Immunogenetics

Introduction
How can the body identify and eliminate foreign invaders. especially since microorganisms are constantly evolving ways to avoid detection? The trick is to be able to distinguish between self and non-self: to recognize molecules in the body that dont belong there. Foreign molecules (often on the surface of foreign organisms) raise an immune response in the body. The primary defense is a set of antibody molecules (also called immunoglobulins, Ig). The human body produces over 1,000,000 different antibodies for this purpose. Antibody molecules bind to antigens, which are molecules that are non-self. Each antibody is specific for a particular antigen. Some antibodies are present in the blood and other body spaces as soluble molecules. The antibodies cause antigens to clump up and form precipitates that scavenger cells pick up and digest. Some soluble antibodies mark foreign cells for attack by the complement system, a series of proteins that punches holes in the cell membranes. Other antibodies are on the surface of immune system cells (lymphocytes), which are stimulated to engulf and digest foreign cells by phagocytosis.

Complement
The complement system is a way of rupturing the membrane of invading cells. Antigens on the surface of the invader bind to soluble antibodies. Then a series of other proteins (already circulating in the blood) is activated: the complement cascade. These proteins bind to the complex in a specific sequence, creating a large hole, which usually kills the cell.

The Immune System

The lymphocytes, or white blood cells, mostly travel through the body in the lymph vessels, a separate circulatory system that is connected to the blood system. The cells collect in lymph nodes, where large numbers of lymphocytes can attack foreign invaders. There are two main branches of immune system: T cells and B cells. Both originate in the bone marrow, from the same stem cells as the red blood cells.

T cells then move to the thymus gland to mature. B cells probably mature in the bone marrow.

B cells secrete soluble antibodies: humoral immunity. T cells interact directly with their targets: cellular immunity In the early 1900s, there are a major debate as to whether the immune response was humoral or cellular. Turned out they were both right.

Antibody Molecules

 Basic structure: 2 heavy chains 2 light chains joined together by disulfide bridges between cysteine amino acids. The molecule has a "Y" shape, with the two ends of the fork being composed of both heavy and light chain regions. These ends are the regions that bind the antigens (Ag). Each Ab molecule has two identical Ag binding regions, and thus the Ab molecules can bind together large groups of Ag's. This makes an insoluble complex that is easy for other cells in the immune system to find and eat.

Antibody Molecules

More Antibody Molecules

Each light (L) chain has 2 domains, a variable (V) region and a constant (C) region. There are only a small number of C regions in each person, but there are very many different V regions. Note that the V and C regions are together on the same polypeptide chain! Each heavy (H) chain has 4 domains, a V domain followed by 3 C domains.

The five major types of antibodies are: IgA. IgA antibodies are found in areas of the body such the nose, breathing passages, digestive tract, ears, eyes, and vagina. IgA antibodies protect body surfaces that are exposed to outside foreign substances. This type of antibody is also found in saliva, tears, and blood. About 10% to 15% of the antibodies present in the body are IgA antibodies. A small number of people do not make IgA antibodies. IgG. IgG antibodies are found in all body fluids. They are the smallest but most common antibody (75% to 80%) of all the antibodies in the body. IgG antibodies are very important in fighting bacterial and viral infections. IgG antibodies are the only type of antibody that can cross the placenta in a pregnant woman to help protect her baby (fetus). IgM. IgM antibodies are the largest antibody. They are found in blood and lymph fluid and are the first type of antibody made in response to an infection. They also cause other immune system cells to destroy foreign substances. IgM antibodies are about 5% to 10% of all the antibodies in the body. IgE. IgE antibodies are found in the lungs, skin, and mucous membranes. They cause the body to react against foreign substances such as pollen, fungus spores, and animal dander. They may occur in allergic reactions to milk, some medicines, and some poisons. IgE antibody levels are often high in people with allergies. IgD. IgD antibodies are found in small amounts in the tissues that line the belly or chest. How they work is not clear.

Generation of Antibody Diversity

There isn't room in the genome for 1,000,000 different antibodies. Coding is done in pieces, with a unique DNA splicing mechanism used to assemble the L and H chains. Each immune system cell splices the DNA differently. Thus, the DNA in the region of the H and L chain genes in B and T cells is not identical to the DNA in other body cells.

Light Chain Splicing

There are two different L chain genes, called kappa and lambda. Immunoglobulins use one or the other. At the kappa L chain gene, there is a single region of DNA that codes for the C domain. Upstream from the C domain is a group of about 250 V domains and another group of 5 J (for "joining") regions. Each V region has a 5UTR segment, a separate exon, attached to it: the leader. During the development of the B cell, a randomly chosen V domain joins with a randomly chosen J domain to form a VJ domain. This occurs by splicing out the DNA between them. Note that this is a very different mechanism from intron spicing that occurs in the RNA of most genes! Once the VJ domain is formed, it can be transcribed into RNA along with the C domain and any DNA that lies between the VJ and C. All the intervening RNA is spliced out as an intron, so the final messenger RNA has VJC all together; this is then translated into a L chain protein.

Lambda light chain genes are slightly different: fewer V regions, and four different C regions each of which has its own J. Lambda chains use only a single DNA splice, to join a randomly selected V region to one of the 4 J-C regions.

Heavy Chains
The process of producing a heavy chain is very similar to L chains, except that there is an additional group of 5 D regions between the V regions and the J regions. Two DNA splices occur for H chains: first a random J joins with a random D to form a DJ region, then a random V region is added to form a VDJ domain. Just as in the L chain, this VDJ is transcribed along with the C region, and any intervening RNA is spliced out as an intron. The final product has VDJC all joined together and gets translated into an H chain protein.

Summary of Splices
Light chain
V-JC joining by DNA splice (lambda) V-J joining by DNA splice (kappa) VJ-C intron removal (RNA splice)

Heavy chain D-J joining by DNA splice V-DJ joining by DNA splice VDJ-C intron removal by RNA splice

Class Switching

Heavy chains fall into 5 classes, based on their C regions. Each H gene has C regions for all 5 classes arranged on the chromosome, with the IgM C region nearest to the V regions. There are several different C regions for some of the classes. IgM is the initial Ab made by each B cell. However, after a while the B cell switches to a different class. This is done using a third DNA splice, in which the DNA between the VDJ and the constant region for the new class is spliced out.

 The T cell receptor or TCR is a molecule found on the surface of T lymphocytes (or T cells) that is, in general, responsible for recognizing antigens bound to major histocompatibility complex (MHC) molecules

TCR, which is anchored in the cell membrane, consists of two halves, which form a pair (or dimer) of protein chains. The halves are called the alpha () and beta () fragments (in / T cells, the halves are gamma () and delta () fragments). Each fragment is divided in turn into a constant (C) and variable (V) region. The constant region has an end that is anchored in the cell membrane. The variable region faces outward and binds to the HLA molecule and the antigen it presents. On the chain, the variable region is called V and the constant region is called C; on the chain, they are called V and C, respectively

T Cell Receptors
The TCR protein has 2 subunits and one antigen binding site. The alpha subunit has V and J segments (similar to Ig light chains) The beta subunit has V, D and J regions, like the Ig heavy chain. Both segments undergo DNA splicing rearrangements like the Ig genes. The joining is not precise and short additions or deletions of bases can occur, as in the Ig genes. However, affinity maturation and somatic hypermutation do not occur. The TCR protein is membrane bound. It is only found on T cells.

 The major histocompatibility complex (MHC) is a large genomic region

or gene family that encodes MHC molecules. MHC molecules play an important role in the immune system and autoimmunity.
Proteins are continually synthesized and destroyed in the cell. These include normal proteins (self) and microbial pathogens (nonself). The MHC proteins act as "signposts" that serve to alert the immune system if foreign material is present inside a cell. They achieve this by displaying fragmented pieces or antigens on the host cell's surface. These antigens may be self or nonself The constitutive presentation of MHC:peptide on cell surfaces allows for pathogen surveillance by immune cells, usually a T cell or natural killer (NK) cell. If activating T or NK cell surface receptors recognize MHC:peptide through binding interactions, it can activate the immune cell and lead to the development of an immune response against the presented antigen There are two general classes of MHC molecules: Class I and Class II. Class I MHC molecules are found on all nucleated cells and present peptides to cytotoxic T cells. Class II MHC molecules are found on certain immune cells themselves, chiefly macrophages, B cells and dendritic cells

MHC Proteins
Class 1 MHC molecules are found on the surface of all nucleated cells. They are involved in cellular immunity. Class 2 MHC molecules are only found on the surface of cells that display antigens: macrophages and B cells. They are involved in humoral immunity.
Structure: Both class 1 and class 2 molecules have 4 domains, but they are divided differently. MHC1 has 3 domains on the alpha subunit and one domain on the beta subunit. MHC2 has two domains on both alpha and beta subunits. The peptide-binding groove is between the alpha-1 and alpha-2 domains on MHC1, and between alpha-1 and beta-1 in MHC2. The MHC proteins are encoded by a series of genes at the MHC locus on chromosome 6. MHC genes are well known to be very polymorphic.
There are three main MHC class 1 genes: A, B, and C, which encode the alpha subunit. The beta subunit is not very polymorphic, and it is encoded elsewhere.. The class 1b genes are mostly monomorphic and their function is not well understood. The class 2 genes are encoded by 6 regions: DM, DN, DO, DP, DQ, and DR. Each region has at least one alpha and one beta gene. There are also some other genes and pseudogenes in the region.

Activation of B and TCells

In the embryo, each B cell undergoes the DNA splicing necessary to produce a single type of antibody. This antibody is an IgM bound to the surface of the cell. No antibody is secreted at this time. Foreign invaders are swallowed (phagocytosis) by macrophages, which are lymphocytes that non-selectively eat particles found in the body. The macrophage partially digests the invader, converting it into peptides and other small molecules. The macrophage then combines the foreign peptides with an MHC class 2 molecule that gets displayed on the surface of the macrophage cell. Helper T cells that have a T cell receptor proteins that match (bind to) the displayed antigen get activated.
Helper T cells are the central regulatory element in humoral immunity. They are also the primary target of the AIDS virus.

The activated helper T cells then divide (proliferate). They also activate B cells. The inactive B cells start the activation process by binding to an antigen with their IgM molecules, engulfing it and processing it. The antigen peptides are displayed on MHC 2 molecules on the cell surface, just like the macrophages do. Activated helper T cells interact with B cells that have the same antigen displayed on their surface: the TCR on the helper T cell binds to the antigen displayed on MHC2 on the surface of the B cell. the CD4 protein on the surface of the helper T cell is also necessary for this interaction. The helper T cells secrete cytokines, which stimulate the B cells to proliferate and differentiate into plasma cells, which secrete antibodies. this is clonal selection: only those B cells with usable antibodies are selected to proliferate.

Some descendants of the activated B cell become plasma cells, while others become memory cells. Memory cells stay present in the blood for long periods of time. The next time their specific antigen appears, the memory cells quickly start proliferating and differentiating into plasma cells. This provides a rapid response to a second appearance of the antigen.

Cellular Immunity
Cytotoxic (or killer) T cells are the main actor in cellular immunity. Cytotoxic cells (also called CD8 cells) kill cells that are infected with viruses or otherwise contain foreign proteins. Cytotoxic T cells are activated in the same way that helper T cells are.
Macrophages eat things in the blood, digest them to peptide fragments, and display the fragments on their surfaces bound to MHC class 1 molecules (as opposed to class 2 for helper T cells). Inactive cytotoxic T cells have a specific T cell receptor protein on their surface. If their TCR binds to the peptide displayed on a macrophage, the cytotoxic T cell is activated. the CD8 preotein on the T cell surface facilitates this interaction.

All cells digest proteins in their lysosomes. Some of the resulting peptide fragments are displayed in MHC 1 proteins on the surface of the cell. Thus, every cell displays a summary of the proteins inside it on its surface. Mostly these are acceptable proteins, but if the cell has been infected by a virus, foreign viral protein fragments will be displayed. If the TCR on an activated cytotoxic T cell binds to a peptide fragment displayed on the surface of a cell, the T cell kills it by secreting perforin proteins that punch holes in the cells membrane.

Self vs. Non-self

If every cellular protein is displayed on the cells surface, and macrophages eat everything nonselectively, why dont we have an immune response against normal cellular proteins? The phenomenon of not attacking self proteins is called tolerance, and it is the result of clonal deletion. Clonal deletion occurs in the thymus. since B cells only become activated by helper T cells, clonal deletion of T cells ensures that B cells that might produce antibodies against self molecules never get activated. Autoimmune diseases are the result of self proteins being incorrectly recognized as non-self.

Immunological Memory
The first time a new antigen is seen, the response is slow and relatively weak. However, a second appearance of that antigen gives a rapid, strong reaction. This is the result of memory cells formed during the first exposure. The memory cells have already proliferated and they quickly start to secrete antibodies.
Note that the secondary response is not general: it is only to the specific antigen that caused the primary response.

This is the basis of vaccinations: introducing a small amount of killed or weakened virus into the body, sometimes several times. The body develops a weak immune response, but builds up memory cells. When the pathogen tries to infect the body, a strong immune response is generated. Cellular immunity has a similar system of memory cells.

Rh Incompatibility

The Rhesus factor is an antigen on the surface of red blood cells. . About 85% of people have the Rh antigen (Rh+) and 15% lack it (Rh-). The Rh+ allele is dominant, so heterozygotes are Rh+. Because the + allele is dominant, it is possible for an Rhmother to have an Rh+ baby. In general, the fetuss blood is separated from the mothers: there is a barrier against blood mixing at the placenta. However, during childbirth some of the fetuss blood often enters the mothers body. This causes her immune system to develop antibodies against the Rh factor. Since antibodies do cross the placental barrier, a subsequent Rh+ fetus will have its blood cells attacked by the mothers anti-Rh antibodies. This leads to hemolytic disease of the newborn, which used to be a major cause of stillbirth. However, these days Rh- mothers are given anti-Rh antiserum shortly after they give birth to an Rh+ baby. This antiserum removes any Rh+ blood cells from the mothers blood, and so she does not develop an immune response against Rh.

Severe Combined Immunodeficiency (SCID)

Severe mixed immunodeficiency syndrome," and "Thymic alymphoplasia" is a genetic disorder in which both "arms" (B cells and T cells) of the adaptive immune systemare impaired due to a defect in one of several possible genes. SCID is a severe form of heritable immunodeficiency. It is also known as the "bubble boy" disease because its victims are extremely vulnerable to infectious diseases There are several types of SCID. The most common form is caused by a mutation in the SCIDX1 gene located on the X chromosome. This gene encodes a protein that is used to construct a receptor called IL2RG (interleukin-2 receptor). Another form of SCID is caused by a mutation on chromosome 20 and is characterized by a deficiency of the enzyme adenosine deaminase

 interleukin-2 receptor : These receptors reside in the plasma membrane of immune cells. Their job is to allow two types of immune cells - T cells and B cells - to communicate. When the gene is mutated, the receptors cannot form and are absent from immune cells. As a result, the immune cells can't communicate with one another about invaders in the environment. Not enough T and B cells are produced to fight off the infection,
and the body is left defenseless.

Where

 Symptoms: usually appear in the first few months of life. Because the immune system cannot protect the baby's body, babies with the disorder tend to get one infection after another. Some of these bacterial infections may be life-threatening, including pneumonia (lung infection), meningitis (brain infection), and sepsis (blood infection). To make matters worse, SCID patients often don't respond to the antibiotics used to treat bacterial infections. They may suffer more frequently from ear infections, sinus infections, a chronic cough, and rashes on the skin. Early diagnosis of SCID is very important, because without quick treatment, children with the disease aren't likely to live past age 2

Types :
1. Autosomal recessive SCID Immunological featuresdefect of the common precursors of T and B cells 2. Defects in HLA II molecular SCID Immunological features increased susceptibility to virus infection no CD4+T cells in peripheral blood decreased Function of the B cells 3. x-linked SCID Pathogenesisgene mutation of IL-2 receptor g chain reduced numbers of peripheral blood T cells and NK cells

Autoimmune Diseases
Autoimmune diseases arise from an overactive immune response of the body against substances and tissues normally present in the body. In other words, the body actually attacks its own cells .A wide spectrum of diseases: rheumatoid arthritis, Crohns disease, type 1 diabetes, lupus, and many others. Normally, immune system cells that react with self antigens are deleted early in life, but when this fails ,it leads to autoimmune disorders

Causes : 1. One cause is sequestered antigens: body proteins that did not reach thymus during the critical period of clonal deletion around birth. Ex :Eye lens crystallin is not generally exposed to the blood, but eye injuries sometimes allow contact and the development of anti-crystallin antibodies. This can result in blindness. 2. Another possible cause is clones of self-reactive immune cells that escape clonal deletion due to chance events. 3. A third possible cause is cross reactive antigens. A pathogen carries an antigen that is similar to a normal body protein. As the body mounts an immune response against the pathogen, the degree of similarity causes cross reaction with the body proteins. An example is scarlet fever, which is caused by a Streptococcus infection. Antibodies produced against these bacteria often cross react with a protein found on heart valve cells. The result is heart damage.

Some autoimmune diseases may have a genetic component and are triggered by external factors (e.g., infection) or injury. Others are probably strictly caused by external factors (e.g., infection) or injury

:Some tissue-specific antigen can be expresses in the thymus causing deletion (death) of thymocytes that recognize those antigens

Autoreactive B cells can arise in germinal centers from cell that are undergoing somatic mutations (a mutation could change the specificity of a BCR from anti-foreign to anti-self).
It is excepted that these autoreactive B cell will bind antigen (signal 1) but should not find a autoreactive T cell to provide help (signal 2) and signal 1 without signal 2 results in allergy and death.

Autoimmune diseases can be organ-specific or systemic

Some commom autoimmune diseases

Graves disease (anti-thyroid stimulating hormone

Normal
receptor; anti-TSHR)

In Graves disease, the antibodies do not destroy the thyroid but act as if they are TSH (i.e., they bind and activate the TSH receptor) (agonist)

Myasthenia gravis (anti-acetylcholine receptors)

In myasthenia gravis the antibodies bind the acetylcholine receptor and cause it to be cleared from the surface of the muscle

For insulin-dependent diabetes mellitus, CTL kill the b cells (cells that make insulin)

Insulin is stained brown

Many autoimmune diseases are associated with certain HLA (MHC) types and with gender

Genetics Gender Environment

Chance

Genetics play an important role but other factors are also important, such as gender, environment and chance

Hypersensitive States
Normally the immune system plays an important role in protecting the body from microorganisms and other foreign substances. If the activity of the immune system is excessive or overreactive, a hypersensitivity reaction develops. The consequences of a hypersensitivity reaction may be injury to the body or death. There are several types.
Anaphylactic reaction is a very rapid response that comes from mast cells releasing large amounts of histamine as a result of binding the antigen to IgE molecules. Histamine causes the blood vessels to leak, causing allergy symptoms such as runny nose and weepy eyes, as well as bronchoconstriction (as in asthma). Some external antigens, especially certain small molecules, accumulate of the surface of cells. The bodys immune response can kill the cells. accumulation of antibody-antigen complexes in body tissues can lead to inflammation and tissue damage.

 The general nature of and symptoms accompanying the reaction depend upon whether antibodies or sensitized T-lymphocytes are involved. When antibodies are involved, the reactions fall under the heading of immediate hypersensitivity. When T-lymphocytes are involved, the reactions are characterized as delayed hypersensitivity. Immediate hypersensitivity reactions include anaphylaxis, allergic reactions, cytotoxic reactions, and immune complex reactions. Delayed hypersensitivity reactions are generally characterized as contact dermatitis or infection allergies.

End