The Epic Tale of the Man who Stepped on Glass

This post took awhile to write and is hopefully accurate. After sifting through lecture notes, my textbook, and internet articles, "The Epic Tale of the Man who Stepped on Glass" compiles the entire immune response as required for understanding of someone enrolled in a first-ever physiology class. While reading, I found that often lists of cells would be provided and then lists of processes. This "tale" takes on both concurrently! Please do note that the focus is on bacterial infection, and not viral infection. However, there is a note at the end, which explains a bit about viral infection as well. 

Once upon a time, there was a man. He may have been a good man or a bad man, I'm not entirely sure, however, the qualifier in this case is irrevelant. On one fateful day the man accidentally (or consciously, but it is highly unlikely this was the case) stepped on a piece of broken glass. The glass had shattered onto the ground, and as he was barefoot, and one of the fragments pierced his skin. http://www.youtube.com/watch?v=Rw0eIG_9tLY

Apart from the man's howl of anguish as the blood dripped down the arch of his foot, other courses of action were taking place in the man's body. Yes, his foot was throbbing and swollen, but at the cellular level, things were at work. The glass had broken through the first line of defence, the coverings of the body. The skin and the mucous membranes usually provide an unpleasant environment for the living conditions of microorganisms, but the glass had successfully penetrated the skin. Little did the man know that the glass had been infected by a bacteria, so the next line of defence had to be called into action.

The fixed tissue macrophage, present at the site of the infection, is the first cell to be involved in the innate immune response. They have toll-like receptors (TLRs), which are attracted by the PAMPs produced by the bacteria. PAMPs, pathogen-associated molecular patterns, are lipopolysaccrides or peptidylglycan molecules present on the surface of bacteria, which are absent in mammals, and are therefore considered foreign. The fixed tissue macrophage will take up some bacteria by phagocytosis, and emit a signal called the MDNCF, the monocyte derived neutrophil cytotaxtic factor, which recruits neutrophils to the site of the infection.

The neutrophils reside in the blood, and travel to the capillaries, but in order to pass through the capillary wall, some modifications are necessary. The neutrophil has to change its receptors and the endophilial cells of the capillaries need to change their receptors. After this, the neutrophil can then adhere to the endophilial cell surface, where it rolls along the capillary cells until it gets to a point where it can squish in between cells called diapedesis. From there the neutrophil travels to the infectious site.

When the neutrophil encounters a bug, it takes it in by phagocytosis. The microbe contacts the membrane of the neutrophil, which envaginates to form a pocket, which then pinches off separately from the membrane to form a phagosome. This is analogous to the foreign particles of food entering your body in a separate pouch known as the stomach, so that digestion does not interfere with the internal processes of the body, or in the case of the neutrophil, so digestion does not interfere with the processes of the cell. A lysosome, filled with digestive enzymes fuses with the phagosome to make (you guessed it!) a phagolysosome, which breaks up the macromolecules into fragments, and oxidative death also occurs. The neutrophil dies in the process of killing bacteria, and then new neutrophils come along and ingest bugs and also die. In the process of dying, the neutrophil extrudes DNA, chromatin and protases, which form a neutrophil extracellular trap or NET. This keeps the bacteria from spreading and contains the bacteria. The dead neutrophil and bugs under skin make pus.

PAMPs can activate complement, which can in turn lead to the killing of pathogens in what is referred to as the alternative pathway. This can be done by a Natural Killer cell, which is also important in the innate immune response. They have a default response of "kill" when they encounter a cell. This function is so strong, they will even act against the body's best interests, and create an auto-immune response against "self." If the ligand of the Natural Killer cell is activated, unless it is turned off by the MHC class I molecule which is present on all nucleated cells, it will kill that cell, which is a problem of auto-immune disease. In many cancerous cells, the MHC class I molecule is faulty, as well as viruses can change the MHC class I molecule. Normally, it is turned off.

The next cell in after the neutrophil is the dendritic cell, which has two functions: phagocytosis and synthesis. It travels with the bacteria on its dendrites to the nearest lymph node, which in the case of the site of infection of the man's foot, happens to be in the groin. The dendritic cell links the innate immune response to the adaptive immune response, the third line of defence. The adaptive immune response is acquired and specific will the humoural aspect of the immunoglobulin mediators. It is also cell-mediated by T cells or lymphocyte effectors.

The adaptive immune response is specific to the antigen and epitope (one site of the antigen where the antibody attaches itself). The antigen presenting cells (APCs) link the antigen by means of a MHC (major histocompatibility complex) class molecule and a peptide. They may be dendritic cells, a macrophages or a B lymphocytes. The MHC molecule is unique to a specific person. There are two kinds of MHC molecules, class I and class II. Recall that class I is present on all cells in the body to turn off the Natural Killer cells. However, class II is only present on three molecules: the dendritic cells, the macrophages, and the B lymphocyte, because it is the antigen presenting molecule. After the antigen is broken down into peptides, it is presented on the dendritic cell, on the MHC class II molecule. The mjaor histocompatibility complex is called the HLA system, for Human Leukocyte Antigens, because that is where it was first seen.

Another way of phagocytosis is done by the dendritic cell. The dendritic cell goes through the same procedures as the neutrophil, except in the phagolysosome, there is the synthesis of the MHC class II molecule with an antigen fragment. The complex then comes to the surface of the cell. This holds any antigenic peptide, without specificity.

Now, before we move into the next steps of the adaptive immune response, it is necessary to take a trip back into the man's past, or more particularly, the past of his T- and B-cells. The T-cells and B-cells are made first in the yolk sac of the fetus, then in the liver and spleen after the first trimester, and finally in the bone marrow after birth. Some of these cells travel to the thymus to become T-cells. In the environment in the thymus and bone marrow, the cells mature, differentiate, and gain specificity for many possibilities of antigens.

Out of all the T-cells which mature in the thymus, only 5% leave the thymus to the blood, where as the rest of the 95% of the cells die. The vast majority of the cells produced in the thymus are anti-self, and must be eliminated to prevent a future auto-immune response. The 5% survivors have specific reactivity to only one peptide.

In the lymph nodes, the B-cells live in the portal part of the lymph node, and the T-cells are located in the madorary part of the molecule. When the dendritic cell leaves the site of infection, it travels to the site in between the B-cells and T-cells. Since the T-cell has a specific receptor that was specified in thymus pre-birth, it will see only one peptide material, one amino acid. This is the MHC peptide, which is recognized by the T-cell receptor, and thus has specificity. The CD4 molecule is involved in binding T-cells to the MHC II region of the MHC-peptide complex on the APC (antigen presenting cell).  As a double-checking mechanism, the T cell synthesizes CD28, which is a co-receptor. If CD28 binds to the B7 molecule on the dendritic cell, the antibody will be produced. However, if the co-receptor is not bound, then no antibodies are made, and the organism becomes tolerant to the protein. Note that the CD28 - B7 binding is not specific.

Also, on the surface of the T-cell is a receptor called CD40L (the L stands for ligand), which is associated with an enzyme that is a ligase called CD40. The B-cell binds to the CD40L, and then the T cell produces at least three interlycukins called IL 4, 5,  and 6, which cause proliferation, further maturation, and induction of the antibody. Next occurs a puzzling step where the B-cell's surface immunoglobin with antibody specificity binds to the bug on the dendrite. This is odd as the B-cell sees the whole bug, but the T-cell sees only a specific protein, yet together they make one antibody. Does this happen at the same time or in sequence? This is a mystery.

Now, both the T-cell and the B-cell have identified the bug as an immunogen, so what happens next? First, it is necessary to consider the structure of the immunogobulin antibody molecule. The molecular was initially found through electrophoresis, where the albumin molecule (a protein in blood), was seen to be homologous, but the other gobulin molecules where found to be heterogenous. The antibody activity is mostly found in the gobulin molecules, with the majority of the activity in gamma globulin and some in other classes. The immunogolbulin molecule has a tetrapeptide structure with four chains, two which are identical and heavy, and two which are identical and light. The light chains give the immunogolbulin its type, whether it is lambda, or kappa. The heavy chains determine the class of molecule: delta, my, gamma, alpha, or epsilon. Interchain and intrachain disulphide bonds are present between and within all chains.

The Fab of the immunogobulin is the antigen binding fragment, which is found at the hypervariable region, and it is divalent, so two antigens can bind. The Fc region is a crystallizable fragment which determines the biological activity of the Ig class. For example, the IgM exibits complement binding (explanation of complement forthcoming!) and is a pentameric molecule. The IgM is the first immunogobulin to respond, but it is inefficent and undergoes class switching. The IgG is present for placental transfer until the fetus can make its own immunoglobulins, is also involved with complement binding and is a dimeric molecule. Also, the IgA is involved with secretory properties including the MALT, and ensures that foreign substances that are encountered from the nasal cavity to the lungs, the digestive tract, do not cause the body to freak out. The IgE deals with mastocytophilic properties, or allergies.

After all of that information about immunoglobulins, it is important to recognize that they are often released by plasma cells, which does not sythesize immunoglobulin (antibody), but just secrete the immunoglobulins (antibodies) made during the earlier part of its B-cell life. The pro-B cell does not have surface immunoglobulin, but the pre-B cell does have this surface immunogobulin that is produced in the bone marrow, and is specific and waiting for the particular antigen to arrive in the cell. The plasma cell loses the surface immunogobulin and secretes antibody from the cell itself.

Four genes determine the structure of the heavy chain message, and each gene has multiple alleles. This is an interesting concept where randomness can actually lead to specificity. There are three regions to choose alleles from on the heavy chain: the variable region, the diversity region, and the constant region, plus an alpha, delta, mu, gamma, epsilon, determining the class. The arrangement of the immunogobulin is carried out by enzymes called the rearrangement activation genes or RAG, and the process happens in the thymus or bone marrow. This allows for hundreds of millions of different specificities, many of which may remain dormant and never be used, and others (95% of all T-cells) which may have a tendency for auto-immune response and be anti-self, so thus are knocked off by the thymus.

So, the helper T-cell has recognized the peptide linkage and the B-cell has recognized the bug, now what? Antibodies are released and then the Fab binds to the antigen, and can start the classical complement pathway (if bound to an IgM or IgG). This is a release of many protein C factors, in a complement cascade. If the factors proceed all the way to factor C9, a hole in the bacterial membrane forms, and the bug explodes. However, if the factors proceed only to C3 and C5, a so-called alternative pathway occurs, which turns on the Innate Immune Reponse, and enhances phagocytosis. Neutrophils are called in to phagocytose the bug, and then the neutrophils die releasing the net. Macrophages then arrive to clean up the pus.

In conclusion, after the immune response has finished, memory cells (either B-cells or T-cells involved in the response) are stored in the apical light zone of the lymph node. The rest of the B-cells commit suicide, called apoptosis.

Note that in the response described above, the T-cell involved was a TH2 cell, or a T Helper 2 cell. Had this not been a bacteria infection, but that of a virus, the TH1 cell would have interacted with a dendritic cell that had taken up a pathogen by means of an MHC II bound to an epitope and a TCR (T-cell receptor) of CD4+. They also have co-receptors of CD28 which binds to B7 on the dendritic cell, as a double-checking mechanism. This is exactly like the TH2 cell. But here is where the process differs: the TH1 cell releases IL-2, TNF, and INF which stimulate the Cytotoxic T-cell. The Cytotoxic T-cell's TCR which is specific for the antigen binds to the virus by recognizing an MHC class I molecule linked to the virus. This only occurs, however, if the MHC class I molecule is linked to CD8. Hence, cT cells are often described as being CD8 positive.