Comprehensive Page-by-Page Immunology Notes (Lectures 10–19)

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• Course: Immunology (Immunology Exam prep). Title suggests content for an Immunology exam review.
• Year/term: 2029
• General structure: Notes derive from a slide deck used for lectures 10–19, covering innate immunity defects, MHC and antigen presentation, antigen receptors and lymphocyte development, cell-mediated and humoral immunity, tolerance, tumor immunology, immunotherapy, and vaccination.

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• Lecture 10: Primary Immunodeficiencies I: Defects in Innate Immunity
• Focus areas include neutropenia, Leukocyte Adhesion Deficiency (LAD) types I and II, Chediak–Higashi syndrome, Chronic Granulomatous Disease (CGD), and related tests (e.g., Nitroblue Tetrazolium test) and other immunodeficiencies.

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• Learning Objectives (key topics):
  • Extravasation/Diapedesis/Transmigration
  • Neutropenia
  • LAD 1 & 2
  • Chediak-Higashi syndrome
  • Chronic granulomatous disease
  • Nitroblue tetrazolium (NBT) test and other immunodeficiencies
• Codes/dates on slide indicate this is part of a series (05 04 03 02 01).

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• Extravasation/Diapedesis overview: neutrophil accumulation at infection site with rolling, tethering, activation, adhesion, and emigration.
• Chemokines and cytokines at infection site activate cell-surface molecules on neutrophils and endothelium to recruit neutrophils to post-capillary venules.
• Migration: neutrophils move from the lumen through endothelium into tissue; three steps: rolling, firm adhesion, transmigration.
• Rolling involves selectins on endothelium and their ligands on neutrophils (e.g., selectin ligands like Sialyl-Lewis-X).
• After rolling, tight adhesion/arrest is mediated by β2-integrins in cooperation with selectins.
• Key players shown: Selectins (on endothelium), addressins (on neutrophils; mucin-like glycoproteins with Sialyl-Lewis-X), and signaling molecules that respond to chemoattractants.
• Diagrammatic note: leukocyte adhesion is a two-way interaction between neutrophils and inflamed endothelial cells; rolling reduces shear forces to allow arrest and transmigration.

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• Rolling details:
  • Addressins on neutrophils; mucin-like glycoproteins with Sialyl-Lewis-X bind selectins on endothelium.
  • Sialyl-Lewis-X includes fucose (a sugar).
  • The interaction slows neutrophils in shear flow (braking action).
• Interaction: Selectins (endothelial) bind addressins (neutrophils) to mediate rolling.

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• Complete adhesion: β2-integrins are heterodimers with α and β subunits; they bind counterligands on endothelium from the Ig superfamily
  • ICAM-1 (Intercellular Adhesion Molecule) and VCAM-1 (Vascular Cell Adhesion Molecule).
  • β2-integrins on neutrophils exist in a low affinity state and convert to high affinity upon activation by cytokines.
  • Endothelial cells express ICAM-1/VCAM-1 when activated by cytokines (TNF, IL-1, endotoxins).
• Structure note: Integrins are heterodimeric receptors (α and β chains) with transmembrane domains and cytosolic signaling domains; they are essential for firm adhesion after rolling.

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• Phagocytosis of bacteria (phagosome formation) and degranulation:
  • Bacteria adhere to neutrophil surface via opsonization.
  • Neutrophil engulfs bacteria with pseudopodia; a phagosome forms.
  • Phagolysosome forms after fusion with granules; lysosomal enzymes and oxidative radicals kill bacteria.
• Key receptors: C3b receptor and Fc receptor on neutrophils aid opsonization and phagocytosis.
• NADPH oxidase is activated during phagocytosis to generate reactive oxygen species (ROS);
  • NADPH/Oxidase complex catalyzes electron transfer to molecular oxygen, forming superoxide O\,2\u22C5- (O2-).
  • Downstream products include H2O2 and hydroxyl radicals; combined with MPO forms potent microbicidal system.
• Primary granules (azurophilic) and secondary granules release contents into phagosome.

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• Intracellular Killing: Oxygen-dependent intracellular killing via NADPH oxidase complex.
• NADPH oxidase components and localization: p22phox and gp91phox (membrane-bound), p47phox, p67phox (cytosolic subunits). The complex assembles at phagosome.
• Steps in ROS production:
  1) Generation of superoxide radical: $O<em>2 + e^- ightarrow O</em>2^{\cdot-}$
  2) Dismutation to hydrogen peroxide: $2 O<em>2^{\cdot-} + 2 H^+ \rightarrow H</em>2O<em>2 + O</em>2$
  3) Hydroxyl radical formation via metal-catalyzed reactions (Fe2+/H2O2) and further reactions.
• Subcellular localization: NADPH oxidase components assemble at the phagosomal membrane.

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• Myeloperoxidase (MPO) system:
  • MPO is in azurophilic granules; uses H2O2 and Cl- to generate hypochlorous acid (HOCl).
  • Reaction: $H<em>2O</em>2 + Cl^- \rightarrow HOCl + H_2O$
  • MPO complex features heme prosthetic groups; MPO gives pus its green color due to heme.
  • The H2O2–MPO–halide system provides a potent bactericidal mechanism.

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• Diseases affecting neutrophil function (pathogenetic classification):
  1) Production defects in bone marrow: Neutropenia
  2) Leukocyte (neutrophil) rolling defects
  3) Adhesion defects
  4) Migration defects
  5) Phagocytosis defects
  6) Degranulation defects
  7) Intracellular killing defects
  8) CGD-related granulomatous disease, etc.
• Specific disorders listed: LAD type I (β2-integrin deficiency), LAD type II (selectin deficiency), Chediak-Higashi syndrome, Chronic granulomatous disease, Myeloperoxidase deficiency, and specific granule deficiencies.
• Other mentions: Localized juvenile periodontitis, and specific granule deficiencies.

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• Neutropenia:
  • Can be genetic (congenital) or acquired (secondary).
  • Causes: decreased production in bone marrow, marrow failure, peripheral destruction, autoimmunity, malignancy, drugs (cytotoxics).
  • Clinical: increased risk of bacterial infections (fever, pneumonia, GI, skin, sepsis); often normal flora involved; not typically increased risk for parasitic or viral infections.

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• Leukocyte (LAD) type I (defect in β2-integrin):
  • Rare autosomal recessive, due to ITGB2 gene mutations encoding the β2 chain of β2-integrin.
  • Leads to moderate to severe deficiency of β2-integrins; inability of neutrophils to migrate from blood to infection sites.
  • Male=female prevalence; classic clinical phenotype includes delayed umbilical cord separation, gingival hyperplasia, severe mucosal infections.
• Visual example: Wild-type vs β2-integrin knockout showing failure of transmigration and neutrophil accumulation within vessels in inflammation.

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• Leukocyte Adhesion Deficiency Type I (clinical phenotypes):
  • Severe type: <2% β2-integrin surface expression; early, frequent, severe infections; high mortality in infancy without treatment.
  • Mild-to-moderate: 2–30% surface expression; fewer severe infections; survival into adulthood.
  • Symptoms: Recurrent bacterial infections localized to skin and mucosa; cutaneous abscesses, gingivitis, stomatitis, aggressive periodontitis; peripheral leukocytosis (e.g., 40,000–100,000/mm3).
  • Infecting organisms: S. aureus, Gram-negative enteric bacteria; fungus may occur.

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• Leukocyte Adhesion Deficiency Type II (LAD II; Sialyl-Lewis X deficiency):
  • Rare autosomal recessive defect in selectin-mediated rolling due to deficiency in Sialyl-Lewis X (addressin component).
  • Mutation in SLC35C1 gene (GDP fucose transporter) leading to failure to convert mannose to fucose and generalized loss of fucosylated carbohydrates; sLeX absent but other fucosylated carbohydrates may be deficient.
  • Pathway context: Golgi GDP-fucose transporter is required to produce fucosylated ligands for selectins; deficient transport disrupts rolling.
• SLC35C1 gene products and the salvage pathway of GDP-Fucose are noted; Sialyl-Lewis X is absent.

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• β-Actin deficiency (ACTB mutation):
  • Autosomal dominant deficiency; β-actin is essential for neutrophil motility; defect in neutrophil migration and chemotaxis.
  • Clinical: recurrent bacterial and fungal infections with poor pus formation; additional features: mental retardation, photosensitivity, periodontitis, tooth loss.

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• Chediak–Higashi syndrome:
  • Rare autosomal recessive defect in membrane fusion of azurophilic granules with phagosomes; LYST gene mutation (lysosomal trafficking regulator).
  • Result: giant azurophilic granules in neutrophils, melanosomes in melanocytes, dense bodies in platelets.
  • Clinical features: recurrent S. aureus infections; oculocutaneous albinism; neurologic impairment; weakness, ataxia, progressive parkinsonism; histology shows giant granules; often lethal due to bacterial infections.
• Visual: images show increased granule size in neutrophils and pigment abnormalities in hair.

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• Chronic Granulomatous Disease (CGD):
  • Genetically heterogeneous group with failure of neutrophils to undergo respiratory burst and generate superoxide; leads to recurrent life-threatening bacterial/fungal infections and granuloma formation.
  • Prevalence: about 1 in 200,000 to 1 in 250,000; ~90% male among CGD patients.
  • Mutations in any of four subunits of NADPH oxidase: gp91phox, p22phox, p47phox, p67phox.
  • Model: NADPH oxidase complex assembly and subunit localization illustrated; the ROS defect underlies CGD.

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• Myeloperoxidase (MPO) deficiency:
  • Increased susceptibility to fungal infections (e.g., Candida, Aspergillus) due to impaired oxidative killing.
  • Diagnosis via immunohistochemistry/flow cytometry for MPO; MPO staining shows negative in MPO-deficient individuals.

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• Transition to Lecture 11: MHC & Antigen Presentation
• Rod map: Introduction to MHC and antigen presentation concepts to follow.

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• Learning Objectives for MHC & Antigen Presentation:
  • MHC Class I & II structure and expression, co-dominant expression, and polymorphism.
  • MHC II sequence and MHC I sequence concepts; alternative antigen presentation strategies and superantigens.

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• How does the immune system react to a microbe?
  • Integrated view: Phagocytosis, Complement, B cells, Neutrophils, MAC, Neutralization by antibodies, Macrophages, Dendritic cells, APCs; T cells and B cells participate in antigen presentation and cytokine signaling.
• Key players mentioned: APCs, T cells (CD4+, CD8+), B cells, NK cells, neutrophils, macrophages, dendritic cells.
• Visual cue: T cells identify microbes via peptide-MHC (pMHC) complexes presented by APCs.

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• The Functions of MHC:
  • MHC enables self vs foreign discrimination and antigen presentation.
  • Selection and presentation roles:
  • I. Developmental selection of T cells (positive/negative) to ensure functional TCRs and self-tolerance.
  • II. Immune response: after endocytosis or infection, processed antigens are loaded onto MHC Class I or II and presented to T cells.

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• The Major Histocompatibility Complex (MHC) Loci:
  • Located on chromosome 6; three sub-loci:
  • I. MHC Class I locus: Classical HLA-A, -B, -C; Non-classical HLA-E, -F, -G
  • II. MHC Class II locus: HLA-DP, -DQ, -DR
  • III. MHC Class III locus: genes encoding cytokines and complement proteins.

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• MHC haplotype and diversity:
  • Demonstrates that each chromosome carries an MHC haplotype; codominance means two sets of alleles are expressed (one from each parent).
  • Population diversity is high (hundreds of alleles per gene); diversity ensures broad antigen recognition.
  • Family diagram illustrates haplotypes across father, mother, siblings and self.

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• Expression and targets of HLA proteins:
  • Classical Class I: expressed on all nucleated cells and platelets; presents antigen to CD8+ T cells when on APCs.
  • Non-classical Class I (HLA-E, F, G): more restricted expression; HLA-G is immunosuppressive.
  • MHC Class II: expressed on dendritic cells, macrophages, B cells; presents antigen to CD4+ T cells.
  • MHC Class III: secreted proteins (complement components, cytokines).

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• MHC Class I structure details:
  • Composed of a chain (α) with three domains plus β2-microglobulin (β2m) which is not MHC-encoded.
  • Domains α1 and α2 form the peptide-binding groove; peptides are typically 8–11 amino acids and sit in the groove.
  • Diagram shows peptide-binding cleft with α1, α2, α3 domains and β2m associated.

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• MHC Class II structure details:
  • Composed of α and β chains with two conserved domains (α1 and β1) that form the peptide-binding groove; peptides usually 14–20 amino acids.
  • Cross-presentation pathway and ER/Golgi processing noted in broader figure; two classic processing pathways:
  • Endogenous (Class I) presents to CD8+ T cells.
  • Exogenous (Class II) presents to CD4+ T cells.
• Cross-presentation: exogenous antigens can be presented via Class I to activate CD8+ T cells (special APCs like dendritic cells).
• Lipid antigen presentation: CD1 molecules (MHC-like) present lipid antigens to NKT cells; CD1 uses a lipid-loading pathway and chaperone molecules distinct from classical MHC.

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• Endogenous (Class I) processing pathway (summary): 1) Cytosolic production of antigen (e.g., viral protein) and ubiquitination. 2) Proteasomal degradation to peptides. 3) Peptides transported into the ER by TAP (Transporter associated with antigen processing). 4) Loading onto HLA-A, -B, or -C in the ER with chaperones and proteasome-derived peptides; complex trafficked to cell surface.
  • Target: CD8+ cytotoxic T lymphocytes (CTLs).

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• Exogenous (Class II) processing pathway (summary):
  1) Exogenous antigens internalized and degraded in endosomes/MIIC compartments.
  2) MHC Class II molecules synthesized in ER and associated with invariant chain (li) in early compartments; CLIP blocks the groove until peptide exchange.
  3) MIIC/endosome fusion allows HLA-DP, -DQ, -DR loading with assistance from HLA-DM, which facilitates CLIP removal.
  4) Peptide-MHC Class II complex trafficked to cell surface for CD4+ T cell recognition.
• Cross-presentation and lipid antigen presentation covered above.

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• Cross-presentation concept (II): Lipid antigen presentation by CD1 molecules (CD1d in particular) to NKT cells.
• Cross-talk: APCs can present exogenous antigens via Class I to activate CD8+ T cells through TAP and proteasome pathways; CD1 presents lipid antigens to NKT cells.

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• T cells and carbohydrate antigen presentation:
  • Carbohydrate antigens (CAPS) such as capsular polysaccharides (CPS) require presentation in context of MHC II via glycopeptides.
  • Carbohydrate portions presented to CD4+ T cells; endocytosed glycoproteins processed via normal MHC Class II pathway; glycopeptide-MHC complex displayed to TCRs on CD4+ T cells.
  • IL-4, IL-2 signaling to drive helper T cell responses; glycopeptide presentation yields specific T cell help.

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• Superantigens:
  • Can activate CD4+ T helper cells by binding to the external surfaces of the TCR β-chain and MHC Class II on APCs, bypassing the peptide groove.
  • Common bacterial toxins (e.g., Staphylococcus aureus enterotoxin B, toxic shock syndrome toxins; Streptococcus pyogenes exotoxin A).
  • Result: activation of large fractions of T cells (up to ~20%), massive cytokine release (e.g., TNF-α, IL-1, IL-2), leading to systemic inflammatory response syndrome (SIRS).

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• Visual of MHC-II with bound peptide and superantigen engaging a non-matching TCR; demonstrates the non-peptide groove interaction and broad T cell activation.

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• Consequences of superantigen binding:
  • Normally, antigen-induced T cell activation activates only a tiny fraction of T cells (≤0.001%).
  • Superantigens can activate up to ~20% of T cells, causing massive cytokine production and potential shock.
• Diagrammatic representation of T cell receptor (TCR), MHC II, and superantigen interactions.

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• Lesson 12: Antigen Receptors & Lymphocyte Development (intro to next major section)
• This page serves as a transition heading to deeper content on antigen receptors and development.

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• Learning Objectives for Antigen Receptors & Lymphocyte Development:
  • Antigen receptor structure for B and T cells
  • Diversity generation mechanisms (V(D)J recombination, gene rearrangements)
  • T-cell maturation, B-cell maturation
  • Negative/positive selection and outputs

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• What to know (high-yield topics):
  • B and T lymphocyte antigen receptors
  • Antigens and epitopes
  • TCR structure
  • Antibody (BCR) structure
  • Generation of diverse antibody and TCR repertoires
  • Ig and TCR gene rearrangements
  • Sources of antigen receptor diversity
  • B and T cell development; anatomic sites; key selection steps; output
  • Consequences of defects

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• Structure of the T cell antigen receptor (TCR):
  • TCR is a membrane-bound heterodimer of α and β chains.
  • Variable regions (Vα and Vβ) contain hypervariable complementarity-determining regions (CDRs) that form the antigen-binding site.
  • TCR αβ is the common form; γδ TCRs are similar in organization albeit with different chains.
  • The TCR is associated with CD3 and has a transmembrane region; disulfide bonds connect subunits.

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• Structure of antibodies (BCR):
  • Membrane-bound antibody comprises a B cell receptor (IgM and IgD on naive B cells).
  • Heavy (H) and light (L) chains form a heterodimer (H2L2).
  • Variable regions (VH, VL) contain HV regions (CDRs).
  • Isotypes (IgM, IgD, IgG, IgA, IgE) differ in constant regions (μ, δ, γ, α, ε).
  • Secreted antibody lacks transmembrane region; effector functions determined by heavy chain isotype.
  • Fab region contains antigen-binding site; Fc region determines effector functions and Fc receptor binding.

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• Structure of antibodies (continued):
  • Hinge region provides flexibility between Fab and Fc.
  • Disulfide bonds stabilize heavy and light chains; VH and VL contribute to antigen binding.

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• Ig and TCR chains recap:
  • V regions encoded by gene segment recombination (VDJ for heavy chains; VDJ for TCR β; VJ for TCR α).
  • TCR αβ organization and rearrangement parallels BCR V(D)J processes but with different gene segments.

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• Immunoglobulin and TCR gene rearrangements (V(D)J recombination):
  • Example: Ig heavy chain gene rearrangement uses V-D-J segments plus joining exons; rearranged VDJ encodes the V region; C region exons encoded by C region gene segments.
  • Mechanism: Recombination signal sequences (RSS) adjacent to V, D, J segments; RAG-1/2 complex mediates cleavage and recombination; non-homologous end joining (NHEJ) repairs coding ends producing VDJ or VJ joints.
  • RAG1/2 are lymphoid-specific enzymes expressed in immature B and T cells.
• Figure references: RSS (12RSS, 23RSS) and joining phases.

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• Ig and TCR gene rearrangements (more details):
  • Ig heavy chain rearranges first (V, D, J) to generate μ heavy chain; followed by light chain rearrangement (V and J) to generate light chain (κ or λ).
  • TCR β chains rearrange first (V, D, J) then TCR α chains rearrange (V and J) to form αβ TCR.

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• Key checkpoints in rearrangement:
  1) RSS sequences adjacent to coding sequences.
  2) V(D)J recombinase (RAG-1 and RAG-2) recognizes RSS and mediates recombination.
  3) DNA breaks repaired by non-homologous end joining (NHEJ) to join coding ends and form functional V-D-J or V-J joints.
• Reiterates the roles of RAG1/2 as lymphoid-specific components of the V(D)J recombinase.

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• Checkpoints in lymphocyte development (summary table):
  • Stages: Stem cell → Pro-lymphocyte → Pre-lymphocyte → Immature lymphocyte → Mature lymphocyte.
  • Major events include antigen receptor gene rearrangement, selection (positive/negative), maturation of functionally distinct receptors, and output to peripheral tissues.
  • Growth factor-mediated commitment and proliferation occur at various stages.

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• Checkpoints in lymphocyte development (continued):
  • Graphical depiction of stages: Generative organ (bone marrow/thymus) to peripheral lymphoid organs.
  • Positive selection: selects cells that recognize self-MHC with appropriate affinity.
  • Negative selection: deletes or alters cells that recognize self too strongly.
  • Development of regulatory T cells (Tregs) in the thymus and periphery.

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• Steps in B lymphocyte development (core points):
  • IG heavy chain rearrangement occurs during B cell development in bone marrow (Pro-B stage).
  • Successful rearrangement of heavy chain leads to μ heavy chain production and pre-BCR formation, which shuts off further H chain rearrangements and initiates light chain rearrangements.
  • Allelic exclusion ensures each B cell expresses a single heavy and a single light chain.
  • Immature B cells express membrane-bound μ heavy chain and light chains (κ or λ) and are IgM+ on surface.
  • Nonreactive immature B cells exit bone marrow and become mature B cells (IgM and IgD on surface).
  • Recombination and alternative splicing allow co-expression of IgM and IgD on mature B cells.

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• Steps in T lymphocyte development (core points):
  • Thymocytes (developing T cells) in thymus experience IL-7–driven proliferation; Pro-T cells are CD4−CD8− (double negative, DN).
  • TCR gene rearrangements begin in Pro-T cells; successful β chain rearrangement leads to Pre-T cell formation and surrogate pre-TCR, signaling progression.
  • Positive selection in thymus yields mature CD4+ T cells and CD8+ T cells that recognize self-MHC with appropriate affinity (TCR-αβ).
  • The process includes allelic exclusion for TCR β and α chains to ensure single TCR specificity.

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• The Need for Selection (conceptual):
  • Positive selection yields useful T cells that recognize MHC; negative selection removes self-reactive T cells; excessive self-recognition is dangerous and triggers negative selection.

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• Detailed T cell maturation anatomy: DN (double negative), DP (double positive), SP (single positive) stages; cortex vs medulla location in thymus; death by neglect if no MHC recognition.
• CD4+ SP and CD8+ SP cells exit thymus as mature T cells.
• Regulatory T cells (Tregs) develop in thymus and periphery to maintain tolerance.

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• Development of Regulatory T cells (Tregs):
  • Thymus-derived Tregs can form from self-reactive immature T cells; Tregs suppress T cell responses to prevent autoimmunity.
  • Tregs express FOXP3; suppress T cell responses via cytokines (IL-10, TGF-β) and cell-contact mechanisms.

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• Failure of Lymphocyte Development (summary):
  • Defects in T cell development lead to immunodeficiency (cell-mediated and antibody-mediated).
  • Defects in B cell development lead to immunodeficiency (antibody-mediated).
  • Consequences: increased susceptibility to infections (bacteria, fungi, viruses).

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• Lesson 13: Cell-Mediated Immunity I: Recognition & Activation (introduction)

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• Learning Objectives for Cell-Mediated Immunity:
  • Roles of key cells; signals needed to activate T cells; ITAM biochemical pathways; big-picture signaling.

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• Overview: Adaptive immunity split into Humoral (antibodies) and Cell-mediated immunity (CMI).
• CMI deals with intracellular microbes (viruses, intracellular bacteria), intracellular pathogens; effector cells include CD4+ Th1, CD8+ CTLs, NK cells, γδ T cells, NKT cells; phagocytes with innate and adaptive collaboration.
• Emphasizes that helper T cells activate macrophages, cytotoxic T cells kill infected cells, and NK/innate cells contribute to early defense.

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• The cells mediating CMI (summary):
  • Innate: NK T cells (recognize lipid antigens on CD1 and lyse target cells), NK cells (kill via receptors like NKG2D, CD16 for ADCC), macrophages (activated by IFN-γ from Th1 and CD8+ T cells).
  • Adaptive: CD4+ Th cells (Th1, Th2, Th17, Tfh, Treg) and CD8+ CTLs; Th1 cells produce IFN-γ to activate macrophages and amplify CTL responses; CTLs kill infected cells and produce IFN-γ.
• Diagrammatic representation (text): Cytokines drive macrophage activation; activated macrophages kill ingested microbes; CTLs kill infected cells; Th1 support immunity; NK cells also contribute early.

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• Activation of Macrophages (M1 vs M2):
  • M1 (classically activated) are induced by IFN-γ and TLR ligands; exhibit microbicidal actions (ROS, NO) and promote inflammation; produce IL-1, IL-12, IL-23 and chemokines.
  • M2 (alternatively activated) are induced by IL-4/IL-13; promote tissue repair, anti-inflammatory responses; produce IL-10, TGF-β; can dampen inflammation.

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• Magnitude and phases of T cell-mediated immunity:
  • Phases: antigen recognition, lymphocyte activation, clonal expansion, differentiation into effector T cells, migration to infection site, effector function, contraction and memory formation.
  • Timeframe: roughly 14–21 days for primary responses; memory persists for faster secondary responses.

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• The Three-Signal Hypothesis for T cell Activation:
  • Signal 1: TCR binding to MHC-peptide complex (pMHC) with co-receptor (CD4/CD8) involvement and Lck signaling.
  • Signal 2: Costimulatory signal (e.g., CD28 on T cell binding CD80/CD86 on APC).
  • Signal 3: Cytokines that drive differentiation (e.g., IL-12 promotes Th1; IL-4 promotes Th2; TGF-β + IL-6 promote Th17/Treg differentiation, etc.).
• Without co-stimulation (Signal 2) or cytokines (Signal 3), T cells become anergic or respond weakly.

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• Receptors and signals for CD4+ T cell activation (Signal 1–3):
  • Signal I: TCR recognizing peptide-MHC Class II on APCs (MHC II) with CD3 and ITAM signaling.
  • Signal II: Co-stimulation with CD28 binding to B7-1/B7-2 on APC; CTLA-4 can inhibit by binding B7-1/B7-2.
  • Signal III: Cytokines such as IL-12, IL-2 family to drive differentiation and survival.
• Diagrammatic note: Adhesion (LFA-1/ICAM-1) stabilizes T cell-APC contact; costimulation provides essential second signal.

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• Signal I: TCR activation details:
  • Lck (associated with CD4/CD8) phosphorylates CD3 zeta ITAMs upon TCR engagement.
  • Phosphorylated ITAMs recruit ZAP-70 and initiate LAT signalosome assembly, propagating three major pathways: Ca2+-calcineurin/NFAT, MAPK/AP-1, and NF-κB signaling.
  • These lead to transcription of IL-2 and other cytokines, promoting T cell activation, proliferation, differentiation, and effector functions.

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• Signal Transduction Architecture (Accessory Molecules):
  • Five key elements in signaling complex: TCR, CD3 ITAM, CD4/CD8 (Lck), Adhesion molecules (stabilize APC-T cell binding), Costimulatory molecules (CD28, B7-1/B7-2) and additional molecules like ICAM-1/LFA-1.
  • Distinct roles: TCR-MHC binding initiates signaling; CD4/CD8 dock with MHC to bring Lck to CD3 zeta; adhesion molecules stabilize interactions; CD28-B7 provides co-stimulation.

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• Step 1 – T Cell Activation: Co-stimulation (Signal 2):
  • Co-stimulatory signals are required for full activation; without signal 2, T cells become anergic or unresponsive.
  • Key molecules: CD80 (B7-1) and CD86 (B7-2) on APC binding CD28 on T cells; other signals: CD40 on APC/B cell engaging CD40L on T cell.
  • CTLA-4 is upregulated and provides inhibitory signal to dampen immune response by binding B7-1/B7-2.
  • A schematic shows APC naive T cell contacting activated APC (with costimulators) leading to IL-2 production and T cell expansion.

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• Step 1 – T Cell Activation: Adhesion (Signal 2 context):
  • Integrins (e.g., LFA-1) activated on T cells by APC-derived cytokines switch from low-affinity to high-affinity states, promoting strong T cell-APC adhesion and allowing TCR signaling to proceed.
  • LFA-1 (CD11a/CD18) on T cell binds ICAM-1 on APC; other integrins (VLA-4/VCAM-1) help in T cell trafficking out of lymph nodes to infection sites.
  • Adhesion strengthens signals and enables TCR clustering.
• Diagrammatic explanation: Integrin activation is enhanced by chemokines and antigen recognition, causing clustering and high-affinity binding.

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• TCR Signaling Cascade (core pathway):
  • Activation of TCR leads to an intracellular signaling cascade including ITAM phosphorylation, ZAP-70 recruitment/phosphorylation, LAT signalosome assembly, and downstream activation of three major pathways:
  • Ca2+-calcineurin → NFAT transcription factor activation
  • MAPK pathway → AP-1 (Fos/Jun) activation and actin polymerization
  • NF-κB pathway → translocation of NF-κB components to the nucleus
  • These events culminate in gene transcription for cytokines (notably IL-2), T cell proliferation, differentiation, and effector functions.
• Key players: Lck, ZAP-70, LAT, SLP-76, PLC-γ1, IP3/DAG, PKC, Ca2+ flux, NFAT, NF-κB, AP-1.

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• Signaling integration: downstream events include phosphorylation, release and degradation of IκB (for NF-κB), and Ca2+-dependent activation of NFAT; MAPK cascade leads to JUN and FOS activation; Ras/Rac signaling influences multiple arms.

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• Step 2 – T Cell Proliferation: NFAT pathway details
  • IP3 triggers Ca2+ release from ER; Ca2+ binds calmodulin, activates the phosphatase calcineurin; calcineurin dephosphorylates NFAT; NFAT translocates to the nucleus to drive gene transcription (e.g., IL-2).
  • Cyclosporine inhibits calcineurin and blocks IL-2 production, suppressing T cell activation.
• Step 2 – Additional signaling: NF-κB and AP-1 (via PKC and MAPK) contribute to IL-2 transcription and anti-apoptotic gene expression.

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• Step 2 – IL-2 Production and T Cell Proliferation:
  • IL-2 receptor (IL-2R) exists as a low-affinity dimer (α and β) or high-affinity trimer (α, β, γ) depending on IL-2Rα (CD25) upregulation after activation.
  • Binding of IL-2 to high-affinity IL-2R drives autocrine and paracrine T cell proliferation (clonal expansion).
  • The IL-2 receptor affinity dynamic is critical for controlling T cell growth.

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• Step 3 – Differentiation of CD4+ T Helper Cells (Th subsets):
  • Th1: IFN-γ signature; driven by IL-12; transcription factor T-bet; promotes macrophage activation and cytotoxic responses.
  • Th2: IL-4-driven; transcription factor GATA3; promotes B cell help and humoral responses; promotes IgG and IgE isotypes; supports eosinophils and mucus production via IL-4/IL-13.
  • Th17: IL-6, TGF-β, IL-23; transcription factor RORγt; produces IL-17 and IL-22; recruits neutrophils; important for defense against extracellular bacteria/fungi; associated with autoimmunity.
  • Tfh (follicular helper T cells): IL-21; helps B cells in germinal centers; expresses CXCR5; supports isotype switching (IgG/IgE) via CD40L interactions and signals (
    e.g., ICOS-L) from activated B cells.
  • Treg: FOXP3; suppressed immune responses via IL-10, TGF-β, and cell-contact mechanisms; maintains tolerance and prevents autoimmunity.
• Altogether, the cytokine milieu during initial antigen exposure defines distinct transcription-factor programs and surface markers for each subset.

Page 70

• CD4+ T cell effector functions and migration:
  • Th1 cells promote macrophage activation and CTL responses; Th2 cells facilitate B cell help and allergic responses; Th17 cells drive neutrophil recruitment; TfH cells assist B cells in germinal centers; Tregs regulate responses.
  • CTLs (CD8+) differentiate into memory and effector CTLs, capable of recognizing antigen on infected cells in context of MHCI and delivering cytotoxic hits (perforin/granzyme, Fas/FasL pathway).
• Overall: Activated CD4+ Th cells coordinate the adaptive response; CD8+ CTLs directly kill infected cells; NK and other innate cells contribute to early defense.

Page 71

• Lesson 14: Cell-Mediated Immunity II: Differentiation & Function (intro)

Page 72

• Learning Objectives for T Cell Subsets and Mechanisms:
  • Subtypes of T cells and their functions.
  • Direct mechanisms of cytotoxicity (Fas/FasL and TNF-mediated pathways).
  • Cytokines and humoral immunity interplay.

Page 73

• T cell subsets (summary figure references):
  • Naive CD4+ T cells differentiate into Th1, Th2, Th17, Tfh, Treg, etc., per cytokine milieu (IL-2, IL-6, TGF-β, IL-4, IL-12, IL-21, etc.).
  • Th1 signature: IFN-γ; Th2: IL-4, IL-5, IL-13; Th17: IL-17, IL-22; Tfh: IL-21; Treg: FOXP3 and IL-10/TGF-β; Th9: IL-9; Thx: other signatures.
• Each subset has distinct effector functions: cytolysis (CD8+ CTLs), cytokine-mediated assistance, anti-inflammatory/regulatory roles, etc.

Page 74

• Step 4 – T Cell Effector Functions (examples):
  • Th1 cells: Driven by IL-12 and IFN-γ; produce IFN-γ; potent activator of CD8 CTLs, NK cells, macrophages; upregulate MHC II and costimulatory molecules; enhance opsonization and phagocytosis.
  • Interaction loop: Dendritic cells present antigen to naive T cells; IL-12 and IFN-γ from NK and Th1 cells amplify responses.

Page 75

• Th2 effector functions:
  • IL-4 promotes B cell help and isotype switching (IgG and IgE); IL-5 supports eosinophils; IL-13 promotes mucus production; IgE binds to FcεR on mast cells/eosinophils; Th2 fosters alternative macrophage activation and tissue repair.
  • Th2 cytokines can antagonize Th1 differentiation (IL-4/IL-13 inhibit cytolytic CD8 activity).

Page 76

• Th17 cells:
  • Induced by IL-6, TGF-β, IL-23; signature IL-17 and IL-22; promotes recruitment of PMNs via IL-8; stimulates antimicrobial peptide release from epithelial cells; important for bacterial/fungal defense; elevated in autoimmune diseases (lupus, RA, IBD).
  • Cytokine network: IL-6, IL-1, TGF-β, IL-23 promote Th17 differentiation; IL-21 acts in amplification.

Page 77

• Regulatory T cells (Tregs) details:
  • CD4+ CD25+ FOXP3+ Tregs; developed in thymus or periphery; suppress T cell responses to prevent autoimmunity; mechanisms include cytokine consumption (IL-2), soluble factors (IL-10, TGF-β), and cell-contact dependent suppression.

Page 78

• Follicular helper T cells (Tfh) and B cell interactions:
  • Tfh cells provide help to B cells during germinal center reactions via IL-21 and surface molecules such as ICOS-L; they promote B cell proliferation, somatic hypermutation, and isotype switching (IgG or IgE depending on cytokines).
  • Germinal centers: dark zone (proliferation and SHM) and light zone (selection and differentiation) with interactions between B cells, Tfh, and follicular dendritic cells.

Page 79

• CD8+ T cell cytotoxicity and helper interactions:
  • CD8+ CTLs recognize antigen presented by MHCI and kill target cells via cytotoxic granules (perforin, granzyme) and cytokines (IFN-γ).
  • CD4+ helper T cells support CTLs by secreting cytokines (e.g., IL-2) and by enhancing APC function (via CD40L-CD40 interactions).
  • CD4+ help also enhances APCs to support CTL differentiation.

Page 80

• NK T (NKT) cells and NK cells in CMI:
  • NKT cells share markers with both T cells (CD3) and NK cells (CD56, CD16, NKG2D); recognize lipid antigens through CD1d and secrete IFN-γ or IL-4; contribute to rapid immune responses and protection against mycobacterial and fungal organisms.
  • NK cells kill via death receptors (e.g., FasL) and through cytotoxic granules (perforin/granzyme); ADCC via CD16 (FcγRIII) recognizes antibody-coated targets.

Page 81

• NK cell cytolysis specifics: two major phenotypes with distinct cytokine profiles:
  • CD56bright NK cells: high cytokine production (IFN-γ, TNF-α) but less cytotoxic; high IL-2 receptor expression.
  • CD56dim NK cells: potent cytotoxic activity; express KIRs and CD16; key in antibody-dependent cellular cytotoxicity (ADCC).
• NK cell receptors: include activating and inhibitory receptors (KIRs); binding balance determines response.

Page 82

• Cytolysis: Perforin/Granzyme pathway (CD8 CTL):
  • Perforin monomers polymerize to form pores in the target cell membrane in the presence of Ca2+; Granzyme and granulysin enter via perforin pores to trigger apoptosis.
  • Cytokines such as TNF-α and IFN-γ are released; granzyme interactions initiate caspase activation and apoptosis.
  • Sequence: Perforin forms pores → Granzyme enters → Caspase cascade → Apoptosis.

Page 83

• Cytolysis: Fas/FasL-induced apoptosis:
  • Activated CD8+ CTLs and NK cells upregulate FasL (CD95L); binding to Fas (CD95) on target cells → activates caspase cascade (caspase-8) → apoptosis via extrinsic pathway (death receptor signaling).
  • Alternative intrinsic pathways include mitochondrial cytochrome c release (activation of caspase-9) in type II cells via BID truncation.

Page 84

• TNF receptor–mediated cytolysis:
  • TNF-α binds TNFR1/TNFR2, forming DISC complex via adaptor proteins (FADD, TRADD) leading to caspase-8 activation and apoptosis.
  • Intracellular signaling can also activate NF-κB and inflammatory gene expression; TNF can have pro-survival or pro-apoptotic outcomes depending on context.
• Overall, cytolysis pathways converge: extrinsic (Fas/TNF) and intrinsic (mitochondrial) pathways can lead to apoptosis in target cells.

Page 85

• Cytolytic pathways converge concept:
  • Multiple activation events converge on shared downstream apoptotic machinery to kill infected or transformed cells. The TNF or Fas/FasL death-receptor pathways and the perforin/granzyme pathway provide complementary routes to cytolysis.
  • Type I cells rely on death receptor signaling; Type II cells integrate mitochondrial (cytochrome c) signals.

Page 86

• Immune checkpoints and balance:
  • PD-1/PD-L1 axis and CTLA-4 provide inhibitory signals to limit T cell activation and maintain peripheral tolerance.
  • PD-1 binds PD-L1/PD-L2 to dampen TCR signaling via ITIM; CTLA-4 binds CD80/CD86 with higher affinity than CD28, inhibiting costimulation.
  • NK cells have inhibitory receptors (KIR, Ly49) that dampen activation.
• The net effect: immune responses are balanced to prevent excessive tissue damage and autoimmunity; dysregulation can lead to cancer or autoimmunity.

Page 87

• Immune-based drug therapies (overview):
  • Immunosuppressive drugs: Cyclosporine (calcineurin inhibitor) and other agents block TCR signaling; Azathioprine inhibits cell cycle; Sirolimus (rapamycin) inhibits mTOR signaling.
  • Targeted biologics: Anti-CD3, anti-CD52; TNF-α inhibitors; IL-2R antibodies; CTLA-4-Ig (abatacept) blocks costimulation by binding CD80/86; Anti-CD154; Anti-CD25; JAK inhibitors; BTK inhibitors (ibrutinib).
  • Immunomodulatory strategies: PD-1/PD-L1 inhibitors, CTLA-4 inhibitors, and combination therapies to enhance anti-tumor responses.

Page 88

• Lesson 15: Humoral Immunity & Antibodies (Abs)
• Focused on B cells and antibodies as a central component of humoral immunity.

Page 89

• Learning Objectives for antibodies and isotypes:
  • ABs and their isotypes, antibody production processes, T-dependent B cell responses, affinity maturation, isotype switching.
  • Big-picture concepts: how diversity is generated; how B cells respond to antigens; how antibodies mediate effector functions.

Page 90

• Key terms: Antigen, immunogen, epitope, hapten concept, linear vs conformational epitopes.
• Epitope types: linear (continuous) and conformational (discontinuous).
• Hapten definition: a molecule that binds antibodies but cannot induce antibody production by itself; needs a carrier protein to become immunogenic.

Page 91

• Haptens and clinical significance:
  • Some drugs (beta-lactam antibiotics) act as haptens when they bind to proteins (e.g., albumin) and form immunogenic complexes, triggering antibodies and potential adverse drug reactions.

Page 92

• Summary of B cell development (simple ladder):
  • Stem cell → Pro-B → Large Pre-B → Small Pre-B → Immature B → Mature B.
  • Key processes: Ig gene rearrangement, negative selection, receptor editing, and activation leading to antigen response.
  • Emphasizes that B cells develop in bone marrow and that negative selection eliminates self-reactive B cells through deletion or receptor editing.

Page 93

• Types of Antibody Responses:
  • T cell-dependent antibody responses require T cell help and protein antigens; occur in follicular B cells in secondary lymphoid organs.
  • T cell-independent antibody responses do not require T cell help and are elicited by polysaccharide, lipid, and nucleic acid antigens; involve B-1 and marginal zone B cells.

Page 94

• T cell-dependent antibody responses (process):
  • Antigen recognition by B cells leads to B cell proliferation and differentiation with helper T cell involvement; plasma B cells secrete IgM initially; isotype switching yields IgG (and others) with affinity maturation.
  • Germinal center reactions produce high-affinity antibodies and memory B cells.

Page 95

• Mature B cells overview:
  • Naive B cells express membrane IgM and IgD; they recirculate in blood and lymphoid tissue; upon antigen encounter, they activate and differentiate into plasma cells (antibody-secreting) and memory B cells.
  • The heavy chain constant region switching (IgM to IgD, IgG, IgA, IgE) results from alternative splicing and class-switch recombination.

Page 96

• BCR signaling (signal 1) and co-receptors:
  • BCR includes surface Ig associated with Igα/Igβ (CD79a/CD79b) with ITAMs that recruit Syk and downstream signaling (BLK, Lyn, Fyn; phospholipase C-γ2, PI3K, Ras, MAPK/ERK).
  • Co-receptor complex CR2 (CD21) with CD19 and CD81 enhances signaling via complement receptor C3d bridging.
  • BCR signaling escalates via PKC and Ca2+-dependent enzymes leading to NFAT, NF-κB, AP-1 transcription factors; requires help from CD40L and cytokines for full activation.

Page 97

• Enhancement of BCR signaling:
  • Complement receptor CD21 (CR2) with CD19 and CD81 forms a co-receptor complex that augments BCR signaling when C3d is bound to antigen.
  • Engagement of CR2 links innate and adaptive immunity; co-signaling via TLRs can further enhance B cell activation.

Page 98

• Helper T cell-mediated B cell activation:
  • Tfh cells recognize class II MHC:peptide on B cells and provide help via CD40L and cytokines (e.g., IL-21).
  • Key outcomes of T cell help: B cell proliferation, differentiation into plasma cells, and germinal center formation with affinity maturation and isotype switching.

Page 99

• B cell–T cell collaboration in the germinal center:
  • Initial T-B interaction happens extrafollicularly; subsequently, germinal center reactions progress with a dark zone (proliferation/SHM) and light zone (selection/affinity maturation).
  • Outcomes include high-affinity antibody-secreting plasma cells and memory B cells.

Page 100

• Germinal centers recap:
  • Formed in secondary lymphoid tissues; intense B cell proliferation; isotype switching; somatic hypermutation; selection for high-affinity B cells; yield plasma cells and memory B cells.

Page 101

• Somatic hypermutation (SHM) of Ig genes:
  • SHM introduces point mutations into V region genes at a much higher rate (105–106×) in activated B cells within germinal centers.
  • Activation-induced deaminase (AID) is the key enzyme.
  • Positive mutations improve antigen-binding and are selected for; deleterious mutations cause death of B cell.
• Outcome: affinity maturation.

Page 102

• Antibody isotype switching (class switch recombination):
  • Example: μ (IgM) to ε (IgE).
  • Mechanism: Switch recombination at Ig heavy chain loci, involving switch regions upstream of constant region genes; AID is essential.
  • Outcome: changes effector function without altering antigen specificity.

Page 103

• Memory B cells and plasma cells:
  • Memory B cells: long-lived, slowly dividing; do not secrete antibody; express surface Ig and memory for rapid responses on re-exposure.
  • Plasma cells: long-lived antibody-secreting cells located in medullary cords and bone marrow; terminally differentiated; secrete large amounts of antibody with same antigen specificity/isotype as parent B cell.

Page 104

• Key Concepts (antibody structure and function):
  • Valency: number of antigen-binding sites; IgG, IgA, IgD have valency 2; IgA dimer has valency 4; IgM pentamer has valency 10.
  • Affinity: strength of a single antigen–antibody interaction; higher for IgG/IgA/IgE generally relative to IgM.
  • Avidity: overall strength of antibody–antigen interaction taking into account valency and multiple epitopes.

Page 105

• Effector functions of antibody isotypes (high-level summaries):
  • IgG: opsonization (Fcγ receptor) and classical complement activation (C1q); ADCC (via FcγRIII) by NK cells; neonatal immunity via FcRn (placental transfer); feedback inhibition via FcγRIIB.
  • IgM: efficient complement activation; first isotype produced.
  • IgA: mucosal immunity; secreted IgA via poly-Ig receptor; neutralization at mucosal surfaces.
  • IgE: mast cell degranulation and eosinophil-mediated defense against helminths; cross-linking triggers allergic responses.

Page 106

• Lesson 16: Mechanisms of Tolerance
• Learning Objectives: Positive/negative selection, AIRE, T and B regulators, molecular mimicry, immunoprivileged tissues.

Page 107

• What is tolerance?
• Tolerance is the unresponsiveness to an antigen; tolerance can be tolerogenic or immunogenic; Autoimmunity results when self-tolerance fails.

Page 108

• Central vs peripheral tolerance:
  • Central tolerance occurs during lymphocyte development in primary lymphoid organs (thymus for T cells, bone marrow for B cells) and eliminates self-reactive cells.
  • Peripheral tolerance occurs in mature lymphoid tissues and effector sites where responses are suppressed or cells are eliminated.
• Mechanisms include deletion (apoptosis), anergy, receptor editing (B cells), and development of regulatory T cells (Tregs).

Page 109

• Central T cell tolerance specifics:
  • Negative selection in thymus deletes immature T cells with high avidity for self antigen.
  • Peripheral tissue antigens are displayed in the thymus by medullary thymic epithelial cells (MTECs) under control of AIRE (Autoimmune Regulator).
  • AIRE promotes expression of tissue-restricted antigens in the thymus, regulating selection.

Page 110

• AIRE and tolerance: negative selection of high-affinity self-reactive T cells; absence of AIRE leads to autoimmune susceptibility; tTreg development may occur for self-antigens; high-affinity self-antigen exposure.

Page 111

• Consequences of deficient AIRE: APS1 (Autoimmune Polyendocrine Syndrome Type 1).
• The balance between deletion and Treg development is influenced by TCR affinity for self-antigen and MHC presentation.

Page 112

• Peripheral T cell tolerance (anergy and co-stimulation):
  • Naive T cells require costimulation (CD28-B7) for activation; without it, T cells become anergic.
  • Inhibitory receptors (CTLA-4, PD-1) dampen signaling to prevent autoimmunity.
  • Anergy is a state of unresponsiveness due to signaling blockade or inhibitory receptor engagement.

Page 113

• Regulatory T cells in peripheral tolerance:
  • Tregs (CD4+CD25+ FOXP3+) can develop in thymus or periphery; suppress effector T cells and maintain tolerance in peripheral tissues.
  • Mechanisms include cytokine production (IL-10, TGF-β) and cell-contact-mediated suppression.

Page 114

• Central B cell tolerance: receptor editing
  • Heavy and light chain gene rearrangements: if self-antigen recognition occurs, light chain can be edited via reactivation of RAG1/2 to generate a new light chain; process repeats until non-self-reactive BCR is produced or apoptosis ensues.

Page 115

• Peripheral B cell tolerance and inhibitory receptors:
  • BCR signaling must reach threshold; insufficient engagement leads to inactivation via inhibitory receptors (e.g., CD32/FcyRII, CD22).
  • SHIP phosphatase dampens PIP3 signaling to block B cell activation; polyvalent antigens can cross-link BCRs and favor activation.

Page 116

• Follicular exclusion and peripheral tolerance:
  • B cells encountering self-antigen in the follicle without T cell help become anergic or excluded from follicles; strategies include receptor editing or deletion.
• Summary: B cell tolerance includes receptor editing, clonal deletion, anergy, and follicular exclusion.

Page 117

• Dysregulation of tolerance: infections and autoimmunity
• Mechanisms: Bystander activation and molecular mimicry can break tolerance and trigger autoimmunity during infection.

Page 118

• Example of molecular mimicry: Guillain-Barré syndrome (GBS)
  • Autoantibody response generated against microbial antigen cross-reacts with nerve glycolipids (GM1) leading to demyelination; involvement of complement and macrophage-mediated inflammation; T cells contribute to pathology.

Page 119

• Immune-privileged tissues:
  • Tissues with reduced immune responses to prevent life-threatening damage (brain, eye, testis, placenta).
  • Examples: brain (blood–brain barrier), eye (blood–retina barrier), testis (blood–testis barrier), placenta (fetal tolerance).

Page 120

• Review questions (to guide study):
  • Central tolerance in T cells; gene roles in peripheral antigen presentation; fates of self-reactive T cells; anergy mechanisms; CTLA-4 vs CD28 engagement; regulatory T cells roles; receptor editing vs affinity maturation; peripheral self-reactivity; HLA roles in autoimmune predisposition; consequences of tolerance failure.

Page 121

• Lesson 17: Tumor Immunology

Page 122

• Learning Objectives for Tumor Immunology:
  • Tumor classes, tumor antigens, immune response, and therapies.

Page 123

• Tumor immunology overview (global):
  • Carcinogenesis involves multi-hit hypothesis; transformation includes loss of growth control, altered cell morphology, and evasion of immune detection.
• Cancer cells show characteristics such as increased cytoplasm, enlarged nucleus, multiple nucleoli, coarse chromatin, and other malignant features.

Page 124

• Tumor antigens: presentation context
  • Tumor Antigens can be classified into tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs).
  • TSAs (neoantigens) arise from oncogenic mutations and are not expressed on normal cells.
  • TAAs are overexpressed normal proteins or aberrantly expressed proteins.
  • Tumor antigens can be mutated, embryonic, or overexpressed self-proteins.

Page 125

• TSAs vs TAAs (definitions):
  • TSAs: expressed only by tumor cells; high specificity; neoantigens from driver mutations or viruses.
  • TAAs: expressed by some normal cells too; overexpressed or mis-timed expression; less tumor-specific.

Page 126

• Tumorigenesis and Immunology (visual overview):
  • Tumor progression stages accompanied by immunoregulation changes; dysplasia -> invasion -> angiogenesis -> metastasis; immune system interactions and tumor microenvironment adaptation.

Page 127

• Immune responses to tumors:
  • T cells (CD8+ CTLs) directly kill tumor cells; CD4+ Th1 cells support CTLs; B cells/antibodies and NK cells contribute to surveillance.
  • Macrophage polarization (M1 vs M2) influences anti-tumor immunity; M1 is tumoricidal; M2 tends to support tumor growth.

Page 128

• Tumor immune surveillance and elimination:
  • Innate and adaptive responses coordinate to detect and eliminate neoplastic cells.
  • Cytolytic mechanisms include perforin/granzyme, Fas/FasL, NKG2D ligands, TNF-α, ROS, and cytokines like IL-12, IFN-γ.

Page 129

• Tumor immune escape mechanisms:
  • Immune evasion: tumor cells alter antigen presentation or immune recognition to escape detection.
  • Immune suppression: tumor cells or tumor-associated cells alter the immune milieu to suppress responses (e.g., Tregs, myeloid-derived suppressor cells).
  • Phenotypic changes such as reduced MHCI expression can help tumors avoid CTLs but may increase NK cell recognition unless compensatory inhibitory signals are dominant.

Page 130

• Immunotherapy: Passive vs Active approaches
  • Passive immunotherapy: administering immune components (mAbs, cytokines, DC vaccines, adoptive cell transfer, CAR-T cells, BiTEs).
  • Active immunotherapy: stimulating the patient’s own immune system (cancer vaccines, checkpoint inhibitors).

Page 131

• Bispecific T-cell Engagers (BiTEs):
  • Fusion of two single-chain antibodies: one binds tumor-associated antigen, the other binds CD3 on T cells.
  • Redirects T cells to tumor cells to form a cytolytic synapse, triggering perforin/granzyme–mediated lysis independent of MHCI.
  • Example schematic: anti-tumor antibody site + anti-CD3 site; hinge and Fc regions included for stability.

Page 132

• T cell–based immunotherapies (overview):
  • T cells engineered to express recombinant TCRs or chimeric antigen receptors (CARs).
  • CAR-T therapy process: isolate T cells, expand, engineer, and re-infuse into patient; can be autologous; targets include CD19, CD20, etc.
  • CAR-T and TCR therapies provide targeted cytotoxicity against tumor cells.

Page 133

• Passive Immunotherapy: Chimeric Antigen Receptors (CAR) continued:
  • CAR structure includes VH and VL domains from antibody, a transmembrane domain, and intracellular CD3ζ signaling plus costimulatory domains.
  • CAR-T strategies are especially effective in hematologic malignancies (e.g., B cell lymphomas, leukemias) but can be associated with toxicities.

Page 134

• Lesson 18: Immunotherapy (transition)

Page 135

• Learning Objectives for Immunotherapies:
  • Mechanisms of action, dendritic cell-targeted immunotherapies, in situ therapies, CAR, BiTEs, and immune checkpoints.

Page 136

• Immunotherapy concepts and rationale:
  • Immunotherapies modify immune responses to either suppress inappropriate responses or enhance anti-disease responses.
  • Types include biological response modifiers, antibody-based therapies, and cellular therapies.
  • Rationale: increasing incidence of immune-mediated diseases and cancer burden.

Page 137

• Drug therapies in immunotherapy (overview):
  • Non-specific immune modulation: Cyclosporine (calcineurin inhibitor), Azathioprine (purine synthesis inhibition), Sirolimus (mTOR inhibition).
  • Specific targeting: Anti-CD3, anti-CD52, TNF-α inhibitors, IL-2 receptor blockers, CTLA-4-Ig (abatacept), Anti-CD154, Anti-CD25, JAK inhibitors, BTK inhibitors.
  • Pathways targeted include TCR signaling, PI3K/Akt, MAPK, mTOR, JAK-STAT, and NFAT/AP-1/NF-κB.

Page 138

• Rationale for therapies:
  • Activating immunotherapies are used to boost immune responses in immunosuppressed patients or where immune responses are needed (e.g., vaccines, cancer therapies).
  • Immunosuppressive therapies are used for autoimmunity, transplantation, and prevention of graft-versus-host disease.
• Conditions and contexts listed: viral infections (HIV, measles, HSV, CMV, VZV), TB, parasitic infections, malignancies, autoimmune diseases (RA, SLE, MS), malnutrition, organ failures, pregnancy, stress, asplenia.

Page 139

• Hematopoietic agents and growth factors:
  • Erythropoietin and GM-CSF/IL-3; G-CSF (filgrastim, pegfilgrastim) and GM-CSF (sargramostim); thrombopoietin (TPO) receptor agonists; vitamins/minerals.
  • Hematopoietic agents support hematopoiesis in immunodeficiencies or after bone marrow suppression.

Page 140

• Type I interferons and other cytokine therapies:
  • IFN-α (e.g., for viral infections and certain cancers), IFN-β (MS, infections), IFN-γ (CGD, malignant osteopetrosis).
  • IL-2, IL-12, IL-15, IL-21 used in various cancers and immune modulation.
  • Type I interferons and other growth factors are used as adjuvants and as direct anti-tumor or antiviral agents.

Page 141

• TLR agonists as adjuvants and immunotherapies:
  • TLR7/8 agonist (Aldara), TLR9 agonist CpG ODN, TLR3/4/5 ligands in trial as adjuvants; BCG (mycobacteria) as adjuvant immunotherapy for bladder cancer.
  • Immunostimulatory strategies aim to enhance innate immune sensing to boost adaptive responses.

Page 142

• JAK-STAT pathway inhibitors and BTK inhibitors:
  • JAK inhibitors (e.g., Tofacitinib/Xeljanz) block cytokine signaling via JAK-STAT, with broad immunomodulatory effects.
  • BTK inhibitors (ibrutinib) block BCR signaling, used in B cell malignancies and autoimmune diseases.

Page 143

• CTLA-4-Ig (abatacept) – costimulation blockade:
  • Fusion protein combining extracellular domain of CTLA-4 with IgG1 Fc; binds CD80/CD86 to prevent CD28 engagement; dampens T cell activation.
  • Therapeutic use in autoimmune diseases (RA, etc.).

Page 144

• Antibody-mediated neutralization and historical notes:
  • Anti-toxins and IVIG; anti-IgE therapies for allergic diseases; Anti-cytokine therapies targeting TNF-α, IL-17, and IL-5; cytokine receptor targeting.
  • Historical example: creation of diphtheria antitoxin via animal immunization and serum purification.

Page 145

• Natalizumab and trafficking control:
  • Anti-α4 integrin antibody inhibits diapedesis; used in MS and Crohn’s disease; linked to risk of PML (progressive multifocal leukoencephalopathy).

Page 146

• Immune checkpoints in cancer therapy:
  • PD-1/PD-L1 axis and CTLA-4 inhibitors unleash T cell activity against tumors.
  • Anti-PD-1 (nivolumab, pembrolizumab), anti-PD-L1 (atezolizumab), anti-CTLA-4 (ipilimumab).
  • Checkpoint blockade can cause immune-related adverse events, including autoimmunity.

Page 147

• Antitumor monoclonal antibodies (mAbs):
  • Trastuzumab (HER2/Neu), Rituximab (CD20), Gemtuzumab ozogamicin (CD33), Alemtuzumab (CD52), Ipilimumab (CTLA-4), Ofatumumab (CD20), Brentuximab vedotin (CD30).
  • Radiolabeled or conjugated mAbs (e.g., 90Y-ibritumomab tiuxetan) used in hematologic malignancies.
  • Cetuximab/Panitumumab (EGFR) and Bevacizumab (VEGFA) as targeted therapies.

Page 148

• Cell-based immunotherapies: overview
  • T cell-based therapies (CAR-T and TCR-transgenic cells); DC-based vaccines; NK cell and macrophage-based approaches.
  • CAR-T cells combine antibody-derived targeting with T cell signaling to recognize tumor antigens irrespective of MHCI.

Page 149

• Latent infections and immune-modulating therapies:
  • TNF inhibitors can reactivate latent infections (e.g., TB); anti-TNF and TB risk risk assessment required.
  • Other agents risk reactivation of JC virus (PML) with anti-CD52 and natalizumab usage.

Page 150

• Disease flares with immune checkpoint inhibitors:
  • Inhibition of immune checkpoints can trigger autoimmune-like flares in patients with pre-existing autoimmune diseases (e.g., myasthenia gravis with ipilimumab).
  • Cases of myocarditis and other autoimmune toxicities have been reported with checkpoint blockade.

Page 151

• Lesson 19: Principles of Vaccination

Page 152

• Administrative slide header; likely an index page.

Page 153

• Passive immunity overview:
  • For at-risk individuals or immunocompromised patients; examples include antidotes, anti-venoms, anti-toxins, IVIG, immune globulins, and therapeutic antibodies.
  • Artificial passive immunity; virus neutralization (RSV, COVID-19), venom/toxin neutralization, and anti-toxin serums.

Page 154

• Passive vs Active immunity (summary):
  • Passive: preformed antibodies; immediate protection; no memory; short-lived; suitable for immunodeficient individuals; no lag but no immunologic memory.
  • Active: infection or immunization; develops memory; slower to confer protection but longer-lasting; memory B and T cells are formed.

Page 155

• Vaccines (definition and goals):
  • Vaccine: preparation of pathogen or its products to induce active immunity; aims to protect individuals and promote herd immunity.
  • Ideal vaccine properties: safe, long-lasting protection, stable, cheap, easy to administer.
  • Two general types: Attenuated (live-attenuated) and Inactivated (dead) vaccines.

Page 156

• Vaccine components:
  • Antigens: target molecules recognized by the immune system.
  • Stabilizers, Adjuvants (e.g., alum, MPL), Antibiotics, Preservatives, Buffers, etc.
  • Adjuvants: enhance immune response by improving antigen delivery, stimulating innate responses, and increasing cytokines.

Page 157

• Adjuvants (detailed):
  • Mechanisms include enhanced delivery, innate immune activation, upregulation of inflammatory cytokines, and general immune potentiation.
  • Classes: inorganic (aluminum salts), organic (squalene), and immunologic/biologic (TLR agonists, cytokines such as IL-2, GM-CSF).

Page 158

• Attenuated vaccines (live-attenuated):
  • Contain weakened form of pathogen; can replicate; usually provide strong, long-lasting immunity with a single dose; potential risk in immunosuppressed individuals; reversion risk.
  • Examples: MMR, varicella, yellow fever, Sabin polio vaccine.

Page 159

• Inactivated vaccines (killed or inactivated):
  • Pathogen cannot replicate; safer but often require booster doses; boosters important due to waning immunity.
  • Use heat- or chemical-inactivated pathogens; more stable and safer for immunocompromised individuals.

Page 160

• Immunity conferred by vaccination (mechanisms):
  • Vaccines stimulate innate and adaptive immune responses; priming of CD4+ T helper cells and CD8+ cytotoxic responses with generation of memory B and T cells.
  • Vaccination routes (parenteral vs mucosal) influence the type of immunity generated (systemic vs mucosal).

Page 161

• Routes of immunization and antibody responses (intramuscular, subcutaneous, intradermal; oral) with examples:
  • IPV (inactivated polio vaccine) and OPV (oral polio vaccine) illustrate systemic vs mucosal immunity differences.
  • Sabin vaccine induces mucosal IgA; Salk vaccine induces serum antibodies.

Page 162

• Goals of immunization programs:
  • Selective immunization: protect those at highest risk.
  • Mass immunization: prevent transmission and spread; leads to eradication, elimination, or control depending on pathogens.

Page 163

• Herd immunity concept:
  • Indirect protection of susceptible individuals when a significant portion of the population is immune.
  • Reduces transmission risk and protects those who cannot be vaccinated.

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• Vaccine hesitancy:

  • Definition: Delay or refusal despite vaccine availability.
  • WHO 2024 top threat list; 2022 infodemic recognized as global health priority.

• MMR vaccination rates by state (graphical data):

  • Illustrates variation across states; Spearman rho and p-value indicate correlation between hesitancy and MMR uptake in certain datasets.

• Equations and key formulas mentioned in slides:

  • Neutrophil respiratory burst and ROS chemistry:
  • Superoxide formation: $O<em>2 + e^- \rightarrow O</em>2^{\cdot-}$
  • Disproportionation to hydrogen peroxide: $2 O<em>2^{\cdot-} + 2 H^+ \rightarrow H</em>2O<em>2 + O</em>2$
  • MPO halide system: $H<em>2O</em>2 + Cl^- \rightarrow HOCl + H_2O$
  • Antibody isotype valencies:
  • IgG/IgA/IgD: valency 2
  • IgM: pentamer (valency 10)
  • IgA (dimer): valency 4
  • Recombination and affinity maturation concepts (general):
  • V(D)J recombination introduces diversity; SHM introduces point mutations in V regions; AID is essential for class switch and SHM processes.

• Connections to foundational principles and real-world relevance:

  • Understanding primary immunodeficiencies (neutrophil defects, CGD, LAD, Chediak–Higashi) informs diagnosis and management of recurrent infections and guides genetic counseling.
  • MHC and antigen presentation underpin T cell–mediated immunity and vaccine design (epitope selection, adjuvants).
  • T and B cell development, selection, and tolerance explain autoimmunity risks and the rationale for immunotherapies (checkpoint inhibitors, abatacept, CAR-T, BiTEs).
  • Tumor immunology highlights immune surveillance and immune escape, informing cancer immunotherapies (PD-1/PD-L1 blockade, CTLA-4 inhibitors, mAbs, CAR-T).
  • Vaccination science (attenuated vs inactivated vaccines, adjuvants, mucosal immunity) underpins public health strategies for herd immunity and disease control.

• Ethical, philosophical, and practical implications:

  • Immunotherapies can unleash autoimmunity; balancing efficacy with adverse events is a clinical priority.
  • Herd immunity relies on vaccine acceptance; hesitancy has real-world consequences for outbreaks and public health.
  • Access to vaccines and biologics (CAR-T, monoclonal antibodies) raises equity considerations across populations and health systems.

• Formulas and LaTeX-friendly notations included in this set:

  • Oxygen radical chemistry in neutrophils:
  • $O<em>2 + e^- \rightarrow O</em>2^{\cdot-}$
  • $2 O<em>2^{\cdot-} + 2 H^+ \rightarrow H</em>2O<em>2 + O</em>2$
  • $H<em>2O</em>2 + Cl^- \rightarrow HOCl + H_2O$
  • Antibody isotype valency:
  • Isotypes: IgM, IgG, IgA, IgD, IgE with valencies as described above.
  • Three signals for T cell activation (conceptual):
  • Signal 1: TCR-MHC-peptide recognition
    n - Signal 2: Costimulation (e.g., CD28–CD80/86)
  • Signal 3: Cytokines (e.g., IL-2, IL-12, TGF-β)

• Note: The above notes are organized page-by-page to mirror the provided transcript. They cover both foundational concepts and specific details (including genetic loci, signaling pathways, and clinical examples) to serve as a comprehensive study guide for exam preparation.