Adaptive Immunology I Lecture 11 PDF

Adaptive Immunology I CHEN4838/5838 Lecture 11 Announcements Muddiest Points #4 Due 10/4 at 11:59pm HW #1 Posted Due 10/10 Grad Project Topic Due 10/8 Key Topics: Adaptive Immunology Parts 1, 2, 3 Adaptive Immune System T Cells Antigen Pres...

Adaptive Immunology I CHEN4838/5838 Lecture 11 Announcements Muddiest Points #4 Due 10/4 at 11:59pm HW #1 Posted Due 10/10 Grad Project Topic Due 10/8 Key Topics: Adaptive Immunology Parts 1, 2, 3 Adaptive Immune System T Cells Antigen Presentation TCR Review of Lymphatics T Cell Activation T Cell Function B cells BCR B&T Cell Interactions B Cell Activation Antibodies Tolerance Memory The Immune System } Humoral Immunity } Cellular Immunity Overarching Cell Response Signal Signal Activation Effector Mechanisms Activation Activation Signaling Mechanisms Cell Signal Key to understanding adaptive immunity Highly complex system is designed logically Think about where effector functions take place and what the cell is targeting: Antibodies are great for pathogens outside of cells CD8/CTL/Cytotoxic T cells kill infected cells – not pathogens directly T helper cells “help” cells kill all pathogens in extracellular space Dendritic cells travel to lymph nodes to activate T cells Macrophages reactivate T cells at sites of infection  Lymphoid Organs Primary Lymphoid Organs: Secondary Lymphoid Organs: Site of Lymphocyte Site of Lymphocyte Generation Activation/Proliferation Maturation Residence Bone marrow – B cells Spleen ~ B cells Thymus – T cells Lymph nodes – B and T cells Lymphatics Passive plumbing system Circulates: Fluid, which contains antigens Naïve B and T cells through lymph nodes to lymphatic ducts to re- enter blood stream B Cell and T Cell Similarities Both use gene recombination and junctional diversity to develop receptors that bind >100 million antigen peptides (but each cell binds ONE antigen) Both are activated by binding antigen: T cells bind antigens presented on MHC molecules B cells bind free antigens (opsonized), antigen presented on follicular dendritic cells Both require co-stimulation for full activation – two signal system Both contribute to immunological memory Principles of Adaptive Immunity Immunoglobulins BCRs/ Antibodies (soluble immunoglobulins) and TCRs have similar structures: Composed of variable region and constant region Each region provides distinct functions BCRs and TCRs go through similar development process – light heavy where diversity is created! chain chain α chain β chain  Immunoglobulins bind to “native” macromolecular antigens Antigen: any molecule that can be bound by an antibody, B cell receptor, or T cell receptor Epitope: the specific piece of the antigen that is directly bound Immunoglobulins can bind any type of macromolecule: protein, carbohydrate, lipid, etc Antibodies and TCRs recognize antigens differently B Cell Receptor (BCR) Two proteins: heavy chain + light chain Structurally identical to antibody + retention sequence on Fc domain Diversity of BCRs arise through: Genetic recombination (VDJ recombination) Heavy Chain Junctional diversity Light Chain Antibody- Binding domain Constant Region (Fab) (Fc) BCR Development All B cells start with the same DNA – how does diversity arise? V(D)J recombination! Heavy chain: Chromosome 14 has 4 types of gene segments: V, D, J, C ~40 V segments, 25Ds, 6Js, 10Cs B cell chooses (at random) one of each segment (VDJ) Light chain: Same process but only with VJ Heavy + light chain combinations = 10 million options Junctional diversity (base pairs added/removed) = 100 million options Creation of BCR V(D)J gene rearrangement: ex. Ig heavy chain 1 V segment, 1 D segment, 1 J segment randomly chosen DNA recombination occurs and removes the DNA between these segments Resulting VDJ recombined segment can actually be transcribed V(D)J gene rearrangement: ex. Ig light chain 1 V segment, 1 J segment randomly chosen DNA recombination occurs and removes the DNA between these segments Resulting VJ recombined segment can actually be transcribed Creation of BCR ACTG X X ACTG Generation of diversity: Immunoglobulins and TCRs  What are some problems with the random generation of Igs and TCRs? How are self-reactive receptors prevented? How is the “right” receptor made at the “right” time? Clonal deletion and selection Diversity is generated during development of B and T cells Cells expressing self-reactive molecules are deleted New antigens on microbes bind to a pre-existing pool of BCRs and TCRs Cells that bind these antigens are selected and expanded When a person gets a vaccine or is infected with a pathogen for the first time— A. She generates newly recombined B cells to make antibodies specifically against new antigens in that pathogen? B. B cells with receptors that have affinity for pathogen antigens already exist in her body before she is injected/infected? BCR Signaling Fab region of BCR binds epitope of cognate antigen: Cognate antigen: antigen that a given B cell binds Epitope: region of the cognate antigen that BCR actually binds (6-12 aas) Signal transduction occurs through Igα and Igβ BCR Activation Step 1: Clustering of BCRs to bring Igα and Igβ together = crosslinking 1. Epitopes repeat on pathogen 2. Many antigens close together 3. Complement opsonization a. Complement receptor = co-receptor b. Amplifies signal Critical for initiating “chain reaction” of signaling from Igα and Igβ BCR Activation Step 2: Second signal – two-signal rule 1. T cell-dependent activation Most common Co-stimulatory signal provided by T helper cell (Th) CD40L on Th cell binds CD40 on B cell 2. T cell-independent activation “Danger signal” co-stimulates cell TLRs Significant BCR crosslinking Mostly found in spleen Useful for detecting lipids, carbohydrates Faster immune response B Cell Maturation Class switching B cell changes the type of antibody it produces B cells initially produce IgM Can change to IgG, IgE, IgA by cutting out more DNA Fc region determines function Affinity Maturation Random mutations to VDJ segments change Fab slightly to create antibodies with higher affinity “Career decision”: plasma cell vs. memory B cell Antibodies 5 basic functions Neutralization of pathogens Opsonization of pathogens Complement activation Innate immune cell activation Protection of internal tissues Antibody class dictates primary effector functions Antibody Classes IgM: Ideal for early infection First antibody produced (before class switching) Good at activating complement (Classical Activation Pathway) Good at neutralizing viruses IgG: Longest lived and most abundant in blood IgG1: opsonizes pathogens for phagocytosis IgG3: fixes complement better than other IgGs and bridges NK cells with target (NK cell binds Fc region = more effective killing) Antibody dependent cellular cytotoxicity Antibody Classes IgA: Mucosal surfaces Cross intestinal wall and resist degradation by acids/enzymes 4 Fab regions = can clump bacteria together for clearance Secreted in breastmilk and coats digestive tract Cannot activate complement IgE: Parasites and Allergens/Toxins Mast cells bind IgE and degranulate Antibody Classes IgM, IgG: Blood IgG: Extracellular fluid, crosses placenta IgA: Mucosal surfaces IgE: Mast cells under epithelial surfaces B Cell Class Switching How does a B cell know what antibody to produce? Cytokines produced by T helper cells IL-4/IL-5 produced in response to worms = IgE IFNγ: bacterial infection = IgG3 TGFβ: viral infection = IgA Affinity Maturation Once BCR is developed – try to improve it! In lymph nodes – B cells undergo somatic hypermutations to DNA in V, D, J gene segments Antibody-antigen affinity is the same Antibody-antigen affinity is the increased Antibody-antigen affinity is the decreased B cells with better antigen binding outcompete for Th binding which leads to more proliferation Abs evolve through a process called Affinity Maturation (AM) in Germinal Centers (GCs) AM in response to a single “strain- antigen or infecting strain: specific” antibodies Th BP III. FDC Survival signal Lymph IV. node Selection signal LZ BM DZ Germinal Center (GC) I. GC seeding Proliferation/ II. mutation B B Cell Review B cells produce antibodies to fight pathogens Antibody class determine effector functions (IgM, IgG, IgA, IgE) Generally: neutralize pathogens, opsonize pathogens, activate complement, activate innate immune cells B cells require activation through binding of antigen to their BCR which leads to BCR clustering + stimulation by a second signal (T helper cell) BCRs develop diversity through Gene segment rearrangement (VDJ recombination) Junctional diversity (addition/deletion of ACTG) Class switching (IgM -> IgX) Affinity maturation (somatic hypermutation) T Cell Receptor Heterodimers - composed of two proteins α/β or γ/δ Each chain has a variable region that binds antigen and a constant region that associates with the membrane TCR assembled by genetic recombination and junctional diversity (like BCR) VJ for α chain, VDJ for β chain Do NOT undergo additional modifications CD4/CD8 Co-Receptors CTLs and Th cells have different functions and look at differing MHC molecules Naïve T cells start as double positive cells (CD4 +CD8+) During maturation choose a lineage: CD8: Killer T Cells – bind MHC class I CD4: Helper T cells – bind MHC class II Differing structure: T Cells Traditional T cells: >95% of T cells α/β TCR CD4 or CD8 co-receptors Non-traditional T cells: γ/δ TCR No CD4 or CD8 Most of their biology is unclear How do naïve T cells become effector T cells? Naïve T cells circulate in the blood and lymph. Interact with antigen-presenting cells (APCs) in secondary lymphoid tissues that present a variety of peptides on MHC molecules: Dendritic cells Macrophages Interaction between T-cell receptor and MHC-peptide complex results in a signaling cascade and leads to T-cell activation. Activation is followed by differentiation of T cell into an effector T cell TCR Binding and MHC Antigen Presentation Recognize presented antigen – must be in complex with MHC molecules TCR binds both antigen AND MHC molecule Class I and Class II MHC Molecules present different antigens to T cells CD8 (CTL): MHC I CD4 (T helper cell): MHC II Class I MHC Class I: Expressed by ALL cells Closed binding groove – bind end amino acids Peptide must be 8-9 amino acids Present intracellular peptide fragments Must complex with β2-microglobulin Displays “chopped up” endogenous proteins “Self” proteins + viral proteins Allows hidden epitopes to be detected Killer T cells inspect MHC I looking for antigens Class II MHC Class II: Expressed only by antigen presenting cells (DCs, macrophages, B cells) Open binding groove – binds middle amino acids Binds larger peptides (13-25 amino acids) Present extracellular peptides (exogenous) Present antigen to T helper cells, naïve T cells Two key system again required to set off T cell proliferation Antigen Loading onto MHC Class I – Endogenous Protein Present: Ordinary cellular proteins Proteins encoded by microbes that have infected cells “Billboard of proteins in the cell” Inspected by CTLs for non-self antigens Expressed by “ordinary” cells and antigen-presenting cells Antigen Loading onto MHC Present: Class II – Exogenous Protein Proteins from the extracellular space Billboard for what’s happening outside the cell Inspected by T helper cells for activation Expressed by antigen presenting cells  intracellular extracellular extracellular The compartment in which the antigen resides impacts route of antigen presentation  Which MHC molecule(s) do DCs use to present antigens?  How do APCs present antigens (pathogens/cancer) that do not infect APCs to CD8 T cells? MHC Cross-Presentation Phagocytic cells (especially dendritic cells, but also macrophages and B cells) can use cross- presentation to present phagocytosed material via MHC class I molecules. Cross-presentation activates the CD8 T cells responsible for combating the intracellular infection. Endocytosed material in a cross-presenting cell is transported to a specialized endosome and ends up in the cytosol – cytosolic diversion. o Diverted material in the cytosol can be processed and presented using the normal MHC class I machinery. Cross-presentation is believed to play an important role in activating naïve CD8 T cells required to mount an adaptive immune response to an intracellular pathogen such as a virus. MHC Cross-Presentation The dendritic cell must be licensed to properly cross-present antigen. Licensing of cross-presentation in dendritic cells is postulated to require CD4 T cells using the following mechanism: Dendritic cells present phagocytosed extracellular antigens on MHC class II and activate a naïve CD4 T cell. Activated CD4 T cells release cytokines, signaling the dendritic cell to begin cross-presentation, potentially activating naïve CD8 T cells. MHC Polymorphism MHC genetic locus = human leukocyte antigen (HLA) locus HLA-A, HLA-B, HLA-C Class I and II MHC genes have many variants throughout the population (~1500 slightly different gene forms for MHC I, ~700 for MHC II) Different people have different versions of MHC proteins = different amino acid sequences, different peptide binding at ends HLA matching – critical for organ transplant CTLs selected to recognize “self” MHC = recognize “foreign” MHC MHC = major histocompatibility complex Antigen Presenting Cells Present antigen + MHC and co-stimulatory signal to activate T cells Dendritic Cells Activated by inflammatory cytokines to load up MHCs and increase B7 production Migrate through lymphatics to lymph node Present antigen to naïve T cells, T helper cells, memory T cells Present antigen on both Class II MHC and Class I MHC (cross presentation) Macrophages Present antigen to killer T cells (CTLs) at sites of infection to re-stimulate them B Cells Present antigen to T helper cells in lymph nodes to re-activate them Dendritic Cells Before infection: DCs patrol tissues with low B7, low MHC Following infection: DCs activated by cytokines released by neutrophils and macrophages, IFNs, pathogens (TLRs) Begin loading MHCs with pathogen Upregulate MHC and B7 Following antigen loading: Migrates to lymph nodes Recruits new monocytes to become DCs in tissue T Cell Development and Selection MHC Restriction “Positive Selection” Cortical thymic epithelial cells ask T cells if they recognize their MHC molecules? Yes -> Live! No -> Die! cTECs display: Class I MHC + endogenous peptides Class II MHC + exogenous peptides Class II MHC + endogenous peptides (not normal) Following MHC restriction – T cells become single positive cells Tolerance of Self “Negative Selection” Do you recognize any of the self-peptides displayed by the MHC molecules? Yes -> Die! No -> Live! Medullary thymic epithelial cells (mTEC) Digest their innards and display proteins Have TF (AIRE) that expresses tissue-specific proteins Thymic dendritic cells (TDCs) Get antigens from environment and are “given” antigens from mTECs T Cell Selection Process  B Cells go through selection as well… Step 1: Check for functional BCR Step 2: Selection against self antigens TCR Signaling TCRs have short intracellular domains (like BCR) Use CD3 to signal: Complex of 4 proteins (γ, δ, ε, ζ) Have signaling motifs TCRs require clustering for activation T cells also use co-receptors for antigen recognition/signaling T cells require co-stimulation for full activation TCR Activation Step 1: Binding of antigen + MHC molecule by TCR + CD coreceptor Step 2: Co-stimulation CD28 on T cells binds B7 on antigen-presenting cell TCR + CD4 + CD28 = immunological synapse Step 3: Release of IL-2 leads to clonal expansion Activation of Helper T Cells (CD4) Produce cytokines to direct the immune response Quarterback Different Th cells produce different subsets of cytokines Th1, Th2, Th17 Positive feedback with cytokine secretion creates more Th Coach DC give cues on which cytokine to produce What kind of invader are we dealing with? Where are they located? DCs use PRRs and cytokine receptors to identify who/where Co-stimulatory molecules on DC informs Th cells Production of Th1 Helper T Cells DCs coming from bacterial/viral infections produce IL-12 -> Th1 Activates Macrophages and NK Cells Restimulates Macrophages, B cells->IgG3 Growth factor for CTLs, NK cells, Th1 Production of Th2 Helper T Cells DCs from sites with parasites Growth factor Th2, B cells and B cells -> IgE B cells -> IgA Produces mucus in intestine Production of Tfh Helper T Cells Activate B cells to produce antibodies in response to extracellular pathogens Interact with B cells in the germinal center Recognizes MHC class II on B cell Release IL-4/IL-21 to stimulate B cells T and B cell must recognize Linked Epitopes – epitopes on the same molecular complex (pathogen) Production of Th17 Helper T Cells DCs fungal or extracellular bacterial infections produce TGFβ, IL-6, or IL-23 Recruits neutrophils to sites of infection Th17 growth factor B cells -> IgG3, IgA Activation of CTL (CD8 T Cells) Biology is still not completely clear Early in infection: 2-cell interaction Antigen presentation on MHC I by DC (cross-presentation) Co-stimulation by the same DC Faster to react but short-lived and limited killing and proliferation potential Later in infection: 3-cell interaction Antigen presentation on MHC I by DC “Help” from T helper cell Proliferate robustly, kill efficiently, can become memory T cells Potentially possible through DC “licensing” or chemokine secretion CD8 Effector T Cells (CTLs) CTLs recognize pathogen on MHC class I on infected cells Carry lytic granules filled with cytotoxins: Perforin Granzyme B CD8 Effector T Cells (CTLs) Induce apoptosis via: Pores in target cell membrane (lytic granules) Fas ligand expression (binds Fas on target cells) Must kill cells without releasing cell contents Also produce IFNγ which upregulates MHC class I expression CD8 Regulatory T cells (Tregs) Restrains the immune response, maintains tolerance to self-antigens, prevents autoimmunity and allergies Induced by TGFβ Secrete IL-10 and TGFβ IL-10 reduces APCs’ PRRs IL-10 reduces APC expression of B7 IL-10 reduces T cell proliferation and CTL killing Shutting Down Cellular Immunity Checkpoint proteins: B7 has competitive binder (CTLA-4) – outcompetes CD28 and shuts down T cell activation PD-1 expressed on T cells following activation, PD-1 binding PD-L1 inhibits T cell function Peripheral Tolerance: T cells with antigen but no co-stimulation = anergy Activation-Induced Cell Death: T cells that are re-activated over and over become sensitive to ligation of their Fas proteins by FasL on other T cells – apoptosis Immunological Memory Immunological Memory B cell memory: Long-lived plasma cells: reside in bone marrow and continually produce low levels of antibodies Central memory B cell: reside in secondary lymphoid tissue and slowly proliferate to replace long-lived plasma cells that die Most have class switched and undergone affinity maturation = best of the best Immunological Memory T Cell memory: Tissue-resident memory T cells: were effector T cells but remain in tissues near site of infection Effector memory T cells: circulate through blood/lymph Central memory T cells: reside in secondary lymphoid organs, move out to tissues upon attack Th1, Th2, Th17 have long memories Review B Cells T Cells Originate and mature in bone Originate in bone marrow, mature marrow in thymus Circulate in lymphatics until Circulate in lymphatics until activated activated Become activated in lymph node Become activated in lymph node Perform effector functions in Perform effector functions in lymph nodes and spleen peripheral tissues (Th1, Th2, CTL) and lymph nodes (Tfh) light heavy chain chain α chain β chain Review – Receptor Diversity generated during development of BCR/TCR B Cells T Cells Generate BCR through VDJ Generates TCR through VDJ recombination, junctional diversity recombination, junctional diversity BCR matures through class No additional TCR maturation switching, affinity maturation T cells also have CD4/CD8 co- receptors Have short transmembrane Have short transmembrane region regions – use Igα and Igβ to signal – use CD3 to signal BCR/TCR Development Cells that bind self-molecules are deleted: tolerance Antigens on microbes bind a pre-existing pool of BCRs and TCRs Cells that bind these antigens are selected and expanded (clonal expansion) Review B Cells T Cells Bind free (opsonized) antigen and Bind presented antigen on MHC antigen on follicular dendritic cells molecules found on APCs (MHC II) Bind native antigens: and all cells (MHC I) Folded proteins Bind small linear peptide antigens Carbohydrates Lipids Review B Cells T Cells Activation requires co-stimulation Activation requires co-stimulation T cells (Th cells) Activated dendritic cells Other “danger” signals B7/CD28 Affinity maturation requires Tfh Activity requires re-activation by binding antigen binding (macrophages/B cells for CD4 T cells) B cells produce antibodies which T cells kill pathogens and help Neutralize pathogens other cells kill pathogens CD8: CTL – kills infected cells and Activate complement eliminates infectious reservoir Activate innate immune cells CD4: Th cells – secrete cytokines to Opsonize pathogens activate other immune cells CD4 vs CD8 The type of infection determines which CD4 subset is made