7. Mast Cells
         5. Pattern Recognition Receptors
            1. Toll-like Receptors
            2. NOD-like Receptors
            3. RIG-I-like Receptors
            4. C-type Lectin Receptors
      2. Adaptive Immunity
         1. Definition and Characteristics
         2. Antigen Specificity
            1. Molecular Recognition
            2. Epitope Binding
         3. Immunological Memory
            1. Primary Immune Response
            2. Secondary Immune Response
            3. Memory Cell Longevity
         4. Clonal Selection Theory
            1. Antigen-Driven Selection
            2. Clonal Expansion
            3. Effector Cell Generation
      3. Immune System Diversity
         1. Generation of Antigen Receptor Diversity
            1. V(D)J Recombination
            2. Somatic Hypermutation
            3. Class Switch Recombination
         2. T Cell Receptor Diversity
         3. B Cell Receptor Diversity
      4. Self versus Non-Self Recognition
         1. Mechanisms of Self-Recognition
            1. MHC Restriction
            2. Self-Antigen Presentation
         2. Danger-Associated Molecular Patterns
         3. Pathogen-Associated Molecular Patterns
         4. Central Tolerance Mechanisms
         5. Peripheral Tolerance Mechanisms
   2. Cellular Components of the Immune System
      1. Lymphocytes
         1. T Lymphocytes
            1. T Cell Development
               1. Thymic Maturation
               2. Positive Selection
               3. Negative Selection
            2. Helper T Cells
               1. Th1 Cells
                  1. Cytokine Profile
                  2. Functions
                  3. Differentiation Signals
               2. Th2 Cells
                  1. Cytokine Profile
                  2. Functions
                  3. Differentiation Signals
               3. Th17 Cells
                  1. Cytokine Profile
                  2. Functions
                  3. Differentiation Signals
               4. Follicular Helper T Cells
                  1. B Cell Help Functions
                  2. Germinal Center Formation
               5. Regulatory T Cells
                  1. Natural Regulatory T Cells
                  2. Induced Regulatory T Cells
                  3. Suppressive Mechanisms
            3. Cytotoxic T Lymphocytes
               1. Antigen Recognition
               2. Cytotoxic Mechanisms
               3. Memory Formation
            4. Memory T Cells
               1. Central Memory T Cells
               2. Effector Memory T Cells
               3. Tissue-Resident Memory T Cells
         2. B Lymphocytes
            1. B Cell Development
               1. Bone Marrow Maturation
               2. Immunoglobulin Gene Rearrangement
               3. Selection Processes
            2. Naive B Cells
               1. Surface Markers
               2. Activation Requirements
            3. Activated B Cells
               1. Germinal Center Formation
               2. Somatic Hypermutation
               3. Class Switching
            4. Plasma Cells
               1. Antibody Production
               2. Lifespan and Location
            5. Memory B Cells
               1. Long-term Protection
               2. Rapid Reactivation
         3. Natural Killer Cells
            1. Recognition Mechanisms
            2. Cytotoxic Functions
            3. Regulatory Functions
      2. Antigen-Presenting Cells
         1. Dendritic Cells
            1. Conventional Dendritic Cells
               1. Subtypes
               2. Antigen Capture
               3. Migration Patterns
            2. Plasmacytoid Dendritic Cells
               1. Type I Interferon Production
               2. Viral Recognition
            3. Dendritic Cell Maturation
               1. Costimulatory Molecule Expression
               2. Cytokine Production
         2. Macrophages
            1. Tissue-Resident Macrophages
               1. Organ-Specific Functions
               2. Homeostatic Roles
            2. Inflammatory Macrophages
               1. Recruitment Mechanisms
               2. Pro-inflammatory Functions
            3. Macrophage Polarization
               1. M1 Polarization
               2. M2 Polarization
         3. B Cells as Antigen-Presenting Cells
            1. Antigen Processing
            2. T Cell Activation
      3. Granulocytes
         1. Neutrophils
            1. Recruitment and Migration
            2. Antimicrobial Functions
            3. Neutrophil Extracellular Traps
         2. Eosinophils
            1. Parasitic Immunity
            2. Allergic Responses
            3. Tissue Remodeling
         3. Basophils
            1. Mediator Release
            2. Allergic Responses
         4. Mast Cells
            1. Tissue Distribution
            2. Degranulation
            3. Inflammatory Mediators
   3. Anatomical Organization
      1. Primary Lymphoid Organs
         1. Bone Marrow
            1. Hematopoiesis
               1. Stem Cell Niches
               2. Lineage Commitment
            2. B Cell Development
               1. Pro-B Cell Stage
               2. Pre-B Cell Stage
               3. Immature B Cell Stage
            3. Central B Cell Tolerance
         2. Thymus
            1. Thymic Architecture
               1. Cortex
               2. Medulla
            2. T Cell Development Stages
               1. Double-Negative Stage
               2. Double-Positive Stage
               3. Single-Positive Stage
            3. Thymic Selection Processes
               1. Positive Selection Mechanisms
               2. Negative Selection Mechanisms
            4. AIRE-Mediated Self-Antigen Expression
      2. Secondary Lymphoid Organs
         1. Spleen
            1. White Pulp Organization
               1. T Cell Zones
               2. B Cell Follicles
               3. Marginal Zone
            2. Red Pulp Functions
               1. Blood Filtration
               2. Erythrocyte Removal
            3. Immune Response Initiation
         2. Lymph Nodes
            1. Structural Organization
               1. Cortex
               2. Paracortex
               3. Medulla
            2. Lymph Flow and Filtration
            3. Germinal Center Formation
               1. Dark Zone
               2. Light Zone
            4. Antigen Presentation
         3. Mucosa-Associated Lymphoid Tissue
            1. Gut-Associated Lymphoid Tissue
               1. Peyer's Patches
               2. Isolated Lymphoid Follicles
               3. Mesenteric Lymph Nodes
            2. Bronchus-Associated Lymphoid Tissue
            3. Skin-Associated Lymphoid Tissue
   4. Molecular Components
      1. Immunoglobulins
         1. Antibody Structure
            1. Heavy Chains
            2. Light Chains
            3. Variable Regions
            4. Constant Regions
         2. Antibody Classes
            1. IgG
               1. Subclasses
               2. Functions
               3. Distribution
            2. IgM
               1. Structure
               2. Functions
               3. Distribution
            3. IgA
               1. Secretory IgA
               2. Functions
               3. Distribution
            4. IgE
               1. Functions
               2. Distribution
            5. IgD
               1. Functions
               2. Distribution
         3. Antibody Functions
            1. Neutralization
            2. Opsonization
            3. Complement Activation
            4. Antibody-Dependent Cellular Cytotoxicity
      2. Cytokines and Chemokines
         1. Pro-inflammatory Cytokines
            1. Tumor Necrosis Factor-α
            2. Interleukin-1β
            3. Interleukin-6
            4. Interferon-γ
         2. Anti-inflammatory Cytokines
            1. Interleukin-10
            2. Transforming Growth Factor-β
            3. Interleukin-4
         3. Chemokines
            1. CC Chemokines
            2. CXC Chemokines
            3. Chemokine Receptors
            4. Leukocyte Migration
      3. Complement System
         1. Classical Pathway
            1. C1 Complex
            2. C4 and C2 Activation
         2. Alternative Pathway
            1. C3 Spontaneous Hydrolysis
            2. Factor B and Factor D
         3. Lectin Pathway
            1. Mannose-Binding Lectin
            2. Ficolin Proteins
         4. Complement Effector Functions
            1. Membrane Attack Complex Formation
            2. Opsonization
            3. Inflammatory Mediator Release
            4. Immune Complex Clearance
      4. Major Histocompatibility Complex
         1. MHC Class I Molecules
            1. Structure and Components
            2. Tissue Distribution
            3. Antigen Processing Pathway
            4. Presentation to CD8+ T Cells
         2. MHC Class II Molecules
            1. Structure and Components
            2. Tissue Distribution
            3. Antigen Processing Pathway
            4. Presentation to CD4+ T Cells
         3. MHC Polymorphism
            1. Genetic Diversity
            2. Population Genetics
            3. Disease Associations