Superantigen

Schematic representation of MHC class II.

Superantigens (SAgs) are a class of antigens which cause non-specific activation of T-cells resulting in polyclonal T cell activation and massive cytokine release. SAgs can be produced by pathogenic microbes (including viruses, mycoplasma, and bacteria as a defense mechanism against the immune system. Compared to a normal antigen-induced T-cell response where .0001.001% of the bodys T-cells are activated, these SAgs are capable of activating up to 25% of the bodys T-cellsFurthermore, Anti-CD3 and Anti-CD28 Antibodies (CD28-SuperMAB) have also shown to be highly potent superantigens (and can activate up to 100% of T cells). The large number of activated T-cells generates a massive immune response which is not specific to any particular epitope on the SAg thus undermining one of the fundamental strengths of the adaptive immune system, that is, its ability to target antigens with high specificity. More importantly, the large number of activated T-cells secrete large amounts of cytokines, the most important of which is Interferon gamma. This excess amount of IFN-gamma in turn activates the macrophages. The activated macrophages, in turn, over-produce proinflammatory cytokines such as IL-1, IL-6 and TNF-alpha. TNF-alpha is particularly important as a part of the body's inflammatory response. In normal circumstances it is released locally in low levels and helps the immune system defeat pathogens. However when it is systemically released in the blood and in high levels (due to mass T-cell activation resulting from the SAg binding), it can cause severe and life-threatening symptoms, including shock and multiple organ failure.

Structure
SAgs are produced intracellularly by bacteria and are released upon infection as extracellular mature toxins. The sequences of these toxins are relatively conserved among the different subgroups. More important than sequence homology, the 3D structure is very similar among different SAgs resulting in similar functional effects among different groups. Crystal structures of the enterotoxins reveals that they are compact, ellipsoidal proteins sharing a characteristic two-domain folding pattern comprising an NH2-terminal barrel globular domain known as the oligosaccharide / oligonucleotide fold, a long -helix that diagonally spans the center of the molecule, and a COOH terminal globular domain. The domains have binding regions for the Major Histocompatibility Complex Class II (MHC Class II) and the T cell receptor (TCR), respectively.

Binding
Superantigens bind first to the MHC Class II and then coordinate to the variable alpha or beta chain of T-cell Receptors (TCR)

MHC Class II
SAgs show preference for the HLA-DQ form of the molecule. Binding to the -chain puts the SAg in the appropriate position to coordinate to the TCR. Less commonly, SAgs attach to the polymorphic MHC class II -chain in an interaction mediated by a zinc ion coordination complex between three SAg residues and a highly conserved region of the HLA-DR chain. The use of a zinc ion in binding leads to a higher affinity interaction. Several staphylococcal SAgs are capable of cross-linking MHC molecules by binding to both the and chains. This mechanism stimulates cytokine expression and release in antigen presenting cells as well as inducing the production of costimulatory molecules that allow the cell to bind to and activate T cells more effectively.

T-cell receptor
T-cell binding region of the SAg interacts with the Variable region on the Beta chain of the Tcell Receptor. A given SAg can activate a large proportion of the T-cell population because the human T-cell repertoire comprises only about 50 types of V elements and some SAgs are capable of binding to multiple types of V regions. This interaction varies slightly among the different groups of SAgs. Variability among different people in the types of T-cell regions that are prevalent explains why some people respond more strongly to certain SAgs. Group I SAgs contact the V at the CDR2 and framework region of the molecule. SAgs of Group II interact with the V region using mechanisms that are conformation-dependent. These interactions are
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for the most part independent of specific V amino acid side-chains. Group IV SAgs have been shown to engage all three CDR loops of certain V forms. The interaction takes place in a cleft between the small and large domains of the SAg and allows the SAg to act as a wedge between the TCR and MHC. This displaces the antigenic peptide away from the TCR and circumvents the normal mechanism for T-cell activation. The biological strength of the SAg (its ability to stimulate) is determined by its affinity for the TCR. SAgs with the highest affinity for the TCR elicit the strongest response. SPMEZ-2 is the most potent SAg discovered to date.

T-cell signaling
The SAg cross-links the MHC and the TCR inducing a signaling pathway that results in the proliferation of the cell and production of cytokines. Low levels of Zap-70 have been found in Tcells activated by SAgs, indicating that the normal signaling pathway of T-cell activation is impaired. It is hypothesized that Fyn rather than Lck is activated by a tyrosine kinase, leading to the adaptive induction of anergy. Both the protein kinase C pathway and the protein tyrosine kinase pathways are activated, resulting in upregulating production of proinflammatory cytokines. This alternative signaling pathway impairs the calcium/calcineurin and Ras/MAPkinase pathways slightly, but allows for a focused inflammatory response.

Direct effects
SAg stimulation of antigen presenting cells and T-cells elicits a response that is mainly inflammatory, focused on the action of Th1 T-helper cells. Some of the major products are IL-1, IL-2, IL-6, TNF-, gamma interferon (IFN-), macrophage inflammatory protein 1 (MIP-1), MIP-1, and monocyte chemoattractant protein 1 (MCP-1). This excessive uncoordinated release of cytokines, (especially TNF-), overloads the body and results in rashes, fever, and can lead to multi-organ failure, coma and death. Deletion or anergy of activated T-cells follows infection. This results from production of IL-4 and IL-10 from prolonged exposure to the toxin. The IL-4 and IL-10 downregulate production of IFNgamma,MHC Class II, and costimulatory molecules on the surface of APCs. These effects produce memory cells that are unresponsive to antigen stimulation. One mechanism by which this is possible involves cytokine-mediated suppression of T-cells. MHC crosslinking also activates a signaling pathway that suppresses hematopoiesis and upregulates Fas-mediated apoptosis. IFN- is another product of prolonged SAg exposure. This cytokine is closely linked with induction of autoimmunity, and the autoimmune disease Kawasaki Disease is known to be caused by SAg infection. SAg activation in T-cells leads to production of CD40 ligand which activates isotype switching in B cells to IgG and IgM and IgE. To summarize, the T-cells are stimulated and produce excess amounts of cytokine resulting in
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cytokine-mediated suppression of T-cells and deletion of the activated cells as the body returns to homeostasis. The toxic effects of the microbe and SAg also damage tissue and organ systems, a condition known as Toxic Shock Syndrome. If the initial inflammation is survived, the host cells become anergic or are deleted, resulting in a severely compromised immune system.

Superantigenicity independent (indirect) effects

Apart from their mitogenic activity, SAgs are able to cause symptoms that are characteristic of infection. One such effect is emesis. This effect is felt in cases of food poisoning, when SAgproducing bacteria release the toxin, which is highly resistant to heat. There is a distinct region of the molecule that is active in inducing gastrointestinal toxicity. This activity is also highly potent, and quantities as small as 20-35ug of SAg are able to induce vomiting. SAgs are able to stimulate recruitment of neutrophils to the site of infection in a way that is independent of T-cell stimulation. This effect is due to the ability of SAgs to activate monocytic cells, stimulating the release of the cytokine TNF-, leading to increased expression of adhesion molecules that recruit leukocytes to infected regions. This causes inflammation in the lungs, intestinal tissue, and any place that the bacteria have colonized. While small amounts of inflammation are natural and helpful, excessive inflammation can lead to tissue destruction. One of the more dangerous indirect effects of SAg infection concerns the ability of SAgs to augment the effects of endotoxins in the body. This is accomplished by reducing the threshold for endotoxicity. Schlievert demonstrated that, when administered conjunctively, the effects of SAg and endotoxin are magnified as much as 50,000 times. This could be due to the reduced immune system efficiency induced by SAg infection. Aside from the synergistic relationship between endotoxin and SAg, the double hit effect of the activity of the endotoxin and the SAg result in effects more deleterious that those seen in a typical bacterial infection. This also implicates SAgs in the progression of sepsis in patients with bacterial infections.

Diseases associated with superantigen production

Diabetes mellitus Eczema Guttate psoriasis Kawasaki Disease Nasal polyps Rheumatic fever Rheumatoid arthritis Scarlet fever Toxic Shock Syndrome

Treatment
The primary goal of medical treatment is to eliminate the microbe that is producing the SAgs. This is accomplished through the use of vasopressors, fluid resuscitation and antibiotics.
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The body naturally produces antibodies to some SAgs, and this effect can be augmented by stimulating B-cell production of these antibodies. Immunoglobulin pools are able to neutralize specific antibodies and prevent T-cell activation. Synthetic antibodies and peptides have been created to mimic SAg-binding regions on the MHC class II, blocking the interaction and preventing T cell activation. Immunosuppressants are also employed to prevent T-cell activation and the release of cytokines. Corticosteroids are used to reduce inflammatory effects.

Evolution of superantigen production

SAg production effectively corrupts the immune response, allowing the microbe secreting the SAg to be carried and transmitted unchecked. One mechanism by which this is done is through inducing anergy of the T-cells to antigens and SAgs. Lussow and MacDonald demonstrated this by systematically exposing animals to a streptococcal antigen. They found that exposure to other antigens after SAg infection failed to elicit an immune response. In another experiment, Watson and Lee discovered that memory T-cells created by normal antigen stimulation were anergic to SAg stimulation and that memory T-cells created after a SAg infection were anergic to all antigen stimulation. The mechanism by which this occurred was undetermined. The genes that regulate SAg expression also regulate mechanisms of immune evasion such as M protein and Bacterial capsule expression, supporting the hypothesis that SAg production evolved primarily as a mechanism of immune evasion. When the structure of individual SAg domains has been compared to other immunoglobulinbinding streptococcal proteins (such as those toxins produced by E. coli) it was found that the domains separately resemble members of these families. This homology suggests that the SAgs evolved through the recombination of two smaller -strand motifs.

Endogenous SAgs
Minor lymphocyte stimulating (Mls) exotoxins were originally discovered in the thymic stromal cells of mice. These toxins are encoded by SAg genes that were incorporated into the mouse genome from the mouse mammary tumour virus (MMTV). The presence of these genes in the mouse genome allows the mouse to express the antigen in the thymus as a means of negatively selecting for lymphocytes with a variable Beta region that is susceptible to stimulation by the viral SAg. The result is that these mice are immune to infection by the virus later in life. Similar endogenous SAg-dependent selection has yet to be identified in the human genome, but endogenous SAgs have been discovered and are suspected of playing an integral role in viral infection. Infection by the Epstein-Barr virus, for example, is known to cause production of a SAg in infected cells, yet no gene for the toxin has been found on the genome of the virus. The virus manipulates the infected cell to express its own SAg genes, and this helps it to evade the host immune system. Similar results have been found with rabies, cytomegalovirus, and HIV.

Freund's adjuvant
Freund's adjuvant is a solution of antigen emulsified in mineral oil and used as an immunopotentiator (booster). The complete form, Freund's Complete Adjuvant,(CFAor FCA is composed of inactivated and dried mycobacteria (usually M. tuberculosis), whereas the incomplete form (IFA or FIAlacks the mycobacterial components (hence just the water in oil emulsion). It is named after Jules T. Freund.

Regulation
Freund's complete adjuvant is effective in stimulating cell-mediated immunity and may lead to the potentiation of the production of certain immunoglobulins, but this effect depends on the animal model used. Its use in humans is forbidden by regulatory authorities, due to its toxicity. Even for animal research there are currently guidelines associated with its use, due to its painful reaction and potential for tissue damage. Injections of CFA should be subcutaneous or intraperitoneal, because intradermal injections may cause skin ulceration and necrosis; intramuscular injections may lead to temporary or permanent muscle lesion, and intravenous injections may produce pulmonary lipid embolism

Effects
When administered to mice, in some laboratory experiments Freund's complete adjuvant was said to have prevented juvenile-onset diabetes and combined with prepared spleen cells was said to have reversed it. In 2006 these claims were challenged by the findings of several other researchers. Although newspapers have described the 2006 findings as confirming the earlier experiments, in substantial ways they conflict with them. A report from NIH was released on November 23, 2006 in Science confirming the participation of spleen cells in reversing end-stage diabetes. It has also been investigated in an animal model of Parkinson's disease.

Mechanism
FCA is known to stimulate production of tumor necrosis factor, which is thought to kill the Tcells responsible for the autoimmune destruction of the pancreatic Beta cells. Still in question is whether the regrowth of functional insulin-producing cells occurs due to differentiation and proliferation of existing pancreatic stem cells, or whether the injected spleen cells re-differentiate to an insulin-producing form. Denise Faustman, whose work has been central to developing the protocol, has suggested that both mechanisms may play a role. However, in experiments to verify and examine her work, Suri reported that DNA-based evidence yielded no sign of spleen cell derivatives in pancreatic islet Beta cells analyzed after treatments.

Each antibody binds to a specific antigen; an interaction similar to a lock and key. An antibody (Ab), also known as an immunoglobulin (Ig), is a large Y-shaped protein produced by B cells that is used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, called an antigen. Each tip of the "Y" of an antibody contains a paratope (a structure analogous to a lock) that is specific for one particular epitope (similarly analogous to a key) on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize its target directly (for example, by blocking a part of a microbe that is essential for its invasion and survival). The production of antibodies is the main function of the humoral immune system. Antibodies are secreted by a type of white blood cell called a plasma cell. Antibodies can occur in two physical forms, a soluble form that is secreted from the cell, and a membrane-bound form that is attached to the surface of a B cell and is referred to as the B cell receptor (BCR). The BCR is only found on the surface of B cells and facilitates the activation of these cells and their subsequent differentiation into either antibody factories called plasma cells, or memory B cells that will survive in the body and remember that same antigen so the B cells can respond faster upon future exposure. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the B cell and, therefore, antibody generation following antigen binding. Soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue to survey for invading microorganisms.

Antibodies are glycoproteins belonging to the immunoglobulin superfamily; the terms antibody and immunoglobulin are often used interchangeably. Antibodies are typically made of basic structural unitseach with two large heavy chains and two small light chains. There are several different types of antibody heavy chains, and several different kinds of antibodies, which are grouped into different isotypes based on which heavy chain they possess. Five different antibody isotypes are known in mammals, which perform different roles, and help direct the appropriate immune response for each different type of foreign object they encounter. Though the general structure of all antibodies is very similar, a small region at the tip of the protein is extremely variable, allowing millions of antibodies with slightly different tip structures, or antigen binding sites, to exist. This region is known as the hypervariable region. Each of these variants can bind to a different antigen. This enormous diversity of antibodies allows the immune system to recognize an equally wide variety of antigens. The large and diverse population of antibodies is generated by random combinations of a set of gene segments that encode different antigen binding sites (or paratopes), followed by random mutations in this area of the antibody gene, which create further diversity. Antibody genes also re-organize in a process called class switching that changes the base of the heavy chain to another, creating a different isotype of the antibody that retains the antigen specific variable region. This allows a single antibody to be used by several different parts of the immune system.

Forms
The membrane-bound form of an antibody may be called a surface immunoglobulin (sIg) or a membrane immunoglobulin (mIg). It is part of the B cell receptor (BCR), which allows a B cell to detect when a specific antigen is present in the body and triggers B cell activation.[9] The BCR is composed of surface-bound IgD or IgM antibodies and associated Ig- and Ig- heterodimers, which are capable of signal transduction.[10] A typical human B cell will have 50,000 to 100,000 antibodies bound to its surface.[10] Upon antigen binding, they cluster in large patches, which can exceed 1 micrometer in diameter, on lipid rafts that isolate the BCRs from most other cell signaling receptors.[10] These patches may improve the efficiency of the cellular immune response.[11] In humans, the cell surface is bare around the B cell receptors for several hundred nanometers,[10] which further isolates the BCRs from competing influences.

Isotypes
Antibodies can come in different varieties known as isotypes or classes. In placental mammals there are five antibody isotypes known as IgA, IgD, IgE, IgG and IgM. They are each named with an "Ig" prefix that stands for immunoglobulin, another name for antibody, and differ in their biological properties, functional locations and ability to deal with different antigens, as depicted in the table.

Antibody isotypes of mammals Name Types Description Antibody Complexes Found in mucosal areas, such as the gut, respiratory tract and IgA 2 urogenital tract, and prevents colonization by pathogens.[ Also found in saliva, tears, and breast milk. Functions mainly as an antigen receptor on B cells that have IgD 1 not been exposed to antigens. It has been shown to activate basophils and mast cells to produce antimicrobial factors.] Binds to allergens and triggers histamine release from mast IgE 1 cells and basophils, and is involved in allergy. Also protects against parasitic worms.[ In its four forms, provides the majority of antibody-based immunity against invading pathogens. The only antibody IgG 4 capable of crossing the placenta to give passive immunity to the fetus. Expressed on the surface of B cells (monomer) and in a secreted form (pentamer) with very high avidity. Eliminates IgM 1 pathogens in the early stages of B cell mediated (humoral) immunity before there is sufficient IgG.

The antibody isotype of a B cell changes during cell development and activation. Immature B cells, which have never been exposed to an antigen, express only the IgM+ isotype in a cell surface bound form. The B lymphocyte, in its mature ready-to-respond form, is known as "naive B lymphocyte." The naive B lymphocyte express both surface IgM+ and IgD+. The coexpression of both these immunoglobulin isotypes renders the B cell 'mature' and ready to respond to antigen. B cell activation follows engagement of the cell bound antibody molecule with an antigen, causing the cell to divide and differentiate into an antibody producing cell called a plasma cell. In this activated form, the B cell starts to produce antibody in a secreted form rather than a membrane-bound form. Some daughter cells of the activated B cells undergo isotype switching, a mechanism that causes the production of antibodies to change from IgM or IgD to the other antibody isotypes, IgE, IgA or IgG, that have defined roles in the immune system.

Structure
Antibodies are heavy (~150 kDa) globular plasma proteins. They have sugar chains added to some of their amino acid residues.] In other words, antibodies are glycoproteins. The basic functional unit of each antibody is an immunoglobulin (Ig) monomer (containing only one Ig unit); secreted antibodies can also be dimeric with two Ig units as with IgA, tetrameric with four Ig units like teleost fish IgM, or pentameric with five Ig units, like mammalian IgM. Several immunoglobulin domains make up the two heavy chains (red and blue) and the two light chains (green and yellow) of an antibody. The immunoglobulin domains are composed of between 7 (for constant domains) and 9 (for variable domains) -strands. The variable parts of an antibody are its V regions, and the constant part is its C region.
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Immunoglobulin domains
The Ig monomer is a "Y"-shaped molecule that consists of four polypeptide chains; two identical heavy chains and two identical light chains connected by disulfide bonds.[12] Each chain is composed of structural domains called immunoglobulin domains. These domains contain about 70-110 amino acids and are classified into different categories (for example, variable or IgV, and constant or IgC) according to their size and function. They have a characteristic immunoglobulin fold in which two beta sheets create a "sandwich" shape, held together by interactions between conserved cysteines and other charged amino acids.

Heavy chain
There are five types of mammalian Ig heavy chain denoted by the Greek letters: , , , , and .[ The type of heavy chain present defines the class of antibody; these chains are found in IgA, IgD, IgE, IgG, and IgM antibodies, respectively. Distinct heavy chains differ in size and composition; and contain approximately 450 amino acids, while and have approximately 550 amino acids.

1. Fab region 2. Fc region 3. Heavy chain (blue) with one variable (VH) domain followed by a constant domain (CH1), a hinge region, and two more constant (CH2 and CH3) domains. 4. Light chain (green) with one variable (VL) and one constant (CL) domain 5. Antigen binding site (paratope) 6. Hinge regions. In birds, the major serum antibody, also found in yolk, is called IgY. It is quite different from mammalian IgG. However, in some older literature and even on some commercial life sciences product websites it is still called "IgG", which is incorrect and can be confusing.

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Each heavy chain has two regions, the constant region and the variable region. The constant region is identical in all antibodies of the same isotype, but differs in antibodies of different isotypes. Heavy chains , and have a constant region composed of three tandem (in a line) Ig domains, and a hinge region for added flexibility; heavy chains and have a constant region composed of four immunoglobulin domains. The variable region of the heavy chain differs in antibodies produced by different B cells, but is the same for all antibodies produced by a single B cell or B cell clone. The variable region of each heavy chain is approximately 110 amino acids long and is composed of a single Ig domain.

Light chain.
In mammals there are two types of immunoglobulin light chain, which are called lambda () and kappa (). A light chain has two successive domains: one constant domain and one variable domain. The approximate length of a light chain is 211 to 217 amino acids. Each antibody contains two light chains that are always identical; only one type of light chain, or , is present per antibody in mammals. Other types of light chains, such as the iota () chain, are found in other vertebrates like sharks (Chondrichthyes) and bony fishes (Teleostei).

CDRs, Fv, Fab and Fc Regions

Some parts of an antibody have the same functions. The arms of the Y, for example, contain the sites that can bind two antigens (in general, identical) and, therefore, recognize specific foreign objects. This region of the antibody is called the Fab (fragment, antigen binding) region. It is composed of one constant and one variable domain from each heavy and light chain of the antibody. The paratope is shaped at the amino terminal end of the antibody monomer by the variable domains from the heavy and light chains. The variable domain is also referred to as the FV region and is the most important region for binding to antigens. More specifically, variable loops of -strands, three each on the light (VL) and heavy (VH) chains are responsible for binding to the antigen. These loops are referred to as the complementarity determining regions (CDRs). The structures of these CDRs have been clustered and classified by Chothia et al.[ and more recently by North et al. In the framework of the immune network theory, CDRs are also called idiotypes. According to immune network theory, the adaptive immune system is regulated by interactions between idiotypes. The base of the Y plays a role in modulating immune cell activity. This region is called the Fc (Fragment, crystallizable) region, and is composed of two heavy chains that contribute two or three constant domains depending on the class of the antibody. Thus, the Fc region ensures that each antibody generates an appropriate immune response for a given antigen, by binding to a specific class of Fc receptors, and other immune molecules, such as complement proteins. By doing this, it mediates different physiological effects including recognition of opsonized particles, lysis of cells, and degranulation of mast cells, basophils and eosinophils.

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Function
Activated B cells differentiate into either antibody-producing cells called plasma cells that secrete soluble antibody or memory cells that survive in the body for years afterward in order to allow the immune system to remember an antigen and respond faster upon future exposures. At the prenatal and neonatal stages of life, the presence of antibodies is provided by passive immunization from the mother. Early endogenous antibody production varies for different kinds of antibodies, and usually appear within the first years of life. Since antibodies exist freely in the bloodstream, they are said to be part of the humoral immune system. Circulating antibodies are produced by clonal B cells that specifically respond to only one antigen (an example is a virus capsid protein fragment). Antibodies contribute to immunity in three ways: they prevent pathogens from entering or damaging cells by binding to them; they stimulate removal of pathogens by macrophages and other cells by coating the pathogen; and they trigger destruction of pathogens by stimulating other immune responses such as the complement pathway.[25]

The secreted mammalian IgM has five Ig units. Each Ig unit (labeled 1) has two epitope binding Fab regions, so IgM is capable of binding up to 10 epitopes.

Activation of complement
Antibodies that bind to surface antigens on, for example, a bacterium attract the first component of the complement cascade with their Fc region and initiate activation of the "classical" complement system. This results in the killing of bacteria in two ways. First, the binding of the antibody and complement molecules marks the microbe for ingestion by phagocytes in a process called opsonization; these phagocytes are attracted by certain complement molecules generated in the complement cascade. Secondly, some complement system components form a membrane attack complex to assist antibodies to kill the bacterium directly. An antibody is a molecule that specificially inactivates an antigen.

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Activation of effector cells

To combat pathogens that replicate outside cells, antibodies bind to pathogens to link them together, causing them to agglutinate. Since an antibody has at least two paratopes it can bind more than one antigen by binding identical epitopes carried on the surfaces of these antigens. By coating the pathogen, antibodies stimulate effector functions against the pathogen in cells that recognize their Fc region. Those cells which recognize coated pathogens have Fc receptors which, as the name suggests, interacts with the Fc region of IgA, IgG, and IgE antibodies. The engagement of a particular antibody with the Fc receptor on a particular cell triggers an effector function of that cell; phagocytes will phagocytose, mast cells and neutrophils will degranulate, natural killer cells will release cytokines and cytotoxic molecules; that will ultimately result in destruction of the invading microbe. The Fc receptors are isotype-specific, which gives greater flexibility to the immune system, invoking only the appropriate immune mechanisms for distinct pathogens.

Natural antibodies
Humans and higher primates also produce "natural antibodies" which are present in serum before viral infection. Natural antibodies have been defined as antibodies that are produced without any previous infection, vaccination, other foreign antigen exposure or passive immunization. These antibodies can activate the classical complement pathway leading to lysis of enveloped virus particles long before the adaptive immune response is activated. Many natural antibodies are directed against the disaccharide galactose (1,3)-galactose (-Gal), which is found as a terminal sugar on glycosylated cell surface proteins, and generated in response to production of this sugar by bacteria contained in the human gut. Rejection of xenotransplantated organs is thought to be, in part, the result of natural antibodies circulating in the serum of the recipient binding to -Gal antigens expressed on the donor tissue.[

Immunoglobulin diversity
Virtually all microbes can trigger an antibody response. Successful recognition and eradication of many different types of microbes requires diversity among antibodies; their amino acid composition varies allowing them to interact with many different antigens. It has been estimated that humans generate about 10 billion different antibodies, each capable of binding a distinct epitope of an antigen.] Although a huge repertoire of different antibodies is generated in a single individual, the number of genes available to make these proteins is limited by the size of the human genome. Several complex genetic mechanisms have evolved that allow vertebrate B cells to generate a diverse pool of antibodies from a relatively small number of antibody genes.

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Domain variability
The region (locus) of a chromosome that encodes an antibody is large and contains several distinct genes for each domain of the antibodythe locus containing heavy chain genes (IGH@) is found on chromosome 14, and the loci containing lambda and kappa light chain genes (IGL@ and IGK@) are found on chromosomes 22 and 2 in humans. One of these domains is called the variable domain, which is present in each heavy and light chain of every antibody, but can differ in different antibodies generated from distinct B cells. Differences, between the variable domains, are located on three loops known as hypervariable regions (HV-1, HV-2 and HV-3) or complementarity determining regions (CDR1, CDR2 and CDR3). CDRs are supported within the variable domains by conserved framework regions. The heavy chain locus contains about 65 different variable domain genes that all differ in their CDRs. Combining these genes with an array of genes for other domains of the antibody generates a large cavalry of antibodies with a high degree of variability. This combination is called V(D)J recombination discussed below.

Medical applications
Disease diagnosis and therapy
Detection of particular antibodies is a very common form of medical diagnostics, and applications such as serology depend on these methods. For example, in biochemical assays for disease diagnosis, a titer of antibodies directed against Epstein-Barr virus or Lyme disease is estimated from the blood. If those antibodies are not present, either the person is not infected, or the infection occurred a very long time ago, and the B cells generating these specific antibodies have naturally decayed. In clinical immunology, levels of individual classes of immunoglobulins are measured by nephelometry (or turbidimetry) to characterize the antibody profile of patient. Elevations in different classes of immunoglobulins are sometimes useful in determining the cause of liver damage in patients for whom the diagnosis is unclear. .

Prenatal therapy
Rhesus factor, also known as Rhesus D (RhD) antigen, is an antigen found on red blood cells; individuals that are Rhesus-positive (Rh+) have this antigen on their red blood cells and individuals that are Rhesus-negative (Rh) do not. During normal childbirth, delivery trauma or complications during pregnancy, blood from a fetus can enter the mother's system. In the case of an Rh-incompatible mother and child, consequential blood mixing may sensitize an Rh- mother to the Rh antigen on the blood cells of the Rh+ child, putting the remainder of the pregnancy, and any subsequent pregnancies, at risk for hemolytic disease of the newborn.

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Isotype (immunology)

Some antibodies form complexes that bind to multiple antigen molecules. An isotype usually refers to any related proteins/genes from a particular gene family. In immunology, the "immunoglobulin isotype" refers to the genetic variations or differences in the constant regions of the heavy and light chains. In humans, there are five heavy chain isotypes and two light chain isotypes:

heavy chain o - IgA 1, 2 o - IgD o - IgG 1, 2, 3, 4 o - IgE o - IgM light chain o o

Immunoglobulin class switching can be used to change the class of the heavy chain, but not of the light chain. Isotypes are distinct forms of light or heavy chains which are present in all members of a species, encoded at distinct genetic loci. Kappa and lambda are isotypes of light chains. Delta (), gamma:1 (1), etc. are isotypes of heavy chains. All isotypes can be readily found in all normal sera.

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Immunoglobulin allotype

The allotype affects the constant region (labeled CL and CH1-3 in the diagram.) In immunology, an immunoglobulin allotype is the allele of the antibody chains found in the individual. The word allotype comes from two Greek roots, allo meaning 'other or differing from the norm' and typos meaning 'mark.' Thus allotype refers to the idea that each immunoglobin has unique sequences particular to the individual's genome that manifest in its constant region (normally). To reduce risk of transplant rejection, tissue typing is used to try to match donors and recipients with the same or similar allotypes. The most important types are Gm (heavy chain) and km (light chain). It can be used in resolving paternity disputes.

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Idiotopes
An idiotope is the unique set of antigenic determinants (epitopes) of the variable portion of an antibody.[1] In some cases it can be the actual antigen-binding site, and in some cases it may comprise variable region sequences outside of the antigen-binding site on the antibody itself. Thus each antibody would have multiple idiotopes; and the set of these individual idiotopes is termed the idiotype of the antibody. Idiotopes contrast with allotopes, which are non-varying structures on the Fc receptor. If a separate antibody is produced that has specific binding capabilities to an idiotope of the previously described antibody, it is said to be an "anti-idiotypic antibody". If such is the case, the anti-idiotypic antibodies will be able to bind to the B lymphocyte receptor for the original antigen and inhibit the immune response to that antigen. This type of regulation was proposed by Niels Jerne in 1974. He termed it the "Network Hypothesis". This type of B lymphocyte regulation may be partially responsible for preventing an immune response from getting out of control, which would elicit damage to host tissue or even cause an autoimmune diseased state. Because of the resemblance of anti-idiotypic antibodies to the original antigen, vaccine studies have been performed. These types of vaccines are called "idiotypic vaccines". None are produced commercially to date.

Idiotype

The idiotype is based upon the variable region (labeled VL and VH in the diagram.) In immunology, an idiotype is a shared characteristic between a group of immunoglobulin or T cell receptor (TCR) molecules based upon the antigen binding specificity and therefore structure of their variable region. The word idiotype comes from two Greek roots, idio meaning 'private, distinctive, peculiar' and typos meaning 'mark.' Thus idiotype describes the distinctive sequence and region that makes any immunoglobing/TCR unique from others of the same type which is its variable region. The variable region of antigen receptors of T cells (TCRs) and B cells
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(immunoglobulins) contains a complementarity determining region (CDR) with a unique amino acid structure that determines the antigen specificity of the receptor. The structure formed by the CDR is known as the idiotope. Immunoglobulins or TCRs with a shared idiotope are the same idiotype. Antibody idiotype is determined by

Gene rearrangement Junctional diversity P-nucleotides (palindromic nucleotides at sites of single-strand breaks) N-nucleotides Somatic hypermutations

The term idiotype is sometimes used to describe the collection of multiple idiotopes, and therefore overall antigen binding capacity, possessed by an antibody. The word idiotype became influential in immunology when Niels Jerne formulated his immune network theory. Jerne was awarded the Nobel Prize for Medicine or Physiology in 1984 largely for being the father of immune network theory. He defined idiotype as the set of epitopes on the V region of an antibody molecule, where epitope means an antigenic determinant. He also defined the "paratope" to be that part of an antibody variable region that binds to an antigen. The best developed version of immune network theory is called the symmetrical network theory, in which the distinction between idiotype and paratope plays no role.

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