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Janeway CA Jr, Travers P, Walport M, et al. Immunobiology: The Immune System in Health and Disease. 5th edition. New York: Garland Science; 2001.

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Immunobiology: The Immune System in Health and Disease. 5th edition.

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Appendix I. Immunologists' Toolbox


Natural adaptive immune responses are normally directed at antigens borne by pathogenic microorganisms. The immune system can, however, also be induced to respond to simple nonliving antigens, and experimental immunologists have focused on the responses to these simple antigens in developing our understanding of the immune response. The deliberate induction of an immune response is known as immunization. Experimental immunizations are routinely carried out by injecting the test antigen into the animal or human subject. The route, dose, and form in which antigen is administered can profoundly affect whether a response occurs and the type of response that is produced, and are considered in Sections A-1A-4. The induction of protective immune responses against common microbial pathogens in humans is often called vaccination, although this term is correctly only applied to the induction of immune responses against smallpox by immunizing with the cross-reactive cowpox virus, vaccinia (see Chapter 14).

To determine whether an immune response has occurred and to follow its course, the immunized individual is monitored for the appearance of immune reactants directed at the specific antigen. Immune responses to most antigens elicit the production of both specific antibodies and specific effector T cells. Monitoring the antibody response usually involves the analysis of relatively crude preparations of antiserum (plural: antisera). The serum is the fluid phase of clotted blood, which, if taken from an immunized individual, is called antiserum because it contains specific antibodies against the immunizing antigen as well as other soluble serum proteins. To study immune responses mediated by T cells, blood lymphocytes or cells from lymphoid organs such as the spleen are tested; T-cell responses are more commonly studied in experimental animals than in humans.

Any substance that can elicit an immune response is said to be immunogenic and is called an immunogen. There is a clear operational distinction between an immunogen and an antigen. An antigen is defined as any sustance that can bind to a specific antibody. All antigens therefore have the potential to elicit specific antibodies, but some need to be attached to an immunogen in order to do so. This means that although all immunogens are antigens, not all antigens are immunogenic. The antigens used most frequently in experimental immunology are proteins, and antibodies to proteins are of enormous utility in experimental biology and medicine. Purified proteins are, however, not always highly immunogenic and to provoke an immune response have to be administered with an adjuvant (see Section A-4). Carbohydrates, nucleic acids, and other types of molecule are all potential antigens, but will often only induce an immune response if attached to a protein carrier. Thus, the immunogenicity of protein antigens determines the outcome of virtually every immune response.

Antisera generated by immunization with even the simplest antigen will contain many different antibody molecules that bind to the immunogen in slightly different ways. Some of the antibodies in an antiserum are cross-reactive. A cross-reaction is defined as the binding of an antibody to an antigen other than the immunogen; most antibodies cross-react with closely related antigens but, on occasion, some bind antigens having no clear relationship to the immunogen. These cross-reacting antibodies can create problems when the antiserum is used to detect a specific antigen. They can be removed from an antiserum by absorption with the cross-reactive antigen, leaving behind the antibodies that bind only to the immunogen. Absorption can be performed by affinity chromatography using immobilized antigen, a technique that is also used for purification of antibodies or antigens (see Section A-5). Most problems of cross-reactivity can be avoided, however, by making monoclonal antibodies (see Section A-12).

Although almost any structure can be recognized by antibody as an antigen, usually only proteins elicit fully developed adaptive immune responses. This is because proteins have the ability to engage T cells, which contribute to inducing most antibody responses and are required for immunological memory. Proteins engage T cells because the T cells recognize antigens as peptide fragments of proteins bound to major histocompatibility complex (MHC) molecules (see Section 3-11). An adaptive immune response that includes immunological memory can be induced by nonpeptide antigens only when they are attached to a protein carrier that can engage the necessary T cells (see Section 9-2 and Fig. 9.4).

Immunological memory is produced as a result of the initial or primary immunization, which evokes the primary immune response. This is also known as priming, as the animal or person is now ‘primed’ like a pump to mount a more potent response to subsequent challenges with the same antigen. The response to each immunization is increasingly intense, so that secondary, tertiary, and subsequent responses are of increasing magnitude (Fig. A.1). Repetitive challenge with antigen to achieve a heightened state of immunity is known as hyperimmunization.

Figure A.1. The dose of antigen used in an initial immunization affects the primary and secondary antibody response.

Figure A.1

The dose of antigen used in an initial immunization affects the primary and secondary antibody response. The typical antigen dose-response curve shown here illustrates the influence of dose on both a primary antibody response (amounts of antibody produced expressed (more...)

Certain properties of a protein that favor the priming of an adaptive immune response have been defined by studying antibody responses to simple natural proteins like hen egg-white lysozyme and to synthetic polypeptide antigens (Fig. A.2). The larger and more complex a protein, and the more distant its relationship to self proteins, the more likely it is to elicit a response. This is because such responses depend on the proteins being degraded into peptides that can bind to MHC molecules, and on the subsequent recognition of these peptide:MHC complexes by T cells. The larger and more distinct the protein antigen, the more likely it is to contain such peptides. Particulate or aggregated antigens are more immunogenic because they are taken up more efficiently by the specialized antigen-presenting cells responsible for initiating a response. Indeed small soluble proteins are unable to induce a response unless they are made to aggregate in some way. Many vaccines, for example, use aggregated protein antigens to potentiate the immune response.

Figure A.2. Intrinsic properties and extrinsic factors that affect the immunogenicity of proteins.

Figure A.2

Intrinsic properties and extrinsic factors that affect the immunogenicity of proteins.

A-1. Haptens

Small organic molecules of simple structure, such as phenyl arsonates and nitrophenyls, do not provoke antibodies when injected by themselves. However, antibodies can be raised against them if the molecule is attached covalently, by simple chemical reactions, to a protein carrier. Such small molecules were termed haptens (from the Greek haptein, to fasten) by the immunologist Karl Landsteiner, who first studied them in the early 1900s. He found that animals immunized with a hapten-carrier conjugate produced three distinct sets of antibodies (Fig. A.3). One set comprised hapten-specific antibodies that reacted with the same hapten on any carrier, as well as with free hapten. The second set of antibodies was specific for the carrier protein, as shown by their ability to bind both the hapten-modified and unmodified carrier protein. Finally, some antibodies reacted only with the specific conjugate of hapten and carrier used for immunization. Landsteiner studied mainly the antibody response to the hapten, as these small molecules could be synthesized in many closely related forms. He observed that antibodies raised against a particular hapten bind that hapten but, in general, fail to bind even very closely related chemical structures. The binding of haptens by anti-hapten antibodies has played an important part in defining the precision of antigen binding by antibody molecules. Anti-hapten antibodies are also important medically as they mediate allergic reactions to penicillin and other compounds that elicit antibody responses when they attach to self proteins (see Section 12-10).

Figure A.3. Antibodies can be elicited by small chemical groups called haptens only when the hapten is linked to an immunogenic protein carrier.

Figure A.3

Antibodies can be elicited by small chemical groups called haptens only when the hapten is linked to an immunogenic protein carrier. Three types of antibodies are produced. One set (blue) binds the carrier protein alone and is called carrier-specific. (more...)

A-2. Routes of immunization

The route by which antigen is administered affects both the magnitude and the type of response obtained. The most common routes by which antigen is introduced experimentally or as a vaccine into the body are injection into tissue by subcutaneous (s.c.) injection between the epidermis and dermal layers, or by intradermal (i.d.) injection, or intramuscular (i.m.) injection; by intravenous (i.v.) injection or transfusion directly into the bloodstream; into the gastrointestinal tract by oral administration; into the respiratory tract by intranasal (i.n.) administration or inhalation.

Antigens injected subcutaneously generally elicit the strongest responses, most probably because the antigen is taken up by Langerhans' cells and efficiently presented in local lymph nodes, and so this is the method most commonly used when the object of the experiment is to elicit specific antibodies or T cells against a given antigen. Antigens injected or transfused directly into the bloodstream tend to induce immune unresponsiveness or tolerance unless they bind to host cells or are in the form of aggregates that are readily taken up by antigen-presenting cells.

Antigen administration via the gastrointestinal tract is used mostly in the study of allergy. It has distinctive effects, frequently eliciting a local antibody response in the intestinal lamina propria, while producing a systemic state of tolerance that manifests as a diminished response to the same antigen if subsequently administered in immunogenic form elsewhere in the body. This ‘split tolerance’ may be important in avoiding allergy to antigens in food, as the local response prevents food antigens from entering the body, while the inhibition of systemic immunity helps to prevent the formation of IgE antibodies, which are the cause of such allergies (see Chapter 12).

Introduction of antigen into the respiratory tract is also used mainly in the study of allergy. Protein antigens that enter the body through the respiratory epithelium tend to elicit allergic responses, for reasons that are not clear.

A-3. Effects of antigen dose

The magnitude of the immune response depends on the dose of immunogen administered. Below a certain threshold dose, most proteins do not elicit any immune response. Above the threshold dose, there is a gradual increase in the response as the dose of antigen is increased, until a broad plateau level is reached, followed by a decline at very high antigen doses (see Fig. A.1). As most infectious agents enter the body in small numbers, immune responses are generally elicited only by pathogens that multiply to a level sufficient to exceed the antigen dose threshold. The broad response optimum allows the system to respond to infectious agents across a wide range of doses. At very high antigen doses the immune response is inhibited, which may be important in maintaining tolerance to abundant self proteins such as plasma proteins. In general, secondary and subsequent immune responses occur at lower antigen doses and achieve higher plateau values, which is a sign of immunological memory. However, under some conditions, very low or very high doses of antigen may induce specific unresponsive states, known respectively as acquired low-zone or high-zone tolerance.

A-4. Adjuvants

Most proteins are poorly immunogenic or nonimmunogenic when administered by themselves. Strong adaptive immune responses to protein antigens almost always require that the antigen be injected in a mixture known as an adjuvant. An adjuvant is any substance that enhances the immunogenicity of substances mixed with it. Adjuvants differ from protein carriers in that they do not form stable linkages with the immunogen. Furthermore, adjuvants are needed primarily for initial immunizations, whereas carriers are required to elicit not only primary but also subsequent responses to haptens. Commonly used adjuvants are listed in Fig. A.4.

Figure A.4. Common adjuvants and their use.

Figure A.4

Common adjuvants and their use. Adjuvants are mixed with the antigen and usually render it particulate, which helps to retain the antigen in the body and promotes uptake by macrophages. Most adjuvants include bacteria or bacterial components that stimulate (more...)

Adjuvants can enhance immunogenicity in two different ways. First, adjuvants convert soluble protein antigens into particulate material, which is more readily ingested by antigen-presenting cells such as macrophages. For example, the antigen can be adsorbed on particles of the adjuvant (such as alum), made particulate by emulsification in mineral oils, or incorporated into the colloidal particles of ISCOMs. This enhances immunogenicity somewhat, but such adjuvants are relatively weak unless they also contain bacteria or bacterial products. Such microbial constituents are the second means by which adjuvants enhance immunogenicity, and although their exact contribution to enhancing immunogenicity is unknown, they are clearly the more important component of an adjuvant. Microbial products may signal macrophages or dendritic cells to become more effective antigen-presenting cells (see Chapter 2). One of their effects is to induce the production of inflammatory cytokines and potent local inflammatory responses; this effect is probably intrinsic to their activity in enhancing responses, but precludes their use in humans.

Nevertheless, some human vaccines contain microbial antigens that can also act as effective adjuvants. For example, purified constituents of the bacterium Bordetella pertussis, which is the causal agent of whooping cough, are used as both antigen and adjuvant in the triplex DPT (diphtheria, pertussis, tetanus) vaccine against these diseases.

The detection, measurement, and characterization of antibodies and their use as research and diagnostic tools

B cells contribute to adaptive immunity by secreting antibodies, and the response of B cells to an injected immunogen is usually measured by analyzing the specific antibody produced in a humoral immune response. This is most conveniently achieved by assaying the antibody that accumulates in the fluid phase of the blood or plasma; such antibodies are known as circulating antibodies. Circulating antibody is usually measured by collecting blood, allowing it to clot, and then isolating the serum from the clotted blood. The amount and characteristics of the antibody in the resulting antiserum are then determined using the assays we will describe in Sections A-5A-11.

The most important characteristics of an antibody response are the specificity, amount, isotype or class, and affinity of the antibodies produced. The specificity determines the ability of the antibody to distinguish the immunogen from other antigens. The amount of antibody can be determined in many different ways and is a function of the number of responding B cells, their rate of antibody synthesis, and the persistence of the antibody after production. The persistence of an antibody in the plasma and extracellular fluid bathing the tissues is determined mainly by its isotype (see Sections 4-15 and 9-12); each isotype has a different half-life in vivo. The isotypic composition of an antibody response also determines the biological functions these antibodies can perform and the sites in which antibody will be found. Finally, the strength of binding of the antibody to its antigen in terms of a single antigen-binding site binding to a monovalent antigen is termed its affinity (the total binding strength of a molecule with more than one binding site is called its avidity). Binding strength is important, since the higher the affinity of the antibody for its antigen, the less antibody is required to eliminate the antigen, as antibodies with higher affinity will bind at lower antigen concentrations. All these parameters of the humoral immune response help to determine the capacity of that response to protect the host from infection.

Antibody molecules are highly specific for their corresponding antigen, being able to detect one molecule of a protein antigen out of more than 108 similar molecules. This makes antibodies both easy to isolate and study, and invaluable as probes of biological processes. Whereas standard chemistry would have great difficulty in distinguishing between two such closely related proteins as human and pig insulin, or two such closely related structures as ortho- and para -nitrophenyl, antibodies can be made that discriminate between these two structures absolutely. The value of antibodies as molecular probes has stimulated the development of many sensitive and highly specific techniques to measure their presence, to determine their specificity and affinity for a range of antigens, and to ascertain their functional capabilities. Many standard techniques used throughout biology exploit the specificity and stability of antigen binding by antibodies. Comprehensive guides to the conduct of these antibody assays are available in many books on immunological methodology; we will illustrate here only the most important techniques, especially those used in studying the immune response itself.

Some assays for antibody measure the direct binding of the antibody to its antigen. Such assays are based on primary interactions. Others determine the amount of antibody present by the changes it induces in the physical state of the antigen, such as the precipitation of soluble antigen or the clumping of antigenic particles; these are called secondary interactions. Both types of assay can be used to measure the amount and specificity of the antibodies produced after immunization, and both can be applied to a wide range of other biological questions.

As assays for antibody were originally conducted with antisera from immune individuals, they are commonly referred to as serological assays, and the use of antibodies is often called serology. The amount of antibody is usually determined by antigen-binding assays after titration of the antiserum by serial dilution, and the point at which binding falls to 50% of the maximum is usually referred to as the titer of an antiserum.

A-5. Affinity chromatography

Specific antibody can be isolated from an antiserum by affinity chromatography, which exploits the specific binding of antibody to antigen held on a solid matrix (Fig. A.5). Antigen is bound covalently to small, chemically reactive beads, which are loaded into a column, and the antiserum is allowed to pass over the beads. The specific antibodies bind, while all the other proteins in the serum, including antibodies to other substances, can be washed away. The specific antibodies are then eluted, typically by lowering the pH to 2.5 or raising it to greater than 11. Antibodies bind stably under physiological conditions of salt concentration, temperature, and pH, but the binding is reversible as the bonds are noncovalent. Affinity chromatography can also be used to purify antigens from complex mixtures by using beads coated with specific antibody. The technique is known as affinity chromatography because it separates molecules on the basis of their affinity for one another.

Figure A.5. Affinity chromatography uses antigen-antibody binding to purify antigens or antibodies.

Figure A.5

Affinity chromatography uses antigen-antibody binding to purify antigens or antibodies. To purify a specific antigen from a complex mixture of molecules, a monoclonal antibody is attached to an insoluble matrix, such as chromatography beads, and the mixture (more...)

A-6. Radioimmunoassay (RIA), enzyme-linked immunosorbent assay (ELISA), and competitive inhibition assay

Radioimmunoassay (RIA) and enzyme-linked immunosorbent assay (ELISA) are direct binding assays for antibody (or antigen) and both work on the same principle, but the means of detecting specific binding is different. Radioimmunoassays are commonly used to measure the levels of hormones in blood and tissue fluids, while ELISA assays are frequently used in viral diagnostics, for example in detecting cases of HIV infection. For both these methods one needs a pure preparation of a known antigen or antibody, or both, in order to standardize the assay. We will describe the assay with a sample of pure antibody, which is the more usual case, but the principle is similar if pure antigen is used instead. In RIA for an antigen, pure antibody against that antigen is radioactively labeled, usually with 125I; for the ELISA, an enzyme is linked chemically to the antibody. The unlabeled component, which in this case would be antigen, is attached to a solid support, such as the wells of a plastic multiwell plate, which will adsorb a certain amount of any protein.

The labeled antibody is allowed to bind to the unlabeled antigen, under conditions where nonspecific adsorption is blocked, and any unbound antibody and other proteins are washed away. Antibody binding in RIA is measured directly in terms of the amount of radioactivity retained by the coated wells, whereas in ELISA, binding is detected by a reaction that converts a colorless substrate into a colored reaction product (Fig. A.6). The color change can be read directly in the reaction tray, making data collection very easy, and ELISA also avoids the hazards of radioactivity. This makes ELISA the preferred method for most direct-binding assays. Labeled anti-immunoglobulin antibodies (see Section A-10) can also be used in RIA or ELISA to detect binding of unlabeled antibody to unlabeled antigen-coated plates. In this case, the labeled anti-immunoglobulin antibody is used in what is termed a ‘second layer.’ The use of such a second layer also amplifies the signal, as at least two molecules of the labeled anti-immunoglobulin antibody are able to bind to each unlabeled antibody. RIA and ELISA can also be carried out with unlabeled antibody stuck to the plates and labeled antigen added.

Figure A.6. The principle of the enzyme-linked immunosorbent assay (ELISA).

Figure A.6

The principle of the enzyme-linked immunosorbent assay (ELISA). To detect antigen A, purified antibody specific for antigen A is linked chemically to an enzyme. The samples to be tested are coated onto the surface of plastic wells to which they bind nonspecifically; (more...)

A modification of ELISA known as a capture or sandwich ELISA (or more generally as an antigen-capture assay) can be used to detect secreted products such as cytokines. Rather than the antigen being directly attached to a plastic plate, antigen-specific antibodies are bound to the plate. These are able to bind antigen with high affinity, and thus concentrate it on the surface of the plate, even with antigens that are present in very low concentrations in the initial mixture. A separate labeled antibody that recognizes a different epitope to the immobilized first antibody is then used to detect the bound antigen.

These assays illustrate two crucial aspects of all serological assays. First, at least one of the reagents must be available in a pure, detectable form in order to obtain quantitative information. Second, there must be a means of separating the bound fraction of the labeled reagent from the unbound, free fraction so that the percentage of specific binding can be determined. Normally, this separation is achieved by having the unlabeled partner trapped on a solid support. Labeled molecules that do not bind can then be washed away, leaving just the labeled partner that has bound. In Fig. A.6, the unlabeled antigen is attached to the well and the labeled antibody is trapped by binding to it. The separation of bound from free is an essential step in every assay that uses antibodies.

RIA and ELISA do not allow one to measure directly the amount of antigen or antibody in a sample of unknown composition, as both depend on the binding of a pure labeled antigen or antibody. There are various ways around this problem, one of which is to use a competitive inhibition assay, as shown in Fig. A.7. In this type of assay, the presence and amount of a particular antigen in an unknown sample is determined by its ability to compete with a labeled reference antigen for binding to an antibody attached to a plastic well. A standard curve is first constructed by adding varying amounts of a known, unlabeled standard preparation; the assay can then measure the amount of antigen in unknown samples by comparison with the standard. The competitive binding assay can also be used for measuring antibody in a sample of unknown composition by attaching the appropriate antigen to the plate and measuring the ability of the test sample to inhibit the binding of a labeled specific antibody.

Figure A.7. Competitive inhibition assay for antigen in unknown samples.

Figure A.7

Competitive inhibition assay for antigen in unknown samples. A fixed amount of unlabeled antibody is attached to a set of wells, and a standard reference preparation of a labeled antigen is bound to it. Unlabeled standard or test samples are then added (more...)

A-7. Hemagglutination and blood typing

The direct measurement of antibody binding to antigen is used in most quantitative serological assays. However, some important assays are based on the ability of antibody binding to alter the physical state of the antigen it binds to. These secondary interactions can be detected in a variety of ways. For instance, when the antigen is displayed on the surface of a large particle such as a bacterium, antibodies can cause the bacteria to clump or agglutinate. The same principle applies to the reactions used in blood typing, only here the target antigens are on the surface of red blood cells and the clumping reaction caused by antibodies against them is called hemagglutination (from the Greek haima, blood).

Hemagglutination is used to determine the ABO blood group of blood donors and transfusion recipients. Clumping or agglutination is induced by antibodies or agglutinins called anti-A or anti-B that bind to the A or B blood-group substances, respectively (Fig. A.8). These blood-group antigens are arrayed in many copies on the surface of the red blood cell, allowing the cells to agglutinate when cross-linked by antibodies. Because hemagglutination involves the cross-linking of blood cells by the simultaneous binding of antibody molecules to identical antigens on different cells, this reaction demonstrates that each antibody molecule has at least two identical antigen-binding sites.

Figure A.8. Hemagglutination is used to type blood groups and match compatible donors and recipients for blood transfusion.

Figure A.8

Hemagglutination is used to type blood groups and match compatible donors and recipients for blood transfusion. Common gut bacteria bear antigens that are similar or identical to blood-group antigens, and these stimulate the formation of antibodies to these (more...)

A-8. Precipitin reaction

When sufficient quantities of antibody are mixed with soluble macromolecular antigens, a visible precipitate consisting of large aggregates of antigen cross-linked by antibody molecules can form. The amount of precipitate depends on the amounts of antigen and antibody, and on the ratio between them (Fig. A.9). This precipitin reaction provided the first quantitative assay for antibody, but is now seldom used in immunology. However, it is important to understand the interaction of antigen with antibody that leads to this reaction, as the production of antigen:antibody complexes, also known as immune complexes, in vivo occurs in almost all immune responses and occasionally can cause significant pathology (see Chapters 12 and 13).

Figure A.9. Antibody can precipitate soluble antigen.

Figure A.9

Antibody can precipitate soluble antigen. Analysis of the precipitate can generate a precipitin curve. Different amounts of antigen are added to a fixed amount of antibody, and precipitates form by antibody cross-linking of antigen molecules. The precipitate (more...)

In the precipitin reaction, various amounts of soluble antigen are added to a fixed amount of serum containing antibody. As the amount of antigen added increases, the amount of precipitate generated also increases up to a maximum and then declines (see Fig. A.9). When small amounts of antigen are added, antigen:antibody complexes are formed under conditions of antibody excess so that each molecule of antigen is bound by antibody and cross-linked to other molecules of antigen. When large amounts of antigen are added, only small antigen:antibody complexes can form and these are often soluble in this zone of antigen excess. Between these two zones, all of the antigen and antibody is found in the precipitate, generating a zone of equivalence. At equivalence, very large lattices of antigen and antibody are formed by cross-linking. While all antigen:antibody complexes can potentially produce disease, the small, soluble immune complexes formed in the zone of antigen excess may persist and cause pathology in vivo.

The precipitin reaction is affected by the number of binding sites that each antibody has for antigen, and by the maximum number of antibodies that can be bound by an antigen molecule or particle at any one time. These quantities are defined as the valence of the antibody and the valence of the antigen: the valence of both the antibodies and the antigen must be two or greater before any precipitation can occur. The valence of an antibody depends on its structural class (see Section 4-19).

Antigen will be precipitated only if it has several antibody-binding sites. This condition is usually satisfied in macromolecular antigens, which have a complex surface with binding sites for several different antibodies. The site on an antigen to which each distinct antibody molecule binds is called an antigenic determinant or an epitope. Steric considerations limit the number of distinct antibody molecules that can bind to a single antigen molecule at any one time however, because antibody molecules binding to epitopes that partially overlap will compete for binding. For this reason, the valence of an antigen is almost always less than the number of epitopes on the antigen (Fig. A.10).

Figure A.10. Different antibodies bind to distinct epitopes on an antigen molecule.

Figure A.10

Different antibodies bind to distinct epitopes on an antigen molecule. The surface of an antigen possesses many potential antigenic determinants or epitopes, distinct sites to which an antibody can bind. The number of antibody molecules that can bind (more...)

A-9. Equilibrium dialysis: measurement of antibody affinity and avidity

The affinity of an antibody is the strength of binding of a monovalent ligand to a single antigen-binding site on the antibody. The affinity of an antibody that binds small antigens, such as haptens, that can diffuse freely across a dialysis membrane can be determined directly by the technique of equilibrium dialysis. A known amount of antibody, whose molecules are too large to cross a dialysis membrane, is placed in a dialysis bag and offered various amounts of antigen. Molecules of antigen that bind to the antibody are no longer free to diffuse across the dialysis membrane, so only the unbound molecules of antigen equilibrate across it. By measuring the concentration of antigen inside the bag and in the surrounding fluid, one can determine the amount of the antigen that is bound as well as the amount that is free when equilibrium has been achieved. Given that the amount of antibody present is known, the affinity of the antibody and the number of specific binding sites for the antigen per molecule of antibody can be determined from this information. The data are usually analyzed using Scatchard analysis (Fig. A.11); such analyses were used to demonstrate that a molecule of IgG antibody has two identical antigen-binding sites.

Figure A.11. The affinity and valence of an antibody can be determined by equilibrium dialysis.

Figure A.11

The affinity and valence of an antibody can be determined by equilibrium dialysis. A known amount of antibody is placed in the bottom half of a dialysis chamber and exposed to different amounts of a diffusible monovalent antigen, such as a hapten. At (more...)

Whereas affinity measures the strength of binding of an antigenic determinant to a single antigen-binding site, an antibody reacting with an antigen that has multiple identical epitopes or with the surface of a pathogen will often bind the same molecule or particle with both of its antigen-binding sites. This increases the apparent strength of binding, since both binding sites must release at the same time in order for the two molecules to dissociate. This is often referred to as cooperativity in binding, but it should not be confused with the cooperative binding found in a protein such as hemoglobin, in which binding of ligand at one site enhances the affinity of a second binding site for its ligand. The overall strength of binding of an antibody molecule to an antigen or particle is called its avidity (Fig. A.12). For IgG antibodies, bivalent binding can significantly increase avidity; in IgM antibodies, which have ten identical antigen-binding sites, the affinity of each site for a monovalent antigen is usually quite low, but the avidity of binding of the whole antibody to a surface such as a bacterium that displays multiple identical epitopes can be very high.

Figure A.12. The avidity of an antibody is its strength of binding to intact antigen.

Figure A.12

The avidity of an antibody is its strength of binding to intact antigen. When an IgG antibody binds a ligand with multiple identical epitopes, both binding sites can bind the same molecule or particle. The overall strength of binding, called avidity, (more...)

A-10. Anti-immunoglobulin antibodies

A general approach to the detection of bound antibody that avoids the need to label each preparation of antibody molecules is to detect bound, unlabeled antibody with a labeled antibody specific for immunoglobulins themselves. Immunoglobulins, like other proteins, are immunogenic when used to immunize individuals of another species. The majority of anti-immunoglobulin antibodies raised in this way recognize conserved features shared by all immunoglobulin molecules of the immunizing species. Others can be specific for immunoglobulin chains, heavy or light chains, for example, or for individual isotypes. Antibodies raised by immunization of goats with mouse IgG are commonly used in experimental immunology. Such goat anti-mouse IgG antibodies can be purified using affinity chromatography, then labeled and used as a general probe for bound IgG antibodies. Anti-immunoglobulin antisera have found many uses in clinical medicine and biological research since their introduction. Fluorescently labeled anti-immunoglobulin antibodies are now widely used both in immunology and other areas of biology as secondary reagents for detecting specific antibodies bound, for example, to cell structures (see Sections A-14 and A-16). Labeled anti-immunoglobulin antibodies can also be used in radioimmunoassay or ELISA (see Section A-6) to detect binding of unlabeled antibody to antigen-coated plates.

Antibodies specific for individual immunoglobulin isotypes can be produced by immunizing an animal of a different species with a pure preparation of one isotype and then removing those antibodies that cross-react with immunoglobulins of other isotypes by using affinity chromatography (see Section A-5). Anti-isotype antibodies can be used to measure how much antibody of a particular isotype in an antiserum reacts with a given antigen. This reaction is particularly important for detecting small amounts of specific antibodies of the IgE isotype, which are responsible for most allergies. The presence in an individual's serum of IgE binding to an antigen correlates with allergic reactions to that antigen.

An alternative approach to detecting bound antibodies exploits bacterial proteins that bind to immunoglobulins with high affinity and specificity. One of these, Protein A from the bacterium Staphylococcus aureus, has been exploited widely in immunology for the affinity purification of immunoglobulin and for the detection of bound antibody. The use of standard second reagents such as labeled anti-immunoglobulin antibodies or Protein A to detect antibody bound specifically to its antigen allows great savings in reagent labeling costs, and also provides a standard detection system so that results in different assays can be compared directly.

A-11. Coombs tests and the detection of Rhesus incompatibility

These tests use anti-immunoglobulin antibodies (see Section A-10) to detect the antibodies that cause hemolytic disease of the newborn, or erythroblastosis fetalis. Anti-immunoglobulin antibodies were first developed by Robin Coombs and the test for this disease is still called the Coombs test. Hemolytic disease of the newborn occurs when a mother makes IgG antibodies specific for the Rhesus or Rh blood group antigen expressed on the red blood cells of her fetus. Rh-negative mothers make these antibodies when they are exposed to Rh-positive fetal red blood cells bearing the paternally inherited Rh antigen. Maternal IgG antibodies are normally transported across the placenta to the fetus, where they protect the newborn infant against infection. However, IgG anti-Rh antibodies coat the fetal red blood cells, which are then destroyed by phagocytic cells in the liver, causing a hemolytic anemia in the fetus and newborn infant.

Since the Rh antigens are widely spaced on the red blood cell surface, the IgG anti-Rh antibodies cannot fix complement and cause lysis of red blood cells in vitro. Furthermore, for reasons that are not fully understood, antibodies to Rh blood group antigens do not agglutinate red blood cells as do antibodies to the ABO blood group antigens. Thus, detecting these antibodies was difficult until anti-human immunoglobulin antibodies were developed. With these, maternal IgG antibodies bound to the fetal red blood cells can be detected after washing the cells to remove unbound immunoglobulin that is present in the fetal serum. Adding anti-human immunoglobulin antibodies to the washed fetal red blood cells agglutinates any cells to which maternal antibodies are bound. This is the direct Coombs test (Fig. A.13), so called because it directly detects antibody bound to the surface of the fetal red blood cells. An indirect Coombs test is used to detect nonagglutinating anti-Rh antibody in maternal serum; the serum is first incubated with Rh-positive red blood cells, which bind the anti-Rh antibody, after which the antibody-coated cells are washed to remove unbound immunoglobulin and are then agglutinated with anti-immunoglobulin antibody (see Fig. A.13). The indirect Coombs test allows Rh incompatibilities that might lead to hemolytic disease of the newborn to be detected, and this knowledge allows the disease to be prevented (see Section 10-25). The Coombs test is also commonly used to detect antibodies to drugs that bind to red blood cells and cause hemolytic anemia.

Figure A.13. The Coombs direct and indirect anti-globulin tests for antibody to red blood cell antigens.

Figure A.13

The Coombs direct and indirect anti-globulin tests for antibody to red blood cell antigens. A Rh- mother of a Rh+ fetus can become immunized to fetal red blood cells that enter the maternal circulation at the time of delivery. In a subsequent pregnancy (more...)

A-12. Monoclonal antibodies

The antibodies generated in a natural immune response or after immunization in the laboratory are a mixture of molecules of different specificities and affinities. Some of this heterogeneity results from the production of antibodies that bind to different epitopes on the immunizing antigen, but even antibodies directed at a single antigenic determinant such as a hapten can be markedly heterogeneous, as shown by isoelectric focusing. In this technique, proteins are separated on the basis of their isoelectric point, the pH at which their net charge is zero. By electrophoresing proteins in a pH gradient for long enough, each molecule migrates along the pH gradient until it reaches the pH at which it is neutral and is thus concentrated (focused) at that point. When antiserum containing anti-hapten antibodies is treated in this way and then transferred to a solid support such as nitrocellulose paper, the anti-hapten antibodies can be detected by their ability to bind labeled hapten. The binding of antibodies of various isoelectric points to the hapten shows that even antibodies that bind the same antigenic determinant can be heterogeneous.

Antisera are valuable for many biological purposes but they have certain inherent disadvantages that relate to the heterogeneity of the antibodies they contain. First, each antiserum is different from all other antisera, even if raised in a genetically identical animal by using the identical preparation of antigen and the same immunization protocol. Second, antisera can be produced in only limited volumes, and thus it is impossible to use the identical serological reagent in a long or complex series of experiments or clinical tests. Finally, even antibodies purified by affinity chromatography (see Section A-5) may include minor populations of antibodies that give unexpected cross-reactions, which confound the analysis of experiments. To avoid these problems, and to harness the full potential of antibodies, it was necessary to develop a way of making an unlimited supply of antibody molecules of homogeneous structure and known specificity. This has been achieved through the production of monoclonal antibodies from cultures of hybrid antibody-forming cells or, more recently, by genetic engineering.

Biochemists in search of a homogeneous preparation of antibody that they could subject to detailed chemical analysis turned early to proteins produced by patients with multiple myeloma, a common tumor of plasma cells. It was known that antibodies are normally produced by plasma cells and since this disease is associated with the presence of large amounts of a homogeneous gamma globulin called a myeloma protein in the patient's serum, it seemed likely that myeloma proteins would serve as models for normal antibody molecules. Thus, much of the early knowledge of antibody structure came from studies on myeloma proteins. These studies showed that monoclonal antibodies could be obtained from immortalized plasma cells. However, the antigen specificity of most myeloma proteins was unknown, which limited their usefulness as objects of study or as immunological tools.

This problem was solved by Georges Köhler and Cesar Milstein, who devised a technique for producing a homogeneous population of antibodies of known antigenic specificity. They did this by fusing spleen cells from an immunized mouse to cells of a mouse myeloma to produce hybrid cells that both proliferated indefinitely and secreted antibody specific for the antigen used to immunize the spleen cell donor. The spleen cell provides the ability to make specific antibody, while the myeloma cell provides the ability to grow indefinitely in culture and secrete immunoglobulin continuously. By using a myeloma cell partner that produces no antibody proteins itself, the antibody produced by the hybrid cells comes only from the immune spleen cell partner. After fusion, the hybrid cells are selected using drugs that kill the myeloma parental cell, while the unfused parental spleen cells have a limited life-span and soon die, so that only hybrid myeloma cell lines or hybridomas survive. Those hybridomas producing antibody of the desired specificity are then identified and cloned by regrowing the cultures from single cells (Fig. A.14). Since each hybridoma is a clone derived from fusion with a single B cell, all the antibody molecules it produces are identical in structure, including their antigen-binding site and isotype. Such antibodies are called monoclonal antibodies. This technology has revolutionized the use of antibodies by providing a limitless supply of antibody of a single and known specificity. Monoclonal antibodies are now used in most serological assays, as diagnostic probes, and as therapeutic agents. So far, however, only mouse monoclonals are routinely produced and efforts to use this same approach to make human monoclonal antibodies have met with very limited success.

Figure A.14. The production of monoclonal antibodies.

Figure A.14

The production of monoclonal antibodies. Mice are immunized with antigen A and given an intravenous booster immunization three days before they are killed, in order to produce a large population of spleen cells secreting specific antibody. Spleen cells (more...)

A-13. Phage display libraries for antibody V-region production

This is a technique for producing antibody-like molecules. Gene segments encoding the antigen-binding variable or V domains of antibodies are fused to genes encoding the coat protein of a bacteriophage. Bacteriophage containing such gene fusions are used to infect bacteria, and the resulting phage particles have coats that express the antibody-like fusion protein, with the antigen-binding domain displayed on the outside of the bacteriophage. A collection of recombinant phage, each displaying a different antigen-binding domain on its surface, is known as a phage display library. In much the same way that antibodies specific for a particular antigen can be isolated from a complex mixture by affinity chromatography (see Section A-5), phage expressing antigen-binding domains specific for a particular antigen can be isolated by selecting the phage in the library for binding to that antigen. The phage particles that bind are recovered and used to infect fresh bacteria. Each phage isolated in this way will produce a monoclonal antigen-binding particle analogous to a monoclonal antibody (Fig. A.15). The genes encoding the antigen-binding site, which are unique to each phage, can then be recovered from the phage DNA and used to construct genes for a complete antibody molecule by joining them to parts of immunoglobulin genes that encode the invariant parts of an antibody. When these reconstructed antibody genes are introduced into a suitable host cell line, such as the nonantibody-producing myeloma cells used for hybridomas, the transfected cells can secrete antibodies with all the desirable characteristics of monoclonal antibodies produced from hybridomas.

Figure A.15. The production of antibodies by genetic engineering.

Figure A.15

The production of antibodies by genetic engineering. Short primers to consensus sequences in heavy- and light-chain variable (V) regions of immunoglobulin genes are used to generate a library of heavy- and light-chain V-region DNAs by the polymerase chain (more...)

In much the same way that a collection of phage can display a wide variety of potential antigen-binding sites, the phage can also be engineered to display a wide variety of antigens; such a library is known as an antigen display library. In such cases, the antigens displayed are often short peptides encoded by chemically synthesized DNA sequences that have mixtures of all four nucleotides in some positions, so that all possible amino acids are incorporated. It is not usual for every position in a peptide to be allowed to vary in this way, since the number of different peptide sequences increases dramatically with the number of variable positions; there are over 2 × 1010 possible sequences of eight amino acids.

A-14. Immunofluorescence microscopy

Since antibodies bind stably and specifically to their corresponding antigen, they are invaluable as probes for identifying a particular molecule in cells, tissues, or biological fluids. Antibody molecules can be used to locate their target molecules accurately in single cells or in tissue sections by a variety of different labeling techniques. When the antibody itself, or the anti-immunoglobulin antibody used to detect it, is labeled with a fluorescent dye the technique is known as immunofluorescence microscopy. As in all serological techniques, the antibody binds stably to its antigen, allowing unbound antibody to be removed by thorough washing. As antibodies to proteins recognize the surface features of the native, folded protein, the native structure of the protein being sought usually needs to be preserved, either by using only the most gentle chemical fixation techniques or by using frozen tissue sections that are fixed only after the antibody reaction has been performed. Some antibodies, however, bind proteins even if they are denatured, and such antibodies will bind specifically even to protein in fixed tissue sections.

The fluorescent dye can be covalently attached directly to the specific antibody, but more commonly, the bound antibody is detected by fluorescent anti-immunoglobulin, a technique known as indirect immunofluorescence. The dyes chosen for immunofluorescence are excited by light of one wavelength, usually blue or green, and emit light of a different wavelength in the visible spectrum. The most common fluorescent dyes are fluorescein, which emits green light, Texas Red and Peridinin chlorophyll protein (PerCP), which emit red light, and rhodamine and phycoerythrin (PE) which emit orange/red light (Fig. A.16). By using selective filters, only the light coming from the dye or fluorochrome used is detected in the fluorescence microscope (Fig. A.17). Although Albert Coons first devised this technique to identify the plasma cell as the source of antibody, it can be used to detect the distribution of any protein. By attaching different dyes to different antibodies, the distribution of two or more molecules can be determined in the same cell or tissue section (see Fig. A.17).

Figure A.16. Excitation and emission wavelengths for common fluorochromes.

Figure A.16

Excitation and emission wavelengths for common fluorochromes.

Figure A.17. Immunofluorescence microscopy.

Figure A.17

Immunofluorescence microscopy. Antibodies labeled with a fluorescent dye such as fluorescein (green triangle) are used to reveal the presence of their corresponding antigens in cells or tissues. The stained cells are examined in a microscope that exposes (more...)

The recent development of the confocal fluorescent microscope, which uses computer-aided techniques to produce an ultrathin optical section of a cell or tissue, gives very high resolution immunofluorescence microscopy without the need for elaborate sample preparation. The resolution of the confocal microscope can be further increased using low-intensity illumination so that two photons are required to excite the fluorochrome. A pulsed laser beam is used, and only when it is focused into the focal plane of the microscope is the intensity sufficient to excite fluorescence. In this way the fluorescence emission itself can be restricted to the optical section.

One important development in the area of microscopy has been the use of time-lapse video microscopy, in which sensitive digital video cameras record the movement of fluorescently labeled molecules in cell membranes and their redistribution when cells come into contact with each other. Cell-surface molecules can be fluorescently labeled in two main ways. One is by the binding of fluorochrome-labeled Fab fragments of antibodies specific for the protein of interest; the other is by generating a fusion protein, in which the protein of interest has been attached to one of a family of fluorescent proteins obtained from jellyfish. The first of these fluorescent proteins to come into wide use was green fluorescent protein (GFP), isolated from the jellyfish, Aequorea victoria. Other variants of this protein with different properties are now available, and the list of available fluorescent labels now includes red, blue, cyan, or yellow fluorescent proteins. Using cells transfected with the genes encoding such fusion proteins, it is possible to show the redistribution of T-cell receptors, co-receptors, adhesion molecules, and other signaling molecules, such as CD45, that takes place when a T cell makes contact with a target cell. It is clear from these observations that the interface between the T cell and its target does not represent a simple apposition of two cell membranes, but is an actively organized and dynamic structure, often now referred to as the ‘immunological synapse.’

A-15. Immunoelectron microscopy

Antibodies can be used to detect the intracellular location of structures or particular proteins at high resolution by electron microscopy, a technique known as immunoelectron microscopy. Antibodies against the required antigen are labeled with gold particles and then applied to ultrathin sections, which are then examined in the transmission electron microscope. Antibodies labeled with gold particles of different diameters enable two or more proteins to be studied simultaneously (see Fig. 5.8). The difficulty with this technique is in staining the ultrathin section adequately, as few molecules of antigen are present in each section.

A-16. Immunohistochemistry

An alternative to immunofluorescence (see Section A-14) for detecting a protein in tissue sections is immunohistochemistry, in which the specific antibody is chemically coupled to an enzyme that converts a colorless substrate into a colored reaction product in situ. The localized deposition of the colored product where antibody has bound can be directly observed under a light microscope. The antibody binds stably to its antigen, allowing unbound antibody to be removed by thorough washing. This method of detecting bound antibody is analogous to ELISA (see Section A-6) and frequently uses the same coupled enzymes, the difference in detection being primarily that in immunohistochemistry the colored products are insoluble and precipitate at the site where they are formed. Horseradish peroxidase and alkaline phosphatase are the two enzymes most commonly used in these applications. Horseradish peroxidase oxidises the substrate diaminobenzidine to produce a brown precipitate, while alkaline phosphatase can produce red or blue dyes depending on the substrates used; a common substrate is 5-bromo-4-chloro-3-indolyl phosphate plus nitroblue tetrazolium (BCIP/NBT), which gives rise to a dark blue or purple stain. As with immunofluorescence, the native structure of the protein being sought usually needs to be preserved, so that it will be recognized by the antibody. Tissues are fixed by the most gentle chemical fixation techniques or frozen tissue sections are used that are fixed only after the antibody reaction has been performed.

A-17. Immunoprecipitation and co-immunoprecipitation

In order to raise antibodies to membrane proteins and other cellular structures that are difficult to purify, mice are often immunized with whole cells or crude cell extracts. Antibodies to the individual molecules are then obtained by using these immunized mice to produce hybridomas making monoclonal antibodies (see Section A-12) that bind to the cell type used for immunization. To characterize the molecules identified by the antibodies, cells of the same type are labeled with radioisotopes and dissolved in nonionic detergents that disrupt cell membranes but do not interfere with antigen-antibody interactions. This allows the labeled protein to be isolated by binding to the antibody in a reaction known as immunoprecipitation. The antibody is usually attached to a solid support, such as the beads that are used in affinity chromatography (see Section A-5), or to Protein A. Cells can be labeled in two main ways for immunoprecipitation analysis. All the proteins in a cell can be labeled metabolically by growing the cell in radioactive amino acids that are incorporated into cellular protein (Fig. A.18). Alternatively, one can label only the cell-surface proteins by radioiodination under conditions that prevent iodine from crossing the plasma membrane and labeling proteins inside the cell, or by a reaction that labels only membrane proteins with biotin, a small molecule that is detected readily by labeled avidin, a protein found in egg whites that binds biotin with very high affinity.

Figure A.18. Cellular proteins reacting with an antibody can be characterized by immunoprecipitation of labeled cell lysates.

Figure A.18

Cellular proteins reacting with an antibody can be characterized by immunoprecipitation of labeled cell lysates. All actively synthesized cellular proteins can be labeled metabolically by incubating cells with radioactive amino acids (shown here for methionine) (more...)

Once the labeled proteins have been isolated by the antibody, they can be characterized in several ways. The most common is polyacrylamide gel electrophoresis (PAGE) of the proteins after dissociating them from antibody in the strong ionic detergent sodium dodecyl sulfate (SDS), a technique generally abbreviated as SDS-PAGE. SDS binds relatively homogeneously to proteins, conferring a charge that allows the electrophoretic field to drive protein migration through the gel. The rate of migration is controlled mainly by protein size (see Fig. A.18). Proteins of differing charges can be separated using isoelectric focusing (see Section A-12). This technique can be combined with SDS-PAGE in a procedure known as two-dimensional gel electrophoresis. For this, the immunoprecipitated protein is eluted in urea, a nonionic solubilizing agent, and run on an isoelectric focusing gel in a narrow tube of polyacrylamide. This first-dimensional isoelectric focusing gel is then placed across the top of an SDS-PAGE slab gel, which is then run vertically to separate the proteins by molecular weight (Fig. A.19). Two-dimensional gel electrophoresis is a powerful technique that allows many hundreds of proteins in a complex mixture to be distinguished from one another.

Figure A.19. Two-dimensional gel electrophoresis of MHC class II molecules.

Figure A.19

Two-dimensional gel electrophoresis of MHC class II molecules. Proteins in mouse spleen cells have been labeled metabolically (see Fig. A.18), precipitated with a monoclonal antibody against the mouse MHC class II molecule H2-A, and separated by isoelectric (more...)

Immunoprecipitation and the related technique of immunoblotting (see Section A-18) are useful for determining the molecular weight and isoelectric point of a protein as well as its abundance, distribution, and whether, for example, it undergoes changes in molecular weight and isoelectric point as a result of processing within the cell.

A-18. Immunoblotting (Western blotting)

Like immunoprecipitation (see Section A-17), immunoblotting is used for identifying the presence of a given protein in a cell lysate, but it avoids the problem of having to label large quantities of cells with radioisotopes. Unlabeled cells are placed in detergent to solubilize all cell proteins and the lysate is run on SDS-PAGE to separate the proteins (see Section A-17). The size-separated proteins are then transferred from the gel to a stable support such as a nitrocellulose membrane. Specific proteins are detected by treatment with antibodies able to react with SDS-solubilized proteins (mainly those that react with denatured sequences); the bound antibodies are revealed by anti-immunoglobulin antibodies labeled with radioisotopes or an enzyme. The term Western blotting as a synonym for immunoblotting arose because the comparable technique for detecting specific DNA sequences is known as Southern blotting, after Ed Southern who devised it, which in turn provoked the name Northern for blots of size-separated RNA, and Western for blots of size-separated proteins. Western blots have many applications in basic research and clinical diagnosis. They are often used to test sera for the presence of antibodies to specific proteins, for example to detect antibodies to different constituents of the human immunodeficiency virus, HIV (Fig. A.20).

Figure A.20. Western blotting is used to identify antibodies to the human immunodeficiency virus (HIV) in serum from infected individuals.

Figure A.20

Western blotting is used to identify antibodies to the human immunodeficiency virus (HIV) in serum from infected individuals. The virus is dissociated into its constituent proteins by treatment with the detergent SDS, and its proteins are separated using (more...)

Co-immunoprecipitation is an extension of the immunoprecipitation technique which is used to determine whether a given protein interacts physically with another given protein. Cell extracts containing the presumed interaction complex are first immunoprecipitated with antibody against one of the proteins. The material identified by this means is then tested for the presence of the other protein by immunoblotting with a specific antibody.

A-19. Use of antibodies in the isolation and identification of genes and their products

As a first step in isolating the gene that codes for a particular protein, antibodies specific for the protein can be used to isolate the purified protein from cells using affinity chromatography (see Section A-5). Small amounts of amino acid sequence can then be obtained from the protein's amino-terminal end or from peptide fragments generated by proteolysis. The information in these amino acid sequences is used to construct a set of synthetic oligo-nucleotides corresponding to the possible DNA sequences, which are then used as probes to isolate the gene encoding the protein from either a library of DNA sequences complementary to mRNA (a cDNA library) or a genomic DNA library (a library of chromosomal DNA fragments).

An alternative approach to gene identification uses antibodies to identify the protein product of a gene that has been introduced into a cell that does not normally express it. This technique is most commonly applied to the identification of genes encoding cell-surface proteins. A set of cDNA-containing expression vectors is first made from a cDNA library prepared from the total mRNA from a cell type that does express the protein of interest. The vectors are used to transfect a cell type that does not normally express the protein of interest, and the vector drives expression of the cDNA it contains without integrating into the host cell DNA. Cells expressing the required protein after transfection are then isolated by binding to specific antibodies that detect the presence of the protein on the cell surface. The vector containing the required gene can then be recovered from these cells (Fig. A.21).

Figure A.21. The gene encoding a cell-surface molecule can be isolated by expressing it in fibroblasts and detecting its protein product with monoclonal antibodies.

Figure A.21

The gene encoding a cell-surface molecule can be isolated by expressing it in fibroblasts and detecting its protein product with monoclonal antibodies. Total mRNA from a cell line or tissue expressing the protein is isolated, converted into cDNA, and (more...)

The recovered vectors are then introduced into bacterial cells where they replicate rapidly, and these amplified vectors are used in a second round of transfection in mammalian cells. After several cycles of transfection, isolation, and amplification in bacteria, single colonies of bacteria are picked and the vectors prepared from cultures of each colony are used in a final transfection to identify a cloned vector carrying the cDNA of interest, which is then isolated and characterized. This methodology has been used to isolate many genes encoding cell-surface molecules.

The full amino acid sequence of the protein can be deduced from the nucleotide sequence of its cDNA, and this often gives clues to the nature of the protein and its biological properties. The nucleotide sequence of the gene and its regulatory regions can be determined from genomic DNA clones. The gene can be manipulated and introduced into cells by transfection for larger-scale production and functional studies. This approach has been used to characterize many immunologically important proteins, such as the MHC glycoproteins.

The converse approach is taken to identify the unknown protein product of a cloned gene. The gene sequence is used to construct synthetic peptides of 10–20 amino acids that are identical to part of the deduced protein sequence, and antibodies are then raised against these peptides by coupling them to carrier proteins; the peptides behave as haptens. These anti-peptide antibodies often bind the native protein and so can be used to identify its distribution in cells and tissues and to try to ascertain its function (Fig. A.22). This approach to identifying the function of a gene is often called ‘reverse genetics’ as it works from gene to phenotype rather than from phenotype to gene, which is the classical genetic approach. The great advantage of reverse genetics over the classical approach is that it does not require a detectable phenotypic genetic trait in order to identify a gene.

Figure A.22. The use of antibodies to detect the unknown protein product of a known gene is called reverse genetics.

Figure A.22

The use of antibodies to detect the unknown protein product of a known gene is called reverse genetics. When the gene responsible for a genetic disorder such as Duchenne muscular dystrophy is isolated, the amino acid sequence of the unknown protein product (more...)

Antibodies can also be used in the determination of the function of gene products. Some antibodies are able to act as agonists, when the binding of the antibody to the molecule mimics the binding of the natural ligand and activates the function of the gene product. For example, antibodies to the CD3 molecule have been used to stimulate T cells, replacing the interaction of the T-cell receptor with MHC:peptide antigens in cases where the specific peptide antigen is not known. Conversely, antibodies can function as antagonists, inhibiting the binding of the natural ligand and thus blocking the function.

Isolation of lymphocytes

A-20. Isolation of peripheral blood lymphocytes by Ficoll-Hypaque™ gradient

The first step in studying lymphocytes is to isolate them so that their behavior can be analyzed in vitro. Human lymphocytes can be isolated most readily from peripheral blood by density centrifugation over a step gradient consisting of a mixture of the carbohydrate polymer Ficoll™ and the dense iodine-containing compound metrizamide. This yields a population of mononuclear cells at the interface that has been depleted of red blood cells and most polymorphonuclear leukocytes or granulocytes (Fig. A.23). The resulting population, called peripheral blood mononuclear cells, consists mainly of lymphocytes and monocytes. Although this population is readily accessible, it is not necessarily representative of the lymphoid system, as only recirculating lymphocytes can be isolated from blood.

Figure A.23. Peripheral blood mononuclear cells can be isolated from whole blood by Ficoll-Hypaque™ centrifugation.

Figure A.23

Peripheral blood mononuclear cells can be isolated from whole blood by Ficoll-Hypaque™ centrifugation. Diluted anticoagulated blood (left panel) is layered over Ficoll-Hypaque™ and centrifuged. Red blood cells and polymorphonuclear leukocytes (more...)

A particular cell population can be isolated from a sample or culture by binding to antibody-coated plastic surfaces, a technique known as panning, or by removing unwanted cells by treatment with specific antibody and complement to kill them. Cells can also be passed over columns of antibody-coated, nylon-coated steel wool and different populations differentially eluted. This technique extends affinity chromatography to cells, and is now a very popular way to separate cells. All these techniques can also be used as a pre-purification step prior to sorting out highly purified populations by FACS (see Section A-22).

A-21. Isolation of lymphocytes from tissues other than blood

In experimental animals, and occasionally in humans, lymphocytes are isolated from lymphoid organs, such as spleen, thymus, bone marrow, lymph nodes, or mucosal-associated lymphoid tissues, most commonly the palatine tonsils in humans (see Fig. 1.7). A specialized population of lymphocytes resides in surface epithelia; these cells are isolated by fractionating the epithelial layer after its detachment from the basement membrane. Finally, in situations where local immune responses are prominent, lymphocytes can be isolated from the site of the response itself. For example, in order to study the autoimmune reaction that is thought to be responsible for rheumatoid arthritis, an inflammatory response in joints, lymphocytes are isolated from the fluid aspirated from the inflamed joint space.

A-22. Flow cytometry and FACS analysis

Resting lymphocytes present a deceptively uniform appearance, all being small round cells with a dense nucleus and little cytoplasm (see Fig. 1.5). However, these cells comprise many functional subpopulations, which are usually identified and distinguished from each other on the basis of their differential expression of cell-surface proteins, which can be detected using specific antibodies (Fig. A.24). B and T lymphocytes, for example, are identified unambiguously and separated from each other by antibodies to the constant regions of the B- and T-cell antigen receptors. T cells are further subdivided on the basis of expression of the co-receptor proteins CD4 and CD8.

Figure A.24. The distribution of lymphocyte subpopulations in human peripheral blood.

Figure A.24

The distribution of lymphocyte subpopulations in human peripheral blood. As shown on the outside of the circle, lymphocytes can be divided into T cells bearing T-cell receptors (detected with anti-CD3 antibodies), B cells bearing immunoglobulin receptors (more...)

An immensely powerful tool for defining and enumerating lymphocytes is the flow cytometer, which detects and counts individual cells passing in a stream through a laser beam. A flow cytometer equipped to separate the identified cells is called a fluorescence-activated cell sorter (FACS). These instruments are used to study the properties of cell subsets identified using monoclonal antibodies to cell-surface proteins. Individual cells within a mixed population are first tagged by treatment with specific monoclonal antibodies labeled with fluorescent dyes, or by specific antibodies followed by labeled anti-immunoglobulin antibodies. The mixture of labeled cells is then forced with a much larger volume of saline through a nozzle, creating a fine stream of liquid containing cells spaced singly at intervals. As each cell passes through a laser beam it scatters the laser light, and any dye molecules bound to the cell will be excited and will fluoresce. Sensitive photomultiplier tubes detect both the scattered light, which gives information on the size and granularity of the cell, and the fluorescence emissions, which give information on the binding of the labeled monoclonal antibodies and hence on the expression of cell-surface proteins by each cell (Fig. A.25).

Figure A.25. The FACS™ allows individual cells to be identified by their cell-surface antigens and to be sorted.

Figure A.25

The FACS™ allows individual cells to be identified by their cell-surface antigens and to be sorted. Cells to be analyzed by flow cytometry are first labeled with fluorescent dyes (top panel). Direct labeling uses dye-coupled antibodies specific for (more...)

In the cell sorter, the signals passed back to the computer are used to generate an electric charge, which is passed from the nozzle through the liquid stream at the precise time that the stream breaks up into droplets, each containing no more than a single cell; droplets containing a charge can then be deflected from the main stream of droplets as they pass between plates of opposite charge, so that positively charged droplets are attracted to a negatively charged plate, and vice versa. In this way, specific subpopulations of cells, distinguished by the binding of the labeled antibody, can be purified from a mixed population of cells. Alternatively, to deplete a population of cells, the same fluorochrome can be used to label different antibodies directed at marker proteins expressed by the various undesired cell types. The cell sorter can be used to direct labeled cells to a waste channel, retaining only the unlabeled cells.

When cells are labeled with a single fluorescent antibody, the data from a flow cytometer are usually displayed in the form of a histogram of fluorescence intensity versus cell numbers. If two or more antibodies are used, each coupled to different fluorescent dyes, then the data are more usually displayed in the form of a two-dimensional scatter diagram or as a contour diagram, where the fluorescence of one dye-labeled antibody is plotted against that of a second, with the result that a population of cells labeling with one antibody can be further subdivided by its labeling with the second antibody (see Fig. A.25). By examining large numbers of cells, flow cytometry can give quantitative data on the percentage of cells bearing different molecules, such as surface immunoglobulin, which characterizes B cells, the T-cell receptor-associated molecules known as CD3, and the CD4 and CD8 co-receptor proteins that distinguish the major T-cell subsets. Likewise, FACS analysis has been instrumental in defining stages in the early development of B and T cells. As the power of the FACS technology has grown, progressively more antibodies labeled with distinct fluorescent dyes can be used at the same time. Three-, four-, and even five-color analyses can now be handled by very powerful machines. FACS analysis has been applied to a broad range of problems in immunology; indeed, it played a vital role in the early identification of AIDS as a disease in which T cells bearing CD4 are depleted selectively (see Chapter 11).

A-23. Lymphocyte isolation using antibody-coated magnetic beads

Although the FACS is superb for isolating small numbers of cells in pure form, when large numbers of lymphocytes must be prepared quickly, mechanical means of separating cells are preferable. A powerful and efficient way of isolating lymphocyte populations is to couple paramagnetic beads to monoclonal antibodies that recognize distinguishing cell-surface molecules. These antibody-coated beads are mixed with the cells to be separated, and run through a column containing material that attracts the paramagnetic beads when the column is placed in a strong magnetic field. Cells binding the magnetically labeled antibodies are retained; cells lacking the appropriate surface molecule can be washed away (Fig. A.26). The bound cells are positively selected for expression of the particular cell-surface molecule, while the unbound cells are negatively selected for its absence.

Figure A.26. Lymphocyte subpopulations can be separated physically by using antibodies coupled to paramagnetic particles or beads.

Figure A.26

Lymphocyte subpopulations can be separated physically by using antibodies coupled to paramagnetic particles or beads. A mouse monoclonal antibody specific for a particular cell-surface molecule is coupled to paramagnetic particles or beads. It is mixed (more...)

A-24. Isolation of homogeneous T-cell lines

The analysis of specificity and effector function in T cells depends heavily on the study of monoclonal populations of T lymphocytes. These can be obtained in four distinct ways. First, as for B-cell hybridomas (see Section A-12), normal T cells proliferating in response to specific antigen can be fused to malignant T-cell lymphoma lines to generate T-cell hybrids. The hybrids express the receptor of the normal T cell, but proliferate indefinitely owing to the cancerous state of the lymphoma parent. T-cell hybrids can be cloned to yield a population of cells all having the same T-cell receptor. When stimulated by their specific antigen these cells release cytokines such as the T-cell growth factor interleukin-2 (IL-2), and the production of cytokines is used as an assay to assess the antigen specificity of the T-cell hybrid.

T-cell hybrids are excellent tools for the analysis of T-cell specificity, as they grow readily in suspension culture. However, they cannot be used to analyze the regulation of specific T-cell proliferation in response to antigen because they are continually dividing. T-cell hybrids also cannot be transferred into an animal to test for function in vivo because they would give rise to tumors. Functional analysis of T-cell hybrids is also confounded by the fact that the malignant partner cell affects their behavior in functional assays. Therefore, the regulation of T-cell growth and the effector functions of T cells must be studied using T-cell clones. These are clonal cell lines of a single T-cell type and antigen specificity, which are derived from cultures of heterogeneous T cells, called T-cell lines, whose growth is dependent on periodic restimulation with specific antigen and, frequently, on the addition of T-cell growth factors (Fig. A.27). T-cell clones also require periodic restimulation with antigen and are more tedious to grow than T-cell hybrids but, because their growth depends on specific antigen recognition, they maintain antigen specificity, which is often lost in T-cell hybrids. Cloned T-cell lines can be used for studies of effector function both in vitro and in vivo. In addition, the proliferation of T cells, a critical aspect of clonal selection, can be characterized only in cloned T-cell lines, where such growth is dependent on antigen recognition. Thus, both types of monoclonal T-cell line have valuable applications in experimental studies.

Figure A.27. Production of cloned T-cell lines.

Figure A.27

Production of cloned T-cell lines. T cells from an immune donor, comprising a mixture of cells with different specificities, are activated with antigen and antigen-presenting cells. Single responding cells are cultured by limiting dilution in the T-cell (more...)

Studies of human T cells have relied largely on T-cell clones because a suitable fusion partner for making T-cell hybrids has not been identified. However, a human T-cell lymphoma line, called Jurkat, has been characterized extensively because it secretes IL-2 when its antigen receptor is cross-linked with anti-receptor monoclonal antibodies. This simple assay system has yielded much information about signal transduction in T cells. One of the Jurkat cell line's most interesting features, shared with T-cell hybrids, is that it stops growing when its antigen receptor is cross-linked. This has allowed mutants lacking the receptor or having defects in signal transduction pathways to be selected simply by culturing the cells with anti-receptor antibody and selecting those that continue to grow. Thus, T-cell tumors, T-cell hybrids, and cloned T-cell lines all have valuable applications in experimental immunology.

Finally, primary T cells from any source can be isolated as single, antigen-specific cells by limiting dilution rather than by first establishing a mixed population of T cells in culture as a T-cell line and then deriving clonal subpopulations. During the growth of T-cell lines, particular T-cell clones can come to dominate the cultures and give a false picture of the number and specificities in the original sample. Direct cloning of primary T cells avoids this artifact.

Characterization of lymphocyte specificity, frequency, and function

B cells are relatively easy to characterize as they have only one function—antibody production. T cells are more difficult to characterize as there are several different classes with different functions. It is also technically more difficult to study the membrane-bound T-cell receptors than the antibodies secreted in large amounts by B cells. All the methods in this part of the appendix can be used for T cells. Some are also used to detect and count B cells.

On many occasions it is important to know the frequency of antigen-specific lymphocytes, especially T cells, in order to measure the efficiency with which an individual responds to a particular antigen, for example, or the degree to which specific immunological memory has been established. There are a number of methods for doing this, either by detecting the cells directly by the specificity of their receptor, or by detecting activation of the cells to provide some particular function, such as cytokine secretion or cytotoxicity.

The first technique of this type to be established was the limiting-dilution culture (see Section A-25), in which the frequency of specific T or B cells responding to a particular antigen could be estimated by plating the cells into 96-well plates at increasing dilutions and measuring the number of wells in which there was no response. However, in this type of assay it became laborious to ask detailed questions about the phenotype of the responding cells, and to compare responses from different cell subpopulations.

A simpler assay for measuring the responses of T-cell populations has been developed from a variant of the antigen-capture ELISA method (see Section A-6), called the ELISPOT assay (see Section A-26). It assays T cells on the basis of cytokine production. In the ELISPOT assay, cytokine secreted by individual activated T cells is immobilized as discrete spots on a plastic plate, which are counted to give the number of activated T cells. The ELISPOT assay suffers from many of the same problems as the limiting-dilution assay in giving information about the nature of the activated cells, and it can be difficult to determine whether individual cells are capable of secreting mixtures of cytokines. It was therefore important to develop assays that could make these measurements on single cells. Measurements based on flow cytometry (see Section A-22) proved the answer, with the development of methods for detecting fluorescently labeled cytokines within activated T cells. The drawback of intracellular cytokine staining (see Section A-27) was that the T cells have to be killed and permeabilized by detergents to enable the cytokines to be detected. This led to the more sophisticated technique of capturing secreted labeled cytokines on the surfaces of the living T cells (see Section A-27).

Finally, methods for directly detecting T cells on the basis of the specificity of their receptor, using fluorochrome-tagged tetramers of specific MHC:peptide complexes (see Section A-28), have revolutionized the study of T-cell responses in a similar way to the use of monoclonal antibodies.

A-25. Limiting-dilution culture

The response of a lymphocyte population is a measure of the overall response, but the frequency of lymphocytes able to respond to a given antigen can be determined only by limiting-dilution culture. This assay makes use of the Poisson distribution, a statistical function that describes how objects are distributed at random. For instance, when a sample of heterogeneous T cells is distributed equally into a series of culture wells, some wells will receive no T cells specific for a given antigen, some will receive one specific T cell, some two, and so on. The T cells in the wells are activated with specific antigen, antigen-presenting cells, and growth factors. After allowing several days for their growth and differentiation, the cells in each well are tested for a response to antigen, such as cytokine release or the ability to kill specific target cells (Fig. A.28). The assay is replicated with different numbers of T cells in the samples. The logarithm of the proportion of wells in which there is no response is plotted against the number of cells initially added to each well. If cells of one type, typically antigen-specific T cells because of their rarity, are the only limiting factor for obtaining a response, then a straight line is obtained. From the Poisson distribution, it is known that there is, on average, one antigen-specific cell per well when the proportion of negative wells is 37%. Thus, the frequency of antigen-specific cells in the population equals the reciprocal of the number of cells added to each well when 37% of the wells are negative. After priming, the frequency of specific cells goes up substantially, reflecting the antigen-driven proliferation of antigen-specific cells. The limiting-dilution assay can also be used to measure the frequency of B cells that can make antibody to a given antigen.

Figure A.28. The frequency of specific lymphocytes can be determined using limiting-dilution assay.

Figure A.28

The frequency of specific lymphocytes can be determined using limiting-dilution assay. Varying numbers of lymphoid cells from normal or immunized mice are added to individual culture wells and stimulated with antigen and antigen-presenting cells (APCs) (more...)

A-26. ELISPOT assays

A modification of the ELISA antigen-capture assay (see Section A-6), called the ELISPOT assay, has provided a powerful tool for measuring the frequency of T-cell responses. Populations of T cells are stimulated with the antigen of interest, and are then allowed to settle onto a plastic plate coated with antibodies to the cytokine that is to be assayed (Fig. A.29). If an activated T cell is secreting that cytokine, it is captured by the antibody on the plastic plate. After a period the cells are removed, and a second antibody to the cytokine is added to the plate to reveal a circle of bound cytokine surrounding the position of each activated T cell; counting each spot, and knowing the number of T cells originally added to the plate allows a simple calculation of the frequency of T cells secreting that particular cytokine, giving the ELISPOT assay its name. ELISPOT can also be used to detect specific antibody secretion by B cells, in this case by using antigen-coated surfaces to trap specific antibody and labeled anti-immunoglobulin to detect the bound antibody.

Figure A.29. The frequency of cytokine-secreting T cells can be determined by the ELISPOT assay.

Figure A.29

The frequency of cytokine-secreting T cells can be determined by the ELISPOT assay. The ELISPOT assay is a variant of the ELISA assay in which antibodies bound to a plastic surface are used to capture cytokines secreted by individual T cells. Usually, (more...)

A-27. Identification of functional subsets of T cells by staining for cytokines

One problem with the detection of cytokine production on a single-cell level is that the cytokines are secreted by the T cells into the surrounding medium, and any association with the originating cell is lost. Two methods have been devised that allow the cytokine profile produced by individual cells to be determined. The first, that of intracellular cytokine staining (Fig. A.30), relies on the use of metabolic poisons that inhibit protein export from the cell. The cytokine thus accumulates within the endoplasmic reticulum and vesicular network of the cell. If the cells are subsequently fixed and rendered permeable by the use of mild detergents, antibodies can gain access to these intracellular compartments and detect the cytokine. The T cells can be stained for other markers simultaneously, and thus the frequency, for example, of IL-10-producing CD25+ CD4 T cells can be easily obtained.

Figure A.30. Cytokine-secreting cells can be identified by intracellular cytokine staining.

Figure A.30

Cytokine-secreting cells can be identified by intracellular cytokine staining. The cytokines secreted by activated T cells can be determined by using fluorochrome-labeled antibodies to detect cytokine molecules that have been allowed to accumulate inside (more...)

A second method, which has the advantage that the cells being analyzed are not killed in the process, is called cytokine capture. This technique uses hybrid antibodies, in which the two separate heavy- and light-chain pairs from different antibodies are combined to give a mixed antibody molecule in which the two antigen-binding sites recognize different ligands (Fig. A.31). In the bispecific antibodies used to detect cytokine production, one of the antigen-binding sites is specific for a T-cell surface marker, while the other is specific for the cytokine in question. The bispecific antibody binds to the T cells through the binding site for the cell-surface marker, leaving the cytokine-binding site free. If that T cell is secreting the particular cytokine, it is captured by the bound antibody before it diffuses away from the surface of the cell. It can then be detected by adding a fluorochrome-labeled second antibody specific for the cytokine to the cells.

Figure A.31. Hybrid antibodies containing cell-specific and cytokine-specific binding sites can be used to assay cytokine secretion by living cells and to purify cells secreting particular cytokines.

Figure A.31

Hybrid antibodies containing cell-specific and cytokine-specific binding sites can be used to assay cytokine secretion by living cells and to purify cells secreting particular cytokines. Hybrid antibodies can be made by mixing together heavy- and light-chain pairs (more...)

A-28. Identification of T-cell receptor specificity using MHC:peptide tetramers

For many years, the ability to identify antigen-specific T cells directly through their receptor specificity eluded immunologists. Foreign antigen could not be used directly to identify T cells, since, unlike B cells, they do not recognize antigen alone but rather the complexes of peptide fragments of antigen bound to self MHC molecules. Moreover, the affinity of interaction between the T-cell receptor and the MHC:peptide complex was in practice so low that attempts to label T cells with their specific MHC:peptide complexes routinely failed. The breakthrough in labeling antigen-specific T cells came with the idea of making multimers of the MHC:peptide complex, so as to increase the avidity of the interaction.

Peptides can be biotinylated using the bacterial enzyme BirA, which recognizes a specific amino acid sequence. Recombinant MHC molecules containing this target sequence are used to make MHC:peptide complexes which are then biotinylated. Avidin, or the bacterial counterpart streptavidin, contains four sites that bind biotin with extremely high affinity. Mixing the biotinylated MHC:peptide complex with avidin or streptavidin results in the formation of an MHC:peptide tetramer—four specific MHC:peptide complexes bound to a single molecule of streptavidin (Fig. A.32). Routinely, the streptavidin moiety is labeled with a fluorochrome to allow detection of those T cells capable of binding the MHC:peptide tetramer.

Figure A.32. MHC:peptide complexes coupled to streptavidin to form tetramers are able to stain antigen-specific T cells.

Figure A.32

MHC:peptide complexes coupled to streptavidin to form tetramers are able to stain antigen-specific T cells. MHC:peptide tetramers are formed from recombinant refolded MHC:peptide complexes containing a single defined peptide epitope. The MHC molecules can (more...)

MHC:peptide tetramers have been used to identify populations of antigen-specific T cells in, for example, patients with acute Epstein-Barr virus infections (infectious mononucleosis), showing that up to 80% of the peripheral T cells in infected individuals can be specific for a single MHC:peptide complex. They have also been used to follow responses over longer timescales in individuals with HIV or, in the example we show, cytomegalovirus infections. These reagents have also been important in identifying the cells responding, for example, to nonclassical class I molecules such as HLA-E or HLA-G, in both cases showing that these nonclassical molecules are recognized by subsets of NK receptors.

A-29. Assessing the diversity of the T-cell repertoire by ‘spectratyping.’

The extent of the diversity of the T-cell repertoire, either generally or during specific immune responses, is often of interest. In particular, as T cells do not undergo somatic hypermutation and affinity maturation in the same way that B cells do, the relationship between the repertoire of T cells making a primary response to antigen and the repertoire of T cells involved in secondary and subsequent responses to antigen has been difficult to determine. This information has usually been obtained through the laborious process of cloning the T cells involved in specific responses (see Section A-24), and the cloning and sequencing of their T-cell receptors.

It is possible, however, to estimate the diversity of T-cell responses by making use of the junctional diversity generated when T-cell receptors are created by somatic recombination, a technique known as spectratyping. Variability in the length of the CDR3 segments is created during the recombination process, both by variation in the exact positions at which the junctions between gene segments occur, and by variation in the number of N-nucleotides added. Both these processes result in the length of the Vβ CDR3 varying by up to nine amino acids. The problem in detecting this variability is that there are 24 families of Vβ gene segments in humans and it is not possible to design a single oligonucleotide primer that will anneal to all of these families. Specific oligonucleotide primers can, however, be designed for each family, and these can be used in the polymerase chain reaction (PCR), together with a primer specific for the Cβ region, to amplify, for each individual family, a segment of the mRNA for the T-cell receptor β chain that spans the CDR3 region. A population of TCR Vβ genes will therefore show a distribution, or ‘spectrum,’ of CD3 lengths, and will give rise to PCR products of different lengths that can be resolved, usually by polyacrylamide gel electrophoresis (Fig. A.33). The deletion and addition of nucleotides during the generation of T-cell receptors by rearrangement is random, and so in a normal individual the CDR3 lengths follow a Gaussian distribution. Deviations from this Gaussian distribution, such as an excess of one particular CDR3 length, indicate the presence of clonal expansions of T cells, such as occurs during a T-cell response.

Figure A.33. The diversity of the T-cell receptor repertoire can be displayed by spectratyping, a PCR-based technique that separates different receptors on the basis of their CDR3 length.

Figure A.33

The diversity of the T-cell receptor repertoire can be displayed by spectratyping, a PCR-based technique that separates different receptors on the basis of their CDR3 length. The process of generation of T-cell receptors is stochastic, giving rise to (more...)

A-30. Biosensor assays for measuring the rates of association and disassociation of antigen receptors for their ligands

Two of the important questions that are always asked of any receptor-ligand interaction is: what is the strength of binding, or affinity, of the interaction, and what are the rates of association and disassociation? Traditionally, measurements of affinity have been made by equilibrium binding measurements (see Section A-9), and measurements of rates of binding have been difficult to obtain. Equilibrium binding assays also cannot be performed on T-cell receptors, which have large macromolecular ligands and which cannot be isolated and purified in large quantity.

It is now possible to measure binding rates directly, by following the binding of ligands to receptors immobilized on gold-plated glass slides, using a phenomenon known as surface plasmon resonance to detect the binding (Fig. A.34). A full explanation of surface plasmon resonance is beyond the scope of this textbook, as it is based on advanced physical and quantum mechanical principles. Briefly, it relies on the total internal reflection of a beam of light from the surface of a gold-coated glass slide. As the light is reflected, some of its energy excites electrons in the gold coating and these excited electrons are in turn affected by the electric field of any molecules binding to the surface of the glass coating. The more molecules that bind to the surface, the greater the effect on the excited electrons, and this in turn affects the reflected light beam. The reflected light thus becomes a sensitive measure of the number of atoms bound to the gold surface of the slide.

Figure A.34. Measurement of receptor-ligand interactions can be made in real time using a biosensor.

Figure A.34

Measurement of receptor-ligand interactions can be made in real time using a biosensor. Biosensors are able to measure the binding of molecules on the surface of gold-plated glass chips through the indirect effects of the binding on the total internal (more...)

If a purified receptor is immobilized on the surface of the gold-coated glass slide, to make a biosensor ‘chip,’ and a solution containing the ligand is flowed over that surface, the binding of ligand to the receptor can be followed until it reaches equilibrium (see Fig. A.34). If the ligand is then washed out, dissociation of ligand from the receptor can easily be followed and the dissociation rate calculated. A new solution of the ligand at a different concentration can then be flowed over the chip and the binding once again measured. The affinity of binding can be calculated in a number of ways in this type of assay. Most simply, the ratio of the rates of association and dissociation will give an estimate of the affinity, but more accurate estimates can be obtained from the measurements of the binding at different concentrations of ligand. From measurements of binding at equilibrium, a Scatchard plot (see Fig. A.11) will give a measurement of the affinity of the receptor-ligand interaction.

A-31. Stimulation of lymphocyte proliferation by treatment with polyclonal mitogens or specific antigen

To function in adaptive immunity, rare antigen-specific lymphocytes must proliferate extensively before they differentiate into functional effector cells in order to generate sufficient numbers of effector cells of a particular specificity. Thus, the analysis of induced lymphocyte proliferation is a central issue in their study. It is, however, difficult to detect the proliferation of normal lymphocytes in response to specific antigen because only a minute proportion of cells will be stimulated to divide. Great impetus was given to the field of lymphocyte culture by the finding that certain substances induce many or all lymphocytes of a given type to proliferate. These substances are referred to collectively as polyclonal mitogens because they induce mitosis in lymphocytes of many different specificities or clonal origins. T and B lymphocytes are stimulated by different polyclonal mitogens (Fig. A.35). Polyclonal mitogens seem to trigger essentially the same growth response mechanisms as antigen. Lymphocytes normally exist as resting cells in the G0 phase of the cell cycle. When stimulated with polyclonal mitogens, they rapidly enter the G1 phase and progress through the cell cycle. In most studies, lymphocyte proliferation is most simply measured by the incorporation of 3H-thymidine into DNA. This assay is used clinically for assessing the ability of lymphocytes from patients with suspected immunodeficiencies to proliferate in response to a nonspecific stimulus.

Figure A.35. Polyclonal mitogens, many of plant origin, stimulate lymphocyte proliferation in tissue culture.

Figure A.35

Polyclonal mitogens, many of plant origin, stimulate lymphocyte proliferation in tissue culture. Many of these mitogens are used to test the ability of lymphocytes in human peripheral blood to proliferate.

Once lymphocyte culture had been optimized using the proliferative response to polyclonal mitogens as an assay, it became possible to detect antigen-specific T-cell proliferation in culture by measuring 3H-thymidine uptake in response to an antigen to which the T-cell donor had been previously immunized (Fig. A.36). This is the assay most commonly used for assessing T-cell responses after immunization, but it reveals little about the functional capabilities of the responding T cells. These must be ascertained by functional assays, as outlined in Sections A-33 and A-34.

Figure A.36. Antigen-specific T-cell proliferation is used frequently as an assay for T-cell responses.

Figure A.36

Antigen-specific T-cell proliferation is used frequently as an assay for T-cell responses. T cells from mice or humans that have been immunized with an antigen (A) proliferate when they are exposed to antigen A and antigen-presenting cells but not when (more...)

A-32. Measurements of apoptosis by the TUNEL assay

Apoptotic cells can be detected by a procedure known as TUNEL staining. In this technique, the 3′ ends of the DNA fragments generated in apoptotic cells are labeled with biotin-coupled uridine by using the enzyme terminal deoxynucleotidyl transferase (TdT). The biotin label is then detected with enzyme tagged streptavidin, which binds to biotin. When the colorless substrate of the enzyme is added to a tissue section or cell culture, it is reacted upon to produce a colored precipitate only in cells that have undergone apoptosis (Fig. A.37). This technique has revolutionized the detection of apoptotic cells.

Figure A.37. Fragmented DNA can be labeled by terminal deoxynucleotidyl transferase (TdT) to reveal apoptotic cells.

Figure A.37

Fragmented DNA can be labeled by terminal deoxynucleotidyl transferase (TdT) to reveal apoptotic cells. When cells undergo programmed cell death, or apoptosis, their DNA becomes fragmented (left panel). The enzyme TdT is able to add nucleotides to the (more...)

A-33. Assays for cytotoxic T cells

Activated CD8 T cells generally kill any cells that display the specific peptide:MHC class I complex they recognize. Thus CD8 T-cell function can be determined using the simplest and most rapid T-cell bioassay—the killing of a target cell by a cytotoxic T cell. This is usually detected in a 51Cr-release assay. Live cells will take up, but do not spontaneously release, radioactively labeled sodium chromate, Na251CrO4. When these labeled cells are killed, the radioactive chromate is released and its presence in the supernatant of mixtures of target cells and cytotoxic T cells can be measured (Fig. A.38). In a similar assay, proliferating target cells such as tumor cells can be labeled with 3H-thymidine, which is incorporated into the replicating DNA. On attack by a cytotoxic T cell, the DNA of the target cells is rapidly fragmented and retained in the filtrate, while large, unfragmented DNA is collected on a filter, and one can measure either the release of these fragments or the retention of 3H-thymidine in chromosomal DNA. These assays provide a rapid, sensitive, and specific measure of the activity of cytotoxic T cells.

Figure A.38. Cytotoxic T-cell activity is often assessed by chromium release from labeled target cells.

Figure A.38

Cytotoxic T-cell activity is often assessed by chromium release from labeled target cells. Target cells are labeled with radioactive chromium as Na251CrO4, washed to remove excess radioactivity and exposed to cytotoxic T cells. Cell destruction is measured (more...)

A-34. Assays for CD4 T cells

CD4 T-cell functions usually involve the activation rather than the killing of cells bearing specific antigen. The activating effects of CD4 T cells on B cells or macrophages are mediated in large part by nonspecific mediator proteins called cytokines, which are released by the T cell when it recognizes antigen. Thus, CD4 T-cell function is usually studied by measuring the type and amount of these released proteins. As different effector T cells release different amounts and types of cytokines, one can learn about the effector potential of that T cell by measuring the proteins it produces.

Cytokines can be detected by their activity in biological assays of cell growth, where they serve either as growth factors or growth inhibitors. A more specific assay is a modification of ELISA known as a capture or sandwich ELISA (see Section A-6). In this assay, the cytokine is characterized by its ability to bridge between two monoclonal antibodies reacting with different epitopes on the cytokine molecule. Cytokine-secreting cells can also be detected by ELISPOT (see Section A-26).

Sandwich ELISA and ELISPOT avoid a major problem of cytokine bioassays, the ability of different cytokines to stimulate the same response in a bioassay. Bioassays must always be confirmed by inhibition of the response with neutralizing monoclonal antibodies specific for the cytokine. Another way of identifying cells actively producing a given cytokine is to stain them with a fluorescently tagged anti-cytokine monoclonal antibody and identify and count them by FACS (see Section A-22).

A quite different approach to detecting cytokine production is to determine the presence and amount of the relevant cytokine mRNA in stimulated T cells. This can be done for single cells by in situ hybridization and for cell populations by reverse transcriptase-polymerase chain reaction (RT-PCR). Reverse transcriptase is an enzyme used by certain RNA viruses, such as the human immunodeficiency virus (HIV-1) that causes AIDS, to convert an RNA genome into a DNA copy, or cDNA. In RT-PCR, mRNA is isolated from cells and cDNA copies made using reverse transcriptase. The desired cDNA is then selectively amplified by PCR using sequence-specific primers. When the products of the reaction are subjected to electrophoresis on an agarose gel, the amplified DNA can be visualized as a band of a specific size. The amount of amplified cDNA sequence will be proportional to its representation in the mRNA; stimulated T cells actively producing a particular cytokine will produce large amounts of that particular mRNA and thus give correspondingly large amounts of the selected cDNA on RT-PCR. The level of cytokine mRNA in the original tissue is usually determined by comparison with the outcome of RT-PCR on the mRNA produced by a so-called ‘housekeeping gene’ expressed by all cells.

A-35. DNA microarrays

Any cell expresses, at any one time, many hundreds or even thousands of genes. Some of the products are expressed at high levels, the actin that forms the cytoskeleton of the cell is one example, while others may only be expressed in a few copies per cell. Different cell types, or cells at different stages of maturation, or even tumor cells compared to their normal counterparts, will express different sets of genes, and trying to identify these differences is an important field of research, in immunology as well as in other areas of biology. One important new technique in analyzing these differences makes use of arrays of hundreds of DNA sequences attached to a glass surface—a so-called DNA microarray or ‘DNA chip.’ The array contains a range of DNA sequences from known genes, arranged in a fixed pattern, and the differential expression of those genes in a particular cell type or tissue is tested by exposing the array to labeled mRNA (or cDNA made from it) from the tissue. Hybridization of labeled mRNAs to their corresponding DNA sequences in the array is detected by standard techniques and the whole technique is readily automated. Many different samples can be examined in parallel, which makes this a powerful analytical technique, as can be seen from the example we illustrate in Fig. A.39. Here the DNA microarray has been constructed with almost 18,000 cDNA clones known to be expressed in either B or T cells and B-cell tumors. This array was then probed with fluorochrome-labeled cDNAs from 96 normal and malignant cells, and the level of expression of approximately 18,000 genes in each of the cell lines was measured simultaneously. In this particular case the patterns of expression of the different genes revealed that the malignant B cells formed discrete subtypes, which were then found to have different clinical prognoses.

Figure A.39. DNA microarrays allow a rapid, simultaneous screening of a great many genes for changes in expression between different cells.

Figure A.39

DNA microarrays allow a rapid, simultaneous screening of a great many genes for changes in expression between different cells. In the experiment whose results are shown here, nearly 18,000 cDNA clones made from lymphoid cells and lymphoid tumors were (more...)

Detection of immunity in vivo

A-36. Assessment of protective immunity

An adaptive immune response against a pathogen often confers long-lasting immunity against infection with that pathogen; successful vaccination achieves the same end. The very first experiment in immunology, Jenner's successful vaccination against smallpox, is still the model for assessing the presence of such protective immunity. The assessment of protective immunity conferred by vaccination has three essential steps. First, an immune response is elicited by immunization with a candidate vaccine. Second, the immunized individuals, along with unimmunized controls, are challenged with the infectious agent (Fig. A.40). Finally, the prevalence and severity of infection in the immunized individual is compared with the course of the disease in the unimmunized controls. For obvious reasons, such experiments are usually carried out first in animals, if a suitable animal model for the infection exists. However, eventually a trial must be carried out in humans. In this case, the infectious challenge is usually provided naturally by carrying out the trial in a region where the disease is prevalent. The efficacy of the vaccine is determined by assessing the prevalence and severity of new infections in the immunized and control populations. Such studies necessarily give less precise results than a direct experiment but, for most diseases, they are the only way of assessing a vaccine's ability to induce protective immunity in humans.

Figure A.40. In vivo assay for the presence of protective immunity after vaccination in animals.

Figure A.40

In vivo assay for the presence of protective immunity after vaccination in animals. Mice are injected with the test vaccine or a control such as saline solution. Different groups are then challenged with lethal or pathogenic doses of the test pathogen (more...)

A-37. Transfer of protective immunity

The tests described in Section A-36 show that protective immunity has been established, but cannot show whether it involves humoral immunity, cell-mediated immunity, or both. When these studies are carried out in inbred mice, the nature of protective immunity can be determined by transferring serum or lymphoid cells from an immunized donor animal to an unimmunized syngeneic recipient (that is, a genetically identical animal of the same inbred strain) (Fig. A.41). If protection against infection can be conferred by the transfer of serum, the immunity is provided by circulating antibodies and is called humoral immunity. Transfer of immunity by antiserum or purified antibodies provides immediate protection against many pathogens and against toxins such as those of tetanus and snake venom. However, although protection is immediate, it is temporary, lasting only so long as the transferred antibodies remain active in the recipient's body. This type of transfer is therefore called passive immunization. Only active immunization with antigen can provide lasting immunity. Moreover, the recipient may become immunized to the antiserum used to transfer immunity. Horse or sheep sera are the usual sources of anti-snake venoms used in humans, and repeated administration can lead either to serum sickness (see Section 12-16) or, if the recipient becomes allergic to the foreign serum, to anaphylaxis (see Section 12-10).

Figure A.41. Immunity can be transferred by antibodies or by lymphocytes.

Figure A.41

Immunity can be transferred by antibodies or by lymphocytes. Successful vaccination leads to a long-lived state of protection against the specific immunizing pathogen. If this immune protection can be transferred to a normal syngeneic recipient with serum (more...)

Protection against many diseases cannot be transferred with serum but can be transferred by lymphoid cells from immunized donors. The transfer of lymphoid cells from an immune donor to a normal syngeneic recipient is called adoptive transfer or adoptive immunization, and the immunity transferred is called adoptive immunity. Immunity that can be transferred only with lymphoid cells is called cell-mediated immunity. Such cell transfers must be between genetically identical donors and recipients, such as members of the same inbred strain of mouse, so that the donor lymphocytes are not rejected by the recipient and do not attack the recipient's tissues. Adoptive transfer of immunity is used clinically in humans in experimental approaches to cancer therapy or as an adjunct to bone marrow transplantation; in these cases, the patient's own T cells, or the T cells of the bone marrow donor, are given.

A-38. The tuberculin test

Local responses to antigen can indicate the presence of active immunity. Active immunity is often studied in vivo, especially in humans, by injecting antigens locally in the skin. If a reaction appears, this indicates the presence of antibodies or immune lymphocytes that are specific for that antigen; the tuberculin test is an example of this. When people have had tuberculosis they develop cell-mediated immunity that can be detected as a local response when their skin is injected with a small amount of tuberculin, an extract of Mycobacterium tuberculosis, the pathogen that causes tuberculosis. The response typically appears a day or two after the injection and consists of a raised, red, and hard (or indurated) area in the skin, which then disappears as the antigen is degraded.

A-39. Testing for allergic responses

Local intracutaneous injections of minute doses of the antigens that cause allergies are used to determine which antigen triggers a patient's allergic reactions. Local responses that happen in the first few minutes after antigen injection in immune recipients are called immediate hypersensitivity reactions, and they can be of several forms, one of which is the wheal-and-flare response (see Fig. 12.14). Immediate hypersensitivity reactions are mediated by specific antibodies of the IgE class formed as a result of earlier exposures to the antigen. Responses that take hours to days to develop, such as the tuberculin test, are referred to as delayed-type hypersensitivity responses and are caused by preexisting immune T cells. This latter type of response was observed by Jenner when he tested vaccinated individuals with a local injection of vaccinia virus.

These tests work because the local deposit of antigen remains concentrated in the initial site of injection, eliciting responses in local tissues. They do not cause generalized reactions if sufficiently small doses of antigen are used. However, local tests carry a risk of systemic allergic reactions, and they should be used with caution in people with a history of hypersensitivity.

A-40. Assessment of immune responses and immunological competence in humans

The methods used for testing immune function in humans are necessarily more limited than those used in experimental animals, but many different tests are available. They fall into several groups depending on the reason the patient is being studied.

Assessment of protective immunity in humans generally relies on tests conducted in vitro. To assess humoral immunity, specific antibody levels in the patient's serum are assayed by RIA or, more commonly, ELISA (see Section A-6), using the test microorganism or a purified microbial product as antigen. To test for humoral immunity against viruses, antibody production is often measured by the ability of serum to neutralize the infectivity of live virus for tissue culture cells. In addition to providing information about protective immunity, the presence of antibody to a particular pathogen indicates that the patient has been exposed to it, making such tests of crucial importance in epidemiology. At present, testing for antibody to HIV is the main screening test for infection with this virus, critical both for the patient and in blood banking, where blood from infected donors must be excluded from the supply. Essentially similar tests are used in investigating allergy, where allergens are used as the antigens in tests for specific IgE antibody by ELISA or RIA (see Section A-6), which may be used to confirm the results of skin tests.

Cell-mediated immunity, that is immunity mediated by T cells, is technically more difficult to measure than humoral immunity. This is principally because T cells do not make a secreted antigen-binding product, so there is no simple binding assay for their antigen-specific responses. T-cell activity can be divided into an induction phase, in which T cells are activated to divide and differentiate, and an effector phase, in which their function is expressed. Both phases require that the T cell interacts with another cell and that it recognizes specific antigen displayed in the form of peptide:MHC complexes on the surface of this interacting cell. In the induction phase, the interaction must be with an antigen-presenting cell able to deliver co-stimulatory signals, whereas, in the effector phase, the nature of the target cell depends on the type of effector T cell that has been activated. Most commonly, the presence of T cells that have responded to a specific antigen is detected by their subsequent in vitro proliferation when reexposed to the same antigen (see Section A-31).

T-cell proliferation indicates only that cells able to recognize that antigen have been activated previously; it does not reveal what effector function they mediate. The effector function of a T cell is assayed by its effect on an appropriate target cell. Assays for cytotoxic CD8 T cells (see Section A-33) and for cytokine production by CD4 T cells (see Sections A-26, A-27, and A-34) are used to characterize the immune response. Cell-mediated immunity to infectious agents can also be tested by skin test with extracts of the pathogen, as in the tuberculin test (see Section A-36). These tests provide information about the exposure of the patient to the disease and also about their ability to mount an adaptive immune response to it.

Patients with immune deficiency (see Chapter 11) are usually detected clinically by a history of recurrent infection. To determine the competence of the immune system in such patients, a battery of tests are usually conducted (see Appendix V); these focus with increasing precision as the nature of the defect is narrowed down to a single element. The presence of the various cell types in blood is determined by routine hematology, often followed by FACS analysis of lymphocyte subsets (see Section A-22), and the measurement of serum immunoglobulins. The phagocytic competence of freshly isolated polymorphonuclear leukocytes and monocytes is tested, and the efficiency of the complement system (see Chapters 2 and 9) is determined by testing the dilution of serum required for lysis of 50% of antibody-coated red blood cells (this is denoted the CH50).

In general, if such tests reveal a defect in one of the broad compartments of immune function, more specialized testing is then needed to determine the precise nature of the defect. Tests of lymphocyte function are often valuable, starting with the ability of polyclonal mitogens to induce T-cell proliferation and B-cell secretion of immunoglobulin in tissue culture (see Section A-31). These tests can eventually pinpoint the cellular defect in immunodeficiency.

In patients with autoimmune diseases (see Chapter 13), the same parameters are usually analyzed to determine whether there is a gross abnormality in the immune system. However, most patients with such diseases show few abnormalities in general immune function. To determine whether a patient is producing antibody against their own cellular antigens, the most informative test is to react their serum with tissue sections, which are then examined for bound antibody by indirect immunofluorescence using anti-human immunoglobulin labeled with fluorescent dye (see Section A-14). Most autoimmune diseases are associated with the production of broadly characteristic patterns of autoantibodies directed at self tissues. These patterns aid in the diagnosis of the disease and help to distinguish autoimmunity from tissue inflammation due to infectious causes.

It is also possible to investigate allergies by administration of possible allergens by routes other than intracutaneous administration. Allergen may be given by inhalation to test for asthmatic allergic responses (see Fig. 12.14); this is mainly done for experimental purposes in studies of the mechanisms and treatment of asthma. Similarly, food allergens may be given by mouth. The administration of allergens is potentially very dangerous because of the risk of causing anaphylaxis, and must only be carried out by trained and experienced investigators in an environment in which full resuscitation facilities are available.

A-41. The Arthus reaction

This is an experimental method using only animal models for studying the formation of immune complexes in tissues and how immune complexes cause inflammation (see Section 12-16). The original reaction described by Maurice Arthus was induced by the repeated injection of horse serum into rabbits. Initial injections of horse serum into the skin induced no reaction, but later injections, following the production of antibodies to the proteins in horse serum, induced an inflammatory reaction at the site of injection after several hours, characterized by the presence of edema, hemorrhage, and neutrophil infiltration, which frequently progressed to tissue necrosis. Most investigators now use passive models of the Arthus reaction in which either antibody is infused systemically and antigen given locally (passive Arthus reaction) or antigen is infused systemically and antibody injected locally (reverse passive Arthus reaction).

Manipulation of the immune system

A-42. Adoptive transfer of lymphocytes

Ionizing radiation from X-ray or γ-ray sources kills lymphoid cells at doses that spare the other tissues of the body. This makes it possible to eliminate immune function in a recipient animal before attempting to restore immune function by adoptive transfer, and allows the effect of the adoptively transferred cells to be studied in the absence of other lymphoid cells. James Gowans originally used this technique to prove the role of the lymphocyte in immune responses. He showed that all active immune responses could be transferred to irradiated recipients by small lymphocytes from immunized donors. This technique can be refined by transferring only certain lymphocyte subpopulations, such as B cells, CD4 T cells, and so on. Even cloned T-cell lines have been tested for their ability to transfer immune function, and have been shown to confer adoptive immunity to their specific antigen. Such adoptive transfer studies are a cornerstone in the study of the intact immune system, as they can be carried out rapidly, simply, and in any strain of mouse.

A-43. Hematopoietic stem-cell transfers

All cells of hematopoietic origin can be eliminated by treatment with high doses of X rays, allowing replacement of the entire hematopoietic system, including lymphocytes, by transfusion of donor bone marrow or purified hematopoietic stem cells from another animal. The resulting animals are called radiation bone marrow chimeras from the Greek word chimera, a mythical animal that had the head of a lion, the tail of a serpent, and the body of a goat. This technique is used experimentally to examine the development of lymphocytes, as opposed to their effector functions, and has been particularly important in studying T-cell development. Essentially the same technique is used in humans to replace the hematopoietic system when it fails, as in aplastic anemia or after nuclear accidents, or to eradicate the bone marrow and replace it with normal marrow in the treatment of certain cancers. In man, bone marrow is the main source of hematopoietic stem cells, but increasingly they are being obtained from peripheral blood after the donor has been treated with hematopoietic growth factors such as GM-CSF, or from umbilical cord blood, which is rich in such stem cells.

A-44. In vivo depletion of T cells

The importance of T-cell function in vivo can be ascertained in mice with no T cells of their own. Under these conditions, the effect of a lack of T cells can be studied, and T-cell subpopulations can be restored selectively to analyze their specialized functions. T lymphocytes originate in the thymus, and neonatal thymectomy, the surgical removal of the thymus of a mouse at birth, prevents T-cell development from occurring because the export of most functionally mature T cells only occurs after birth in the mouse. Alternatively, adult mice can be thymectomized and then irradiated and reconstituted with bone marrow; such mice will develop all hematopoietic cell types except mature T cells.

The recessive nude mutation in mice is caused by a mutation in the gene for the transcription factor Wnt and in homozygous form causes hairlessness and absence of the thymus. Consequently, these animals fail to develop T cells from bone marrow progenitors. Grafting thymectomized or nude/nude mice with thymic epithelial elements depleted of lymphocytes allows the graft recipients to develop normal mature T cells. This procedure allows the role of the nonlymphoid thymic stroma to be examined; it has been crucial in determining the role of thymic stromal cells in T-cell development (see Chapter 7).

A-45. In vivo depletion of B cells

There is no single site of B-cell development in mice, so techniques such as thymectomy cannot be applied to the study of B-cell function and development in rodents. However, bursectomy, the surgical removal of the Bursa of Fabricius in birds, can inhibit the development of B cells in these species. In fact, it was the effect of thymectomy versus bursectomy that led to the naming of T cells for thymus-derived lymphocytes and B cells for bursal-derived lymphocytes. There are no known spontaneous mutations (analogous to the nude mutation) in mice that produce animals with T cells but no B cells. However, such mutations exist in humans, leading to a failure to mount humoral immune responses or make antibody. The diseases produced by such mutations are called agammaglobulinemias because they were originally detected as the absence of gamma globulins. The genetic basis for one form of this disease in humans has now been established (see Chapter 11), and some features of the disease can be reproduced in mice by targeted disruption of the corresponding gene (see Section A-47). Several different mutations in crucial regions of immunoglobulin genes have already been produced by gene targeting and have provided mice lacking B cells.

A-46. Transgenic mice

The function of genes has traditionally been studied by observing the effects of spontaneous mutations in whole organisms and, more recently, by analyzing the effects of targeted mutations in cultured cells. The advent of gene cloning and in vitro mutagenesis now make it possible to produce specific mutations in whole animals. Mice with extra copies or altered copies of a gene in their genome can be generated by transgenesis, which is now a well established procedure. To produce transgenic mice, a cloned gene is introduced into the mouse genome by microinjection into the male pronucleus of a fertilized egg, which is then implanted into the uterus of a pseudopregnant female mouse. In some of the eggs, the injected DNA becomes integrated randomly into the genome, giving rise to a mouse that has an extra genetic element of known structure, the transgene (Fig. A.42).

Figure A.42. The function and expression of genes can be studied in vivo by using transgenic mice.

Figure A.42

The function and expression of genes can be studied in vivo by using transgenic mice. DNA encoding a protein of interest, here the mouse MHC class II protein Eα, is purified and microinjected into the male pronuclei of fertilized eggs. The eggs (more...)

The transgene, to be studied in detail, needs to be introduced onto a stable, well-characterized genetic background. However, it is difficult to prepare transgenic embryos successfully in inbred strains of mice, and transgenic mice are routinely prepared in F2 embryos (that is, the embryo formed after the mating of two F1 animals). The transgene must then be bred onto a well-characterized genetic background; this requires 10 generations of back-crossing with an inbred strain to assure that the integrated transgene is largely (>99%) free of heterogeneous genes from the founder mouse of the transgenic mouse line (Fig. A.43).

Figure A.43. The breeding of transgenic co-isogeneic or congenic mouse strains.

Figure A.43

The breeding of transgenic co-isogeneic or congenic mouse strains. Transgenic mouse strains are routinely made in F2 mice. To produce mice on an inbred background, the transgene is introgressively back-crossed onto a standard strain, usually C57BL/6 (B6). (more...)

This technique allows one to study the impact of a newly discovered gene on development, to identify the regulatory regions of a gene required for its normal tissue-specific expression, to determine the effects of its over-expression or expression in inappropriate tissues, and to find out the impact of mutations on gene function. Transgenic mice have been particularly useful in studying the role of T-cell and B-cell receptors in lymphocyte development, as described in Chapter 7.

A-47. Gene knockout by targeted disruption

In many cases, the functions of a particular gene can be fully understood only if a mutant animal that does not express the gene can be obtained. Whereas genes used to be discovered through identification of mutant phenotypes, it is now far more common to discover and isolate the normal gene and then determine its function by replacing it in vivo with a defective copy. This procedure is known as gene knockout, and it has been made possible by two fairly recent developments: a powerful strategy to select for targeted mutation by homologous recombination, and the development of continuously growing lines of embryonic stem cells (ES cells). These are embryonic cells which, on implantation into a blastocyst, can give rise to all cell lineages in a chimeric mouse.

The technique of gene targeting takes advantage of the phenomenon known as homologous recombination (Fig. A.44). Cloned copies of the target gene are altered to make them nonfunctional and are then introduced into the ES cell where they recombine with the homologous gene in the cell's genome, replacing the normal gene with a nonfunctional copy. Homologous recombination is a rare event in mammalian cells, and thus a powerful selection strategy is required to detect those cells in which it has occurred. Most commonly, the introduced gene construct has its sequence disrupted by an inserted antibiotic-resistance gene such as that for neomycin resistance. If this construct undergoes homologous recombination with the endogenous copy of the gene, the endogenous gene is disrupted but the antibiotic-resistance gene remains functional, allowing cells that have incorporated the gene to be selected in culture for resistance to the neomycin-like drug G418. However, antibiotic resistance on its own shows only that the cells have taken up and integrated the neomycin-resistance gene. To be able to select for those cells in which homologous recombination has occurred, the ends of the construct usually carry the thymidine kinase gene from the herpes simplex virus (HSV-tk). Cells that incorporate DNA randomly usually retain the entire DNA construct including HSV-tk, whereas homologous recombination between the construct and cellular DNA, the desired result, involves the exchange of homologous DNA sequences so that the nonhomologous HSV-tk genes at the ends of the construct are eliminated. Cells carrying HSV-tk are killed by the antiviral drug ganciclovir, and so cells with homologous recombinations have the unique feature of being resistant to both neomycin and ganciclovir, allowing them to be selected efficiently when these drugs are added to the cultures (see Fig. A.44).

Figure A.44. The deletion of specific genes can be accomplished by homologous recombination.

Figure A.44

The deletion of specific genes can be accomplished by homologous recombination. When pieces of DNA are introduced into cells, they can integrate into cellular DNA in two different ways. If they randomly insert into sites of DNA breaks, the whole piece (more...)

This technique can be used to produce homozygous mutant cells in which the effects of knocking-out a specific gene can be analyzed. Diploid cells in which both copies of a gene have been mutated by homologous recombination can be selected after transfection with a mixture of constructs in which the gene to be targeted has been disrupted by one or other of two different antibiotic-resistance genes. Having obtained a mutant cell with a functional defect, the defect can be ascribed definitively to the mutated gene if the mutant phenotype can be reverted with a copy of the normal gene transfected into the mutant cell. Restoration of function means that the defect in the mutant gene has been complemented by the normal gene's function. This technique is very powerful as it allows the gene that is being transferred to be mutated in precise ways to determine which parts of the protein are required for function.

To knock out a gene in vivo, it is only necessary to disrupt one copy of the cellular gene in an ES cell. ES cells carrying the mutant gene are produced by targeted mutation (see Fig. A.44), and injected into a blastocyst which is reimplanted into the uterus. The cells carrying the disrupted gene become incorporated into the developing embryo and contribute to all tissues of the resulting chimeric offspring, including those of the germline. The mutated gene can therefore be transmitted to some of the offspring of the original chimera, and further breeding of the mutant gene to homozygosity produces mice that completely lack the expression of that particular gene product (Fig. A.45). The effects of the absence of the gene's function can then be studied. In addition, the parts of the gene that are essential for its function can be identified by determining whether function can be restored by introducing different mutated copies of the gene back into the genome by transgenesis.

Figure A.45. Gene knockout in embryonic stem cells enables mutant mice to be produced.

Figure A.45

Gene knockout in embryonic stem cells enables mutant mice to be produced. Specific genes can be inactivated by homologous recombination in cultures of embryonic stem cells (ES cells). Homologous recombination is carried out as described in Fig. A.44. In (more...)

The manipulation of the mouse genome by gene knockout and transgenesis is revolutionizing our understanding of the role of individual genes in lymphocyte development and function.

Because the most commonly used ES cells are derived from a poorly characterized strain of mice known as strain 129, the analysis of the function of a gene knockout often requires extensive back-crossing to another strain, just as in transgenic mice (see Fig. A.43). One can track the presence of the mutant copy of the gene by the presence of the neor gene. After sufficient back-crossing, the mice are intercrossed to produce mutants on a stable genetic background.

A problem with gene knockouts arises when the function of the gene is essential for the survival of the animal; in such cases the gene is termed a recessive lethal gene and homozygous animals cannot be produced. However, by making chimeras with mice that are deficient in B and T cells, it is possible to analyze the function of recessive lethal genes in lymphoid cells. To do this, ES cells with homozygous lethal loss-of-function mutations are injected into blastocysts of mice lacking the ability to rearrange their antigen-receptor genes because of a mutation in their recombinase-activating genes (RAG knockout mice). As these chimeric embryos develop, the RAG-deficient cells can compensate for any developmental failure resulting from the gene knockout in the ES cells in all except the lymphoid lineage. So long as the mutated ES cells can develop into hematopoietic progenitors in the bone marrow, the embryos will survive and all of the lymphocytes in the resulting chimeric mouse will be derived from the mutant ES cells (Fig. A.46).

Figure A.46. The role of recessive lethal genes in lymphocyte function can be studied using RAG-deficient chimeric mice.

Figure A.46

The role of recessive lethal genes in lymphocyte function can be studied using RAG-deficient chimeric mice. ES cells homozygous for the lethal mutation are injected into a RAG-deficient blastocyst (top panel). The RAG-deficient cells can give rise to (more...)

A second powerful technique achieves tissue-specific or developmentally regulated gene deletion by employing the DNA sequences and enzymes used by bacteriophage P1 to excise itself from a host cell's genome. Integrated bacteriophage P1 DNA is flanked by recombination signal sequences called loxP sites. A recombinase, Cre, recognizes these sites, cuts the DNA and joins the two ends, thus excising the intervening DNA in the form of a circle. This mechanism can be adapted to allow the deletion of specific genes in a transgenic animal only in certain tissues or at certain times in development. First, loxP sites flanking a gene, or perhaps just a single exon, are introduced by homologous recombination (Fig. A.47). Usually, the introduction of these sequences into flanking or intronic DNA does not disrupt the normal function of the gene. Mice containing such loxP mutant genes are then mated with mice made transgenic for the Cre recombinase, under the control of a tissue-specific or inducible promoter. When the Cre recombinase is active, either in the appropriate tissue or when induced, it excises the DNA between the inserted loxP sites, thus inactivating the gene or exon. Thus, for example, using a T-cell specific promoter to drive expression of the Cre recombinase, a gene can be deleted only in T cells, while remaining functional in all other cells of the animal. This is an extremely powerful genetic technique that while still in its infancy, was used to demonstrate the importance of B-cell receptors in B-cell survival. It is certain to yield exciting results in the future.

Figure A.47. The P1 bacteriophage recombination system can be used to eliminate genes in particular cell lineages.

Figure A.47

The P1 bacteriophage recombination system can be used to eliminate genes in particular cell lineages. The P1 bacteriophage protein Cre excises DNA that is bounded by recombination signal sequences called loxP sequences. These sequences can be introduced (more...)

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Copyright © 2001, Garland Science.
Bookshelf ID: NBK10755


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