Immunogenomics

B-Cells (produced by the bone marrow in humans, but discovered in the bursa of birds)

• • B-Cells recognize non-body stuff - which is called antigen - by either binding to a part of the the antigen called epitope with receptors on their cell membrane or by secreting these receptors in the form of antibodies into the blood (or mucus) where the antibodies can bind themselves.
  • B-Cell Proteins
    • An Antibody comes in five different flavors (in placental mammals) IgA, IgD, IgE, IgG, IgM. They all share the same basic structure, but differ in their additions. Somehow we assume that IgG is the most important, because it is the most common type and we don't know that much about the other types anyways.
    • IgG is one of those antibody types that looks like a Y. The *ends* of the arms of the Y recognize the antigen, the *ends* not the middle part.
    • The two arms of the Y of all antibodies - and so IgG - are composed of two identical Heavy and two identical Light Chains
    • The two ends of the Y, the part that recognizes the antigen are together called Fab. One Fab comprises a bit of the heavy chain and a bit of the light chain. Not everything touches the antigen, so the most important region in the Fab fragment is called Fv (variable).
    • The Fv can be split into its three main parts, the [complementary determining regions], called CDR1, CDR2 and CDR3. Remember that there is a light and a heavy chain in one Fv, so there are six complementary determining regions in total.
    • For a long time, no one knew how the body produces the right Fa fragments that bind to "non-self" but not to "self". A popular theory was that proteins "fold" themselves into the right shape, around some part of antigen (epitope). This turned out to be wrong.

B-cell genomes

• • Apart from transposable elements, virus insertions and random mutations, most cells have the same genome
  • During embryonic development, B-cells are one of the two cell types that can recombine parts of their genome, in what is called somatic recombination. The loci that recombine are called IGH@ (heavy chains), IGK@ and IGL@ (light chains) (how the heck do you pronounce the @ here?). They are located on chromosomes 14, 2 and 22. (NB: do not confuse IGH, the locus, with the antibody types IgA, IgE, IgM, IgD and IgG).
  • On these loci many (somewhere between 6-40) little genes are located next to each other. From left to right, they are separated into a stretch of V genes, then D genes, then J genes, though light chain loci do not have D genes, so we usually write it as V(D)J. On the genome browser, these loci don't look great, because all VDJ genes are all very similar, so the RefSeq sequences match everywhere and are filtered out.
  • All Vs, Ds and Js are separated by recombination signal sequences. The recombinase is activated for a short time during embryonic B-cell development (the mammals probably got that enzyme that from a transposase) and first recombines a D to J and then a V to this DJ combination.
  • While this is going on, a terminaldeoxyneucleotidetransferase adds and deletes some nucleotides between the different segments to add a little bit of noise between them.

Basic Immunology

• • As a result, each B-cell has its own unique combination of VDJ genes in all of their loci
  • This V(D)J-combination is transcribed to produce a heavy or light chain immunoglobulin protein and assembled into receptors
  • At around 2 months of embryonic development, all B-cells that bind something in the body kill themselves. At our age, only B-cells circulate in our blood that bind to stuff that is *not* part of the body. All others have been eliminated already.
  • In any of these B-cells, when the receptors built from the VDJ combinations bind to some antigen, this particular B-cell will start to divide and many of the daughter cells will produce antibodies from this VDJ combination. In addition, the daughter cells will hypermutate their VDJ segments and those that bind better will turn out to produce even more daughter cells and more antibodies. Macrophages will then kill the cells that are marked with antibodies.
• Immunogenomics
  • To amplify the VDJ fragment with PCR, primers are designed for each V and each J gene in the genome
  • Blood is extracted and PCR is run on the mixed cells
  • The resulting DNA is sequenced and the identity of each V, D, J determined by blasting against a database of VDJ genes
  • The number of each VDJ combination can be determined as a result
  • The big dream is to help identify the origin of allergies (which antibody? what does it bind to?) with this, to detect diseases before they produce symptoms (e.g. by finding antibodies in them) or to find antibodies against tumors. No one has achieved this yet.

• • Q: Somehow we think that the heavy chains are more important than the light chains, and CDR3 more important than CDR1 and CDR2

• • The heavy chains are encoded by one of the few loci that can recombine somatically, the IGH-locus