Antibodies, Lymphocytes, and the Generation of Diversity

• The adaptive immune system isn't as fast as the innate immune system, but it is more specific to individual antigens and it has memory.
• The adaptive immune system operates based on lymphocytes, of which there are two types: T-lymphocytes and B-lymphocytes (or T-cells and B-cells).
• The specific receptor for antigens on a T-cell is the T-cell receptor.

  The T-cell receptor is comprised of an alpha-chain and a beta-chain. This makes the T-cell receptor a heterodimer because it is made up off 2 different polypeptide chains.

  The alpha and beta chains of the T-cell receptor contribute to the formation of the specific antigen binding site. Each T-cell will have it's own unique T-cell receptor, and hence, each T-cell will bind to its own specific antigen.
• The receptor for antigens on a B-cell is a B-cell receptor, also known as an antibody.

  An antibody is comprised of 2 identical heavy chains and 2 identical light chains joined together by disulphide bridges. The heavy and light chain pairs from the antigen binding sites, and a single antibody has 2 antigen binding sites.
• Adaptive immunity depends on the diversity of lymphocyte receptors that can match the diversity of antigen shapes that the body might encounter.

  Circulation of lymphocytes with diverse receptors through blood and lymphoid tissues increases the probability that they will encounter their corresponding antigens.
• Specific T cells will recognise specific antigens due to the specificity of the T-cell receptor. Once the antigen has bound to the T-cell receptor, the T-cell is stimulated to divide by mitosis so that there will be more of the necessary T-cell receptor to bind to the antigen.

  These clonal cells are memory cells. They're quiescent (inactive), but they are in abundance, so the T-cell receptor concentration has increased. Hence, when the same antigen is present in the body again, it is dealt with more quickly.
• Memory works the same way with both T-cells and B-cells. Clonal cells mean there is a higher frequency of the specific cells needed to deal with the pathogen. If the same pathogen/antigen is present in the body again, these memory cells will induce a more rapid response.

  Memory is a unique feature of the adaptive immune system.
• The adaptive immune system is slower than the innate immune system.

  The innate immune system work within a number of hours. The adaptive immune system can take 12 days for the primary immune response occur, and the secondary immune response can take 5-7 days.
• Both T-cell receptors and antibodies can be split into two distinct regions: the variable region at the top, and the constant region at the bottom. The uniqueness of the receptor is typically determined by the variable region.
• In order for the adaptive immune response to be effective, the diversity of the receptors need to match or exceed the diversity of the microbes. However, microbe diversity exceeds millions, and they can mutate and adapt. The total number of human genes in the genome is approximately 25000.

  Hence, if the receptors were only dependent on the DNA within the genome, there wouldn't be enough variability in the receptor to match the diversity of the antigens. Therefore, to increase the receptor diversity to match that of the pathogens, a process called gene rearrangement is used.
• The variable region of the heavy chain is composed of 3 parts: a variable part, diversity part, and joining part (this sequence is abbreviated to VDJ).
• The base sequence that codes for the antibody heavy chain is located in chromosome 14 on every cell in the body. The genes coding for the variable region are arranged into groups of segments. The are different alternatives for the V, D, and J segments that complete the antibody heavy chain variable region.

  There are 48 different segments for V, 27 different segments for D, and 6 different segments for J. Combining these, this gives a total of 7776 different VDJ combinations for the heavy chain variable region.
• The antibody light chain variable region is comprised on only a variable and a joining segment. In total, there are 340 different combinations of V and J segments to make up the light chain variable regions.
• Combining the combinations of the VDJ segments in the heavy chain and the VJ segments in the light chain, this gives a total of 2,643,840 variants of the receptors.

  This combination of the heavy and light chain gene rearrangement is known as combinatorial diversity.
• In addition to combinatorial diversity, further diversity is created by the mechanism that joins the VDJ and VJ segments together. The joining of segments is not precise; nucleotides can be added or removed from junctions during rearrangement. This adds further diversity termed junctional diversity.
• Gene rearrangement creates the unique specificity of B and T cell receptors. B cell development with gene rearrangement happens in the bone marrow.. T cell development with gene rearrangement happens in the thymus.
• The mechanism for generating the receptor is the same for both T-cells and B-cells. However, the binding/ligating of the T-cell receptors and the B-cell receptors have different consequences.
• There are 2 groups of T-cells: cytotoxic T cells and helper T cells.
• When cytotoxic T cells are activated via their T-cell receptor, they differentiate to produce cytotoxic granules.

  When helper T cells are activated via their T-cell receptors, they differentiate into many different types of T-cells that each produce their own set of cytokines.

  None of these pathways involve the T-cell receptor after recognition of the pathogen. All the T-cell receptor does is recognise its corresponding antigen.
• Activation of a B cell via its antibodies can turn it into either a memory cell, or a plasma cell.

  Plasma B cells produce and secrete antibodies that have the same specificity as expressed by the B cell that used it as its B-cell receptor. Therefore, a B-cell receptor is involved after it recognises the pathogenic antigen, and ultimately becomes the effector molecule.
• Antibodies are immunoglobulins. They're made up of 2 identical light chains and 2 identical heavy chains. The light chains can be Kappa or Lambda, and each are encoded by different loci on different chromosomes. B cells only express one of them.

  The variable region of the light chains is the area encoded by the V and J segments by gene rearrangement.
• The variable region gives the antibody its specificity. The constant region gives the antibody its function. It's the constant region that determines whether the antibody is IgM, IgG, IgA, IgE, or IgD.
• IgM, IgG, IgA, IgD, and IgE are referred to as classes or isotypes determined by the constant regions of their heavy chains.

  The IgG subclasses are IgG1, IgG2, IgG3, and IgG4.

  The IgA subclasses are IgA1, and IgA2.

  The subclasses are coded by different constant region gene segments.
• The Fc is a term describing paired constant region segments. Some cells such as macrophages have Fc receptors and these are the receptors for the Fc regions of antibodies.
• Antibodies bind to antigens through the tips of the variable regions. The interaction between antibody and antigen is a direct physical interaction between the antigen shape that the B-cells are able to bind to.

  Antigen-antibody binding can be by shape, electrostatic interaction/attraction, and hydrostatic interaction.
• General functions of antibodies:

  • Neutralises toxins and viruses by binding to them and blocking their interaction with other cells.
  • Opsonise pathogens (make them more suspectable to phagocytosis) by binding to them to promote phagocytosis and killing by other cells via Fc receptor recognition.
  • Activate the complement cascade.
  • Agglutinates particles.
• IgG is the main antibody found in serum. Measurement of antibody titre in serum in response to vaccine is generally a measurement of specific IgG antibodies.
• IgG antibodies are good at opsonisation, as they coat pathogens so phagocytic cells can recognise them, as many phagocytes have Fc receptors for IgG.

  Pathogens coated in IgG antibodies also become targets for Natural Killer cells. This is known as antibody-dependent cellular cytotoxicity. This also depends on Fc receptors.

  There are 4 main subclasses of IgG antibodies: IgG1, IgG2, IgG3, and IgG4. IgG1 is the most abundant in serum, and IgG4 is the least abundant in serum.
• IgA antibodies can be found in the serum as monomers. Dimeric IgA antibodies (two IgA molecules joined together by a J-molecule) is associated with mucosal surfaces.
• In the example of the gut, bacteria are present in the intestinal lumen and plasma cells are present on the other side of the epithelial surface. These plasma cells release dimeric IgA. The IgA combine with receptors located on the basal lateral surface of the epithelial cells known as secretory components. The dimeric IgA can then be transported through the epithelium into the gut lumen. In this microenvironment, IgA combine and agglutinate the intestinal bacteria and regulate their population.
• Dimeric IgA regulate gut bacteria population in 2 ways:

  1. Dimeric IgA has 4 antigen binding sites, so it can agglutinate and neutralise bacteria efficiently.
  2. The secretory component of the secreted IgA can bind very well to mucus. In this way, they can retain antigens on the mucosal surface and prevent them from doing more damage.
• IgM is the first antibody made in the immune responses, and it's pentameric, meaning it's made up of 5 individual IgM molecules joined together. Each IgM molecule is composed of 2 identical heavy chains and 2 identical light chains arranged in a y-shape.
• Pentameric IgM has 10 antigen binding sites, giving it a high avidity (high ability for the whole of the molecule to bind to antigens). Agglutination can result in extensive lattices of pathogens. Pentameric IgM is also a very good fixer of complement.
• IgE is associated with allergic responses. Mast cells have Fc receptors for IgE on their surface, and this binding happens in the presence of an allergen.

  An allergen can cross-link IgE on the surface of the mast cell and this results in muscle degranulation. Granules are released by the mast cell that gives the symptoms of allergy.

  Individuals with allergies tend to have a higher concentration of IgE antibodies in serum.
• IgD isn't really considered a secreted antibody, as there is very little IgD in serum. However, IgD can be found on the surface of B-cells as part of the B-cell receptor. On newly formed B cells, the B-cell receptor can be IgM and IgD expressed together.
• The specificity of B cells can be improved by a process called affinity maturation. Affinity maturation only occurs with B cells.
• Lymphocytes constantly circulate through blood and lymphoid tissues. Secondary lymphoid tissues contain zones of dividing B cells called germinal centres.

  Germinal centres are areas that contain highly proliferative B cells that have been activated by antigens with the help of T-cells. These centres can vary in size.
• If B cells encounter specific antigens and they have help from T cells, they can enter germinal centres of dividing B cells. B cells in the germinal centre start to divide rapidly, and as they do so, they start to mutate their immunoglobulin variable region genes by somatic hypermutation. This produces a lot of variants, and the high affinity variants are selected in the germinal centre to be cloned.

  This concept of somatic hypermutation followed by selection is known as affinity maturation.
• In addition to somatic hypermutation, antibodies can switch from the use of one constant region to another in the germinal centre. All B cells start with the IgM at their surface, and IgM is the first antibody made in the primary immune response. However, to achieve the range of functions required, the constant region can swap in the germinal centre so that B-cells can keep the same variable region, but is now associated with the constant region of, for example, IgG or IgA.
• The germinal centre is where B-cells do to rapidly divide. B cells can differentiate into 2 types of cells, and these are the types of cells that also leave the germinal centre: memory cells and plasma cells.