Innate vs. Adaptive Immunity

Innate vs. Adaptive Immunity

• Innate immunity is a non-specific immune response that recognizes pathogens by patterns & commonalities
• Adaptive immunity is a specific, learned immune response that occurs after initial exposure to a pathogen

Physical Barriers Against Infection

• Physical barriers include hairs, oils, and antimicrobial substances on the skin and mucosal surfaces

Antigens and Epitopes Defined

• Antigens are substances recognized as foreign by the body
• Epitopes are markers on antigens, recognized by specific proteins

Immune Cells

• Leukocytes are white blood cells

Granulocytes

• Granulocytes contain granules that package proteins for destroying pathogens
• Granulocytes include neutrophils, basophils, eosinophils, and mast cells

Neutrophils

• Neutrophils are the majority of white blood cells and perform phagocytosis

Phagocytosis

• Phagocytosis is cell eating performed by neutrophils, monocytes, macrophages, and dendritic cells

Eosinophils

• Eosinophils defend against parasitic worms

Basophils

• Basophils defend against worm infections and play a role in T cell activation for parasitic infections

Mast Cells

• Mast cells are granular cells in connective tissue, act as inflammatory mediators, and release histamine

Lymphocytes

• Lymphocytes are a type of agranulocyte that include B cells, T cells, and NK cells

Monocytes

• Monocytes are a type of agranulocyte that migrates to tissues and differentiates into macrophages or dendritic cells

Hematopoiesis

• Hematopoiesis is the production of blood cells

Erythrocytes

• Erythrocytes are red blood cells and contain hemoglobin to transport oxygen

Megakaryocytes

• Megakaryocytes are cells that specialize in the production of platelets

Platelets

• Platelets are non-nucleated products of megakaryocytes and specialize in blood clotting

Myeloid Progenitor

• Myeloid progenitors give rise to most cells involved in innate immunity and antigen presentation
• Hematopoietic stem cells differentiate into myeloid progenitor cells, which then divide and differentiate

Antigen-Presenting Cells

• Antigen-presenting cells are phagocytic cells of the innate immune system

Macrophages

• Macrophages are agranulocytes specializing in phagocytosis of foreign antigens and apoptotic cells

Cytokines

• Cytokines are soluble proteins secreted by cells and aid the immune system
• They increase inflammation, chemotaxis, immune cell signalling, and differentiation

Dendritic Cells

• Dendritic cells are white blood cells specializing in phagocytosis
• They phagocyte foreign pathogens and present antigen epitopes to the adaptive immune system

Lymphoid Progenitor

• Lymphoid progenitors give rise to T cells, B cells, innate lymphoid cells, and NK cells
• Hematopoietic stem cells that differentiate into lymphoid progenitor cells give rise to cells involved in both innate and adaptive immune responses

NK Cells

• NK cells are responsible for killing virally infected and cancer cells.
• They target the source of infection for destruction

Cytotoxic T Cells

• Cytotoxic T cells are CD8-positive T cells activated by recognition of a specific epitope
• They target cells with intracellular infections, utilizing cytokines and cytotoxins

Helper T Cells

• Helper T cells assist in the activation of other cells
• These include macrophages, B cells, and cytotoxic T cells

Plasma Cells

• Plasma cells are B cells activated after encountering their specific antigen
• They secrete soluble antibodies that recognize the original B cell's antigen

B Cells

• B cells are lymphocytes involved in the humoral adaptive immune response.
• They recognize specific antigens via cell surface immunoglobulins and differentiate into plasma cells/centrocytes when activated
• B cells can act as antigen-presenting cells, using MHC class II after engulfing the antigen

Steps of Inflammation

• Innate immune cells recognize an infection.
• Cytokines or inflammatory mediators are released, activating cells with corresponding receptors.
• Activated immune cells and plasma proteins migrate to the infection site through vasodilation.
• Dendritic cells and soluble pathogen antigens move to nearby lymphoid tissue.

Clonal Selection

• Clonal selection is the process where a specific T or B cell recognizes its antigen via its receptor
• Only lymphocytes with matching receptors are activated, proliferate, and create clones

Clonal Expansion

• Clonal expansion is the proliferation and differentiation of a T/B cell after its receptor interacts with its antigen

Naive T Cell

• Naive T cells are immature T cells, have not encountered an antigen, and are undifferentiated
• Mature T cells have undergone positive and negative selection where they encountered their specific antigen

Naive B Cell

• Naive B cells are immature B cells, haven't encountered an antigen, and express B cell receptors
• Once B cells encounter their antigen they can differentiate into plasma cells or memory cells

Plasma Cells

• Plasma cells secrete soluble immunoglobulins for the antigen

Memory Cells

• Memory cells are long-lived cells, that mount a secondary immune response

Immunological Memory and Vaccines

• The immune response is highly efficient the second time due to immunological memory
• Memory T and B cells generated during clonal expansion act in a faster, robust response upon re-exposure
• Vaccines prime the adaptive immune system with a non-pathogenic form of a pathogen

Primary Lymphoid Tissue

• Primary lymphoid tissue is where lymphocytes develop; this includes the bone marrow and thymus

Secondary Lymphoid Tissue

• Secondary lymphoid tissue is where lymphocytes are activated, meet antigens, and differentiate
• Secondary lymphoid tissue includes lymph nodes, spleen, tonsils, and MALT

Immune Cell Trafficking

• Immune cell trafficking involves the movement of immune cells throughout the body
• This allows them to reach infection, inflammation, or damage sites to initiate a response.
• Immune cells that traffic include T and B cells

Lymph Node - Structure and Function

• Lymph nodes are bean-shaped structures that filter lymph fluid and support immune responses
• The paracortex contains T cells interacting with antigen-presenting cells
• The superficial part contains B cells
• Follicles are areas for germinal centers, where immune responses occur.
• Germinal centers are sites of B cell proliferation and differentiation

Spleen's Relation to Lymph Nodes

• The spleen filters red blood cells and monitors the bloodstream for pathogens.
• Without a spleen, a person is prone to bloodstream bacterial infections

Hypersensitivity Reactions

• Hypersensitivity reactions occur when the immune system malfunctions
• This is an exaggerated or misdirected immune response

Type I Hypersensitivity

• Type I is immediate hypersensitivity
• This is an overreaction to harmless allergens that involves IgE and leads to inflammation
• Examples include allergies and anaphylaxis

Type II Hypersensitivity

• Type II is cytotoxic hypersensitivity
• Antibodies (IgG/IgM) attack self-cells
• An example of this is hemolytic anemia

Type III Hypersensitivity

• Type III involves immune complex hypersensitivity
• Antigen-antibody complexes deposit in tissues, creating inflammation
• One example is lupus

Type IV Hypersensitivity

• Type IV is delayed hypersensitivity
• T-cell-mediated inflammation damages tissues
• An example is contact dermatitis

Lysozyme Function

• Lysozyme breaks down bacterial cell walls

Psoriasin Function

• Psoriasin destroys or inhibits microorganism growth and can cause bacterial lysis

Phagocytosis Process

• Phagocytosis starts with pathogen recognition by a receptor on a phagocyte
• Receptors recognize opsonins or patterns on the pathogen's surface
• The pathogen binds to the phagocyte through the receptors which causes receptor clustering
• The cell membrane invaginates to engulf the pathogen into a phagosome
• The phagosome fuses with a lysosome, forming a phagolysosome where digestion occurs

PRRs Definition

• PRRs (Pattern Recognition Receptors) are immune receptors recognizing conserved molecular patterns on pathogens
• PRRs trigger innate immune responses

PAMPs Definition

• PAMPs (Pathogen-Associated Molecular Patterns) are molecular structures found on pathogens, like bacterial cell walls
• PAMPs are recognized by PRRs to initiate immune activation

TLR Definition

• TLR (Toll-Like Receptor) is a type of PRR
• This PRR detects PAMPs
• This PRR activates immune signalling pathways, contributing to inflammation

Lectin Definition

• Lectin is a carbohydrate-binding protein important for pathogen recognition, cell signaling, and immune responses

CD Definition

• CD (Cluster of Differentiation) refers to surface markers on immune cells
• These markers are used to identify and classify cell types and stages of differentiation

LPS Definition

• LPS (Lipopolysaccharide) is a component of the outer membrane of Gram-negative bacteria.
• It activates TLR4 to trigger strong immune responses

Fc Receptor Definition

• Fc Receptor is a receptor on immune cells that binds the Fc region of antibodies
• It facilitates phagocytosis, antibody-dependent cellular cytotoxicity, and immune regulation

IL-1 Functions

• IL-1 stimulates inflammation, induces fever by acting on the hypothalamus, and activates T cells to enhance immune responses
• It also promotes the production of acute phase proteins that are key to systemic inflammation

TNF-alpha Functions

• TNF-alpha drives inflammation, increases vascular permeability for immune cell migration, triggers apoptosis in infected cells, and supports acute-phase protein release
• Although crucial for immune coordination, excessive production can be harmful, as seen in chronic inflammatory diseases

TLRs

• TLRs are transmembrane proteins with intracellular and extracellular domains
• They are located on the cell surface or within the cell (endosomes and lysosomes)
• TLRs recognize ligands that cause changes in gene expression and help activate the innate immune system
• The cytokine release bridges the adaptive and innate immune responses
• Extracellular TLRs recognize PAMPs, intracellular TLRs recognize foreign nucleic acids

Macrophage Activation

• Macrophages can be activated by toll-like receptors or PRRs (Pattern Recognition Receptors)

Macrophage Cytokines

• IL-1β and TNF-ɑ: Inflammatory response
• IL-6: Activates liver cells which produce complement proteins
• CXCL8: Recruits neutrophils
• IL-12: Recruits and activates NK cells

Neutrophil Receptors

• CR3 and CR4 are receptors on the surface of a neutrophil

Neutrophil Extravasation - Steps

• Slow rolling requires selectins binding to carbohydrates on neutrophils
• Tight binding needs CXCL8 binding to neutrophil, increasing LFA-1 expression
• Tight binding needs LFA-1 that is present on the neutrophil, which tightly binds to ICAM-1 on endothelial cells
• Diapedesis is where the neutrophil squeezes between endothelial cells which is mediated by LFA-1 and CR3
• Migration is where the gradient of CXCL8 directs the neutrophil towards the infection

NETs Function

• NETs are extracellular fibers consisting of DNA and antimicrobial proteins that trap pathogens
• They increase pathogen destruction without requiring phagocytosis

NK Cell Targets

• NK cells target intracellular pathogens

Interferon Function

• Interferons (IFN) are cytokines, activate cells, and are important in targeting viral infections
• TLRs sense viral molecules
• Signal transduction leads to IFN-α and IFN-β expression which induces NK cell proliferation and activates interferon-stimulated genes

NK Cell Activation

• The protein NKG2D binds to two ligands (MIC-A and MIC-B) and activates NK cells

NK Cell Killing

• NK cells release cytotoxic granules with molecules like perforin and granzymes when killing a cell
• Perforin forms small holes
• Granzymes initiate apoptosis

Dendritic Cells and T Cells

• DCs uptake/process antigens and then present the processed antigen on MHC class I or II to T cells in secondary lymphoid tissue, thus connecting innate and adaptive responses

Immune Response Differences vs Pathogen

• Extracellular pathogens trigger dendritic cells to release IL-6 and TGF-B and activate Th (helper) cells which activate neutrophils
• Intracellular pathogens trigger dendritic cells to release IL-12 and IFN-γ, which activate macrophages and cytotoxic T cells

Complement Fixation

• Complement fixation is the covalent attachment of a complement protein to the surface of a pathogen

C3 Function

• C3 is a complement protein that is cleaved during complement activation into C3a and C3b

C3a Function

• C3a functions as an anaphylatoxin

C3b Function

• C3b functions as an opsonin

Complement Activation - Alternative Pathway

• The alternative pathway is the first pathway that is activated
• C3 is spontaneously converted to iC3
• iC3 ultimately becomes C3 convertase and cleaves other C3 proteins into C3a and C3b

Complement Activation - Lectin Pathway

• Triggers inflammatory cytokines
• Initiated by mannose binding lectin

Complement Activation - Classical Pathway

• Initiated by C-reactive protein interacting with another complement protein
• The initiating component can be either an innate immune protein or a soluble immunoglobulin

C3 Convertase

• C3 convertase is an enzyme responsible for cleaving the C3 protein

Alternative Pathway - First to Act

• The alternative pathway is first to act because C3 is always present

Tickover

• Tickover is the process when C3 turns into iC3, which cleaves C3 into C3a and C3b

"a" Complement Proteins

• "a" complement proteins are anaphylatoxins
• "a" fragments promotes immune cell recruitment

"b" Complement Proteins

• "b" complement proteins function as opsonins
• "b" fragments are involved in pathogen elimination and the formation of the membrane attack complex

Alternate C3 Convertase

• Alternative C3 convertase makes C3a and C3b

Properdin

• Properdin stabilizes alternative C3 convertase on pathogen surfaces, creating more C3a and C3b

Opsonin Molecules

• C3b, C4b, and C1q are complement molecules that act as opsonins

Alternative C5 Convertase Formation

• C3b interacts with the alternative C3 convertase to form the alternative C5 convertase

MAC Initiating Factor

• MAC initiating factor is C5b binding to the pathogen surface

MAC Formation

• C5b, C6, and C7 join to form C7b67, which inserts into the pathogen membrane
• C8 binds, then C9, followed by more C9 molecules to create a pore
• The osmotic balance is disrupted and causes the pathogen to die

C5a and C3a

• Induce inflammatory responses
• Increase vascular permeability
• Cause smooth muscle contractions and mast cell degranulation
• Secrete histamine

Lectin/Classical Pathways

• Induce inflammatory response

MBL

• Acts as site of attachment and serves as an opsonin

Classical C3 Convertase

• Composed of C2b and C4b

Classical Complement Pathway Initiation

• Begins with binding of C-reactive protease and its associates (C1q/C1r/C2s) to phosphocholine on the surface of the pathogen
• The protease C1r/C1s can act similarly to MASP-1/MASP-2 to cleave C4 and C2, forming C3 convertase

TCR vs Toll-Like Receptor Function

• Toll-like receptors are part of innate immunity and are specific to types of ligands and patterns, not to one type of antigen
• TCRs differentiate after exposure to a pathogen and have more diversity in T cells/TCRs
• TCR antigen-binding sites bind to both the MHC II and the antigen

T Cell Receptor Structure

• Transmembrane proteins located extracellularly, with alpha and beta chains, both constant and variable regions
• The constant region is the same among all TCRs
• A variable region contains different amino acids based on the TCR and antigen-binding site
• Specificity comes from antigen-binding sites on the structure

MHC Class I

• Present on intracellular antigens
• Consist of 2 polypeptides

CD8

• T-cell coreceptor that binds to MHC class I molecules

MHC Class II

• Present on extracellular antigens
• Also has a and b chains

CD4

• T-cell coreceptor that binds to MHC class II molecules

MHC II

• Expressed by antigen-presenting cells (e.g., macrophages, mast cells, dendritic cells)

MHC I

• Expressed by any cells besides erythrocytes/RBCs

Immunoglobulins

• Immunoglobulins, also known as antibodies, can act as B-cell receptors (BCRs) if expressed on the B cell surface
• They can also act as soluble effector molecules secreted by plasma cells

Soluble Immunoglobulin Functions

• Neutralization of foreign particles or pathogens
• Opsonization of foreign particles or pathogens
• Complement activation.
• Activation of innate immune cells
• Protection of internal/mucosal tissues

Longer Adaptive Immune Response

• Events that require identification, activation, the proliferation of B/T cells takes many days

Affinity Maturation

• Alterations in B cell genes promote the production of B cells with high affinity immunoglobulins

Somatic Recombination

• Somatic recombination cuts out the regions of DNA and is an error prone process

Isotype Switching

• B cells can change their immunoglobulin isotype, like IgA to IgE

T Cell Function over Lifetime

• An individual's T cell population develops as an infant
• Amount of creation decreases by ~3% from birth until ages 35-45
• After, the amount decreases by 1% per year.

Thymocytes

• Immature T cells found in the thymic cortex
• Thymocytes undergo development and selection to become T cells

Thymic Epithelial Cells

• Thymic epithelial cells are a resident cell type in the thymus.
• They interact with thymocytes to activate genes for thymocyte development
• These play a role in differentiation checkpoints.

TCR Checkpoints - Overview

• There are two checkpoints, one for beta chain and the other for the alpha chain
• If the gamma-delta receptor rearranges first in either, the cell becomes gamma-delta

TCR Checkpoints - Step 1

• Starts with a double-negative thymocyte (no CD4 or CD8 coreceptor)
• 1st checkpoint addresses gamma-delta vs beta subunit
• If the gamma-delta recombines first, it stays double-negative and becomes a gamma-delta T cell
• If Beta recombines first, the T cell becomes double-positive and moves to the next checkpoint

TCR Checkpoints - Step 2

• 2nd checkpoint address gamma-delta vs alpha subunit
• If the gamma-delta recombines first, the cell stays double-negative and becomes a gamma-delta T cell
• If alpha recombines first, the T cell stays double-positive and becomes and continues onto positive and negative selection

T Cell Selection in Cortex

• 1st Round of Positive and Negative Selection (Cortex) which tests the TCR affinity for MHC class I or II molecules presenting the antigen
• Death by Neglect is the inability for the TCR to interact with any self MHC-peptide complexes to be useful
• Negative Selection is where the TCR binds too tightly
• Positive Selection is where the TCR interacts

Lineage Commitment - T Cell Selection

• When the unknown process cell becomes single-positive (only CD4 OR CD8 coreceptor)

T Cell Selection in Medulla

• 2nd Round of Positive and Negative Selection (Medulla) positively selects for tolerance to self-antigens done the transcriptional activator AIRE allowing Thymic epithelial cells to express antigens from different parts of the body
• Negative Selectionis when TCR binds too tightly
• Positive Selection is when TCR does not interact

MHC vs TCR Diversity

• MHC diversity is due to the presence of MHC gene families and genetic polymorphism.
• Different yet related T genes encode MHC class I and class II subunits.
• Multiple alleles of each gene encode each subunit
• TCR diversity as a result of random rearrangements of V, D, and J gene segments during T cell development random addition/deletion of nucleotides

Hypervariable Region in the TCR

• Two different polypeptide chains in the structure: Alpha/Beta Subunit or Gamma/Delta Subunit; each has constant/variable region
• Hypervariable regions are the junction of V, D, and J segments
• CDRs = Complementary Determining Regions; each domain contains three hypervariable regions
• Formed through random V, D, and J gene segment rearrangements with random nucleotide additions/deletions

Alpha/Beta vs Gamma/Delta T Cells

• All alpha-beta receptors recognize peptide antigens presented by MHC molecules
• Gamma-delta receptors recognize their antigen without the presence of an MHC molecule

CD3 Role

• Consists of gamma, delta, and epsilon chains, as well as two zeta chains
• This is used in signaling when T cell is activated

CD4 Role

• It's a coreceptor on helper T cells that is important for recognition and binding to MHC class II

CD8 Role

• Coreceptor on cytotoxic T cells that's vital for recognizing and binding to MHC class I

CD28 Role

• In naive cells, it provides a costimulatory signal to the T cell

CTLA4 Role

• It binds the same receptors as CD28 to downregulate T cell activation

MHC I Structure

• Alpha transmembrane chain
• Soluble beta microglobulin
• Binding groove is located in the alpha chain

MHC II Structure

• Alpha transmembrane chain
• Beta transmembrane chain
• The binding groove is the interface between a and b chains

Peptide Loading - MHC I

• A peptide-loading complex is formed
• Calnexin is a chaperone protein that keeps MHC class I molecules folded correctly in the ER
• Tapasin allows efficient loading and promotes peptide association with the MHC class I molecule
• Intracellular antigen is digested in proteasome.
• The peptide is transported via TAP

Peptide Loading - MHC II

• MHC class II molecule assembly in the ER includes the invariant chain, which blocks the peptide-binding groove
• CLIP production occurs, with the CLIP which remains bound to the peptide-binding groove
• Phagocytosis of extracellular antigen into a phagolysosome where the vesicle housing the MHC class II moleule
• HLA-DM promotes CLIP exchange

Invariant Chain

• Blocks peptide binding groove, prevents proteasomal peptide binding
• MHC I peptides are prohibited from binding to MHC II molecules in the ER because of the invariant chain.

Cross Presentation Purpose

• Allows activation of cytotoxic T cells and enable presentation of exogenous antigens, solving intracellular infections

Isotype

• Different protein versions of a gene family with related functions

Allotype

• Protein product of a particular allele of a gene

Haplotype

• Expressed isotypes of all alleles of a gene family within an individual

Directional Selection

• Shifts selective pressure to increase frequency of a single alelle and reduces the MHC diversity

Mature vs Immature DCs

• Immature dendritic cells are involved in the peripheral tissues with phagocytosis of foreign pathogens and specialize in antigen uptake/processing
• Mature dendritic cells are when DCs migrate into secondary lymphoid tissue via cellular projections

CCR7 and CCL21 Role

• CCR7 is a receptor, used by DCs to help migrate to lymph nodes during infection.
• CCL21 is chemokine for the CCR7 receptor as a signal

B7 Role

• Mature DCs express B7, needed to activate B and T cells, triggered by CCL21, affinity for proliferation

Macrophages vs DCs

• DCs specialize in phagocytosis and T-cell activation to naïve T cells
• Macrophages remain main site for phagocytosis with limited T-cell activation

LFA-1 and ICAM-1

• It facilitates binding and formation of the immune synapse
• Facilitates diapedesis using the proteins that allow connections of molecules

CTLA4 and CD28

• It's on the APCs, and CD28 will signal on T Cells for T cell differentiation
• After activation, T cells express CTLA4 as inhibitory to regulate this

S1P expression

• To guide T cells that are in the secondary lymphoid tissue to signal
• The receptor is suppressed during activation

Interleukins

• Amino acid sequences on CD3 proteins and crucial for signal transduction
• When phosphorylated, they create docking sites
• IL-2 Binds to create cellular divisions
• Regulate via activating and inhibitory

T Cell Anergy

• When T cells no longer have an effect to non-stimulating B7
• B7 causes anergy or T cell energy

C88 and T Cells with B7

• Activate though DCs with MHC-I molecules on B7 which allow T cell activation
• Cytokines are released by APC to encourage this activity and differentiation

Signals for Cytotoxic functions

• B7 molecules
• After maturing, they don't need this for combat pathogens

TH1 function

• For defense of intracellular pathogens
• IL 2
• activating macrophages and cytotoxic T cells

TH2 Function

• For extracellular pathogens
• Activate B cells to produce antibodies

TFH function

• Follicular helper for CD4 cell activation
• Differentiation for plasma calls in high affinity

TH17 function

• Fight fungus and infections
• Promote inflammation