The Immune System

• • The four principles of immune response are: recognition, response, memory & recognition
• • The principles of immune response are applied by: recognition, allows cells to identify between 'self' & 'non-self', as well as 'danger' & 'non-danger'; response, rapid, pathogen-appropriate, immunological actions initiated as soon as pathogen exposure occurs; immunological memory, cells have memory of pathogen encountered for faster response to infection if encountered again; & regulation, for immune responses to come & go to prevent chronical inflammation from overactive immune responses targeted at 'own' cells.
• • Immune system is able to discriminate between 'self' & 'non-self' by different microorganisms (i.e. virus, bacteria, protozoans) expressing unique molecules (i.e. proteins, lipids, carbohydrates), because these components are not found in the human body, so can discriminate from self-components. These components also allows distinction between different microorganisms.
• • The differences between innate & adaptive immune system, in terms of microbial recognition, is that innate immune systems recognise pathogen associated molecular patterns (PAMP's), unique microbial molecules shared within taxonomic groups, using pattern recognition receptors (PRR) found on innate immune system cells.
  • While adaptive immune system recognises specific antigens, unique microbial molecules specific to a particular organism, using specific antigen receptors (antibodies) on lymphocytes (adaptive immune system cells).
• • The primary lymphoid tissues are bone marrow and thymus. Their roles are to generate immune cells.
• • The secondary lymphoid tissues are: lymph node; lymphatic vessels; adenoids; Peyer's patches; skin; spleen; & tonsils. Their roles are to store mature lymphocytes.
• • The characteristic features of innate immunity are: pathogen specificity, by recognising (via PRR) PAMP's shared by microbes or damaged host cells; limited immunological diversity by being germline encoded; no immunological memory; & rapid immunological response with constant magnitude.
• • The components of innate immunity are: cellular & chemical barriers (i.e. skin, mucosa, antimicrobial molecules); proteins in blood, complement proteins for complement cascade; innate immune cells (i.e. macrophages, neutrophils, dendritic cells, natural killer cells).
• • The characteristics of adaptive immunity are: pathogen specificity, recognises microbial & non-microbial antigens; large immunological diversity by having somatic recombination of gene segments; immunological memory; & slower immunological response with increasing magnitude from multiple exposures.
• • The components of adaptive immunity are: cellular & chemical barriers (i.e. lymphocytes in epithelia, antibodies secreted at epithelial surfaces); proteins in blood, antibodies that can bind to & prevent pathogen attachment to host cells; adaptive immune cells (i.e. B lymphocytes, T lymphocytes).
• • The structure of antibody molecules is made up of two heterodimer bonded through disulfide bonds, where each heterodimer consists of a heavy chain & a light chain. Antibodies have two distinct regions: variable region (Fab), which takes up one of an infinite number of forms as binding site with one H domain & one L domain; & constant region (Fc), which takes up one of five isotypes with longer H chain domain.
• • The structure of antibody relates to the function of antibodies by Fab region of heavy chain & light chain associating with a specific shape to form specific antigen-binding sites that only recognise one type of antigen, so variable regions of B cell surface antibody receptors don't change. Because antigen recognition is the function of Fab regions, this causes B cells to eventually only expresses one type of antibody surface receptor & secrete that one antibody type to bind to toxins/pathogen themselves to prevent attachment to cells for neutralisation
• • The antibody isotypes are: IgM, found on membranes of naïve B cells & secreted into plasma as pentamer; IgA, found in high concentrations in mucosal secretion often as dimer; IgD, not secreted so only found on B cell surface; IgG, found in high concentrations in plasma & tissue fluids; & IgE, found in low levels in plasma, tissue fluids & bound to mast cells.
  • Isotypes are determined by changes in heavy chains in Fc regions of antibody.
• • By Fab region: secreted IgA prevents pathogen binding at mucosal surfaces for neutralisation; secreted IgG & IgM neutralises toxins secreted by bacteria.
  • By Fc region: secreted IgG & IgM trigger classical pathway; secreted IgG bind to Fc receptors on phagocytes, for opsonisation, to trigger phagocytosis; secreted IgG provides protection for transplacental immunity; secreted IgE triggers mast cell degranulation for inflammation response that activates eosinophils, which recognises & kills pathogen; & secreted IgG, binds to FcR of macrophages & NK cells to induce cytotoxin product release.
• • B cells are activated by specific antigens, via antigen epitope (i.e. natural conformational shape), binding to multiple identical copies of B cell surface antibody (i.e. IgM). This ligation can trigger B cell's antigen presentation, allowing external T cell signals to help determine B cell isotype for activation, through irreversible DNA recombination. This effector B cell/plasma cell can then undergo clonal expansion (i.e. proliferation) with clonal selection (i.e. same antibody) to secrete that specific isotypic antibody, via binding site remaining the same but Fc regions changing.
• • The elements of immunoglobin gene locus for heavy chains are: V, D & J elements, which give binding sites for Fab regions under somatic recombination; & C elements, five different elements (i.e. mu, delta, alpha, gamma & epsilon) that gives constant region of antibody when recombined with VDJ element.
  • The elements of immunoglobin gene locus for light chains are: V & J elements, which give binding sites for Fab regions under somatic recombination; & C elements, one element for constant region of antibody when recombined with VJ elements.
• • Immunoglobin gene locus achieve their functions by random recombination of the three segments (i.e. V, D & J) in heavy chains first, then of the two segments (i.e. V & J) in light chains forming specific antibody variable regions for binding specific antigens. This occurs during antigen independent B cell development from pluripotent stem cells in bone marrow, as rearrangement is accompanied by rapid division, many cell deaths & enzymes (i.e. recombinase activating genes (RAG's), terminal deoxynucleotide transferase (TdT) & exonuclease).
• • The principles of gene arrangement in Ig genes involve: random recombination in DNA, with V&J recombine in L chain, & D&J recombine + V&DJ recombine in H chain; Fc region gene element recombine with Fab region; introns between gene segments are spliced out of mature mRNA; final antibody peptide with recombined VJ elements (L chain), VDJ elements (H chain) form Fab region & constant elements form Fc regions.
• • In DNA stage, gene rearrangements occur by first recombining VDJ elements in Fab domain of H, where B cells then check if functional heavy chain is produced. Then recombining VJ elements in Fab domain of L, where B cells check if functional antibody molecule is produced. If these have passed, B cells tests if newly generated B cell receptor can bind to antigens.
• • Diversity in antigen binding sites of antibodies are generated by: each chain having multiple segments (i.e. V for variable, D for diversity & J for joining); two light chain alleles (i.e. kappa & lambda), to choose recombination from; & having multiple VDJ & VJ genes.
• • Isotype switching involve gene arrangement by occurring after the stimulation of B cells by specific antigens (i.e. helper T cells), as VDJ elements are always recombined first with C_mu elements for IgM molecules in naïve B cells. VDJ elements then recombine with a new C element type, which is accompanied by DNA deletion of other C elements from Ig locus, for irreversible DNA recombination. This allows new antibody isotype to be transcribed & translated, but VDJ gene is the same.
• • Gene rearrangement of Ig genes impact B lymphocyte population by immature B cells potentially displaying auto-reactive antibodies that result in cell apoptosis, which decreases B lymphocyte population. This is because most B cells that bind to self-molecules are deleted through apoptosis before leaving the bone marrow. As when these cells become mature, it migrates to circulation & expresses/binds to IgM of single specificity, for no antigen recognition.
• • B cells no longer undergo any DNA recombination after it leaves the lymph node because Rag genes are turned off when B cells go in circulation. So antigen binding sites are not changed, even if binding is self-binding.
• • Diversity in antigen binding sites of T cell receptors (TCR), that are always membrane bound, are generated by recombination in: alpha chain, random VJ element recombination, of Fab domain for specific binding site, with one C element, of Fc domain; & beta chain, random VDJ element recombination, of Fab domain for specific binding site, also with one C element. This creates specific binding sites for specific antigens per T cell.
• • T lymphocytes recognise antigen by antigen peptides being loaded into MHC (major histocompatibility complexes) molecules, on antigen presenting cell (APC) membranes, to present it to T cell receptors. As antigens are first degraded into peptides in APC, before binding onto MHC molecules, where bound-complex is then transported, via vesicles, to APC membrane for presentation.
• • The similarities between antigen recognition by B & T lymphocytes are that both must be activated before performing effector functions. Cells of both also display multiple copies of single clonally distinct receptor (i.e. antibody for B cells, TCR for T cells), which regonises one specific antigen on membrane only.
• • The differences between antigen recognition by B & T lymphocytes are that B cells are activated by free antigens that drain through lymphatics to lymph nodes, where antibody receptors directly recognise/bind to natural conformational shape of antigens. While T cells are activated by APC internalising antigen in tissues before migrating to lymph nodes via lymphatics, where MHC on cell surface presents the antigen peptide for TCR to recognise & bind for activation.
• • The interaction between MHC molecules & TCR occurs by MHC with bound pathogen peptide acting as a signal for TCR, so TCR can recognise & bind the peptide to initiate reactions.
  • Class I MHC is expressed on cell surface of all nucleating cell, including infected cells & T cells themselves. While Class II MHC is expressed on cell surface of antigen presenting cells (APC), of macrophages, dendritic cells & B cells.
• • The role of MHC molecules in antigen presentation is to bind to internalised, antigen peptides by embedding these peptides in MHC cleft, which holds peptides in place using anchor residues.
  • This occurs by antigen processing, which is the intracellular proteolytic generation of degraded antigen. This involves: endosomal processing (i.e. for presentation to MHC Class II ) that bind to longer chains to signal what's happening in external environment; & cytosolic processing (i.e. for presentation to MHC Class I) that bind to shorter chains to signal to outside what's happening on the inside.
• • MHC expression patterns occur by individuals with different MHC alleles binding to a restricted range of diverse peptides. This is due to MHC alleles in humans involving polymorphisms & are inherited by gene arrangements.
• • MHC-I antigen processing occurs by antigens being taken up by APC, as cytosolic protein, before being degraded by proteasome as peptides that are transported to ER. Peptides then bind to/loaded onto MHC in ER.
• • MHC-II antigen processing occurs by antigens being endocytosed into the APC, forming an endosome with enzymes (i.e. lysosomal hydrolase) that degrade antigen into peptides, before fusing with trans-Golgi to allow peptide binding/loading onto MHC, that was synthesised in ER before being transported to trans-Golgi.
• • MHC-II presentation occurs by loaded MHC being transported to plasma membrane via vesicle from trans-Golgi. MHC then binds to TCR with co-receptor CD4+ proteins, that recognise MHC-II complex. This allows activation of CD4+ helper T cells from naïve T cells, that help B cell antibody production, help macrophage activation, help immune response regulation & aids cytotoxic T cells.
• • MHC-I presentation occurs by a vesicle, containing loaded MHC, budding off ER & transported to cell surface, where MHC associates with TCR & co-receptor CD8+ proteins, which helps recognise MHC-I complex. This allows activation of cytotoxic CD8 T cells from naïve T cells, that bind to/kill infected & neoplastic cells.
• • The three signals for activating T lymphocytes are: antigen presentation via MHC complex, which activates effector T cells; co-stimulation, where CD80/86 cell surface proteins from APC associate with CD28 cell surface proteins from T cells for T cell survival (i.e. apoptosis otherwise); & cytokine secretion, where cytokines are released from APC for effector T cell differentiation.
• • The role of dendritic cells in antigen presentation to T lymphocytes is to take up antigens from site of infection in tissues, internalise it as peptides, migrate to lymph nodes & present the peptides to activate effector T cells. This occurs by immature DC's highly phagocytic internal taking up antigens, via PAMP binding to its PRR, for its own activation allowing increased antigen processing & surface expression of MHC I & II.
  • It also activates effector B cells, since soluble antigen would still be draining from tissues to lymph node for B cell to bind & activate through secretion.
• • Dendritic cells are considered the best APC for naïve T cells because it is quiescent in normal tissues with low MHC, no/low CD80, no/low CD86 & low levels of adhesion molecules. But it has high pinocytosis rate, as DC is constantly sampled from the environment, so increases antigen processing & MHC I/II surface expression.
• • The role of APC in T cell activation is to present antigen peptides to TCR, via MHC molecules, to bind/activate T cells. Binding results in upregulation of adhesion molecules (i.e. CD28 for T cells, CD80/86 for APC) for co-stimulation of T cell survival. Upregulation results in selected cytokines being secreted to differentiate activated T cells, for acquiring effector functions.
• • The cytokine (signal 3) determines the outcome of adaptive immune response by different levels of polarising cytokine released being dependent on the type of PAMP that's recognised by PRR of APC. Where high levels of polarising cytokines would skew the subset the naïve T cells would become when matured, since these signal T cells to adopt a form of effector T cells that would secrete/produce different cytokines for immune response. This ensures that responses are appropriate for the pathogen encountered, since different PRR recognise different PAMP on different microbials.
• • The cytokines involved in inducing some T helper cell responses are: Th1, induced by IL-12; Th2, induced by IL-4; & Th17 induced by IL-6.