Immunology_Janeway

Immunology_Janeway. Label target cells with Na2 51CrO4 Killed cells release radioactive chromium Add cytotoxic T cells to labeled target cells Fig. 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 by the release of radioactive chromium into the medium, detectable within 4 hours of mixing target cells with T cells. 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.


Immunology_Janeway

Immunology_Janeway. An alternative to these in vitro cytotoxicity assays is to measure target-cell killing by cytotoxic T cells in intact experimental animals. This assay is generally performed with mice that have been infected with a pathogen known to induce a strong cytotoxic T-cell response, such as a virus. Target cells are incubated with the antigenic peptide, which will bind to MHC class I on the target-cell surface. These cells are then incubated with a low concentration of the fluorescent dye CFSE (see Section A-26). A control population of cells that is not given the antigenic peptide is incubated with a high concentration of CFSE, allowing these cells to be distinguished from the antigen-bearing target cells. The two cell populations are mixed 1:1 and injected into the experimental animals. Four hours later, spleen cells are recovered from the animals and analyzed by FACS, allowing the specific target-cell lysis to be calculated from the ratio of the two CFSE-labeled cell populations (Fig.


Immunology_Janeway

Immunology_Janeway. hours later, spleen cells are recovered from the animals and analyzed by FACS, allowing the specific target-cell lysis to be calculated from the ratio of the two CFSE-labeled cell populations (Fig. A.39).


Immunology_Janeway

Immunology_Janeway. Target cells and control cells are labeled with different concentrations of dye, mixed 1:1, and injected into mice


Immunology_Janeway

Immunology_Janeway. Fig. A.39 Assay for cytotoxic T-cell activity using CFSE-labeled target cells. To detect cytotoxic T-cell activity in intact experimental animals, mice that have been infected with a virus are injected with a mixture of target cells labeled with the fluorescent dye CFSE. One group of target cells is pre-incubated with a viral peptide that binds to MHC class I on the target cells; this group of cells is labeled with a low concentration of CFSE. A second group of cells is incubated with a control (nonviral) peptide and is labeled with a high concentration of CFSE. The two groups of cells are mixed together in a 1:1 ratio, and injected into the infected mice. After 4 hours, the mice are sacrificed and the target cells are recovered and analyzed by flow cytometry. Examination of the ratio of the two target-cell populations provides a measure of specific lysis of viral peptide-coated target cells. A-29 Assays for CD4 T cells.


Immunology_Janeway

Immunology_Janeway. A-29 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 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 cytokine released. Because different effector T cells release different amounts and types of cytokines, one can learn about the effector potential of a T cell by measuring the proteins it produces.


Immunology_Janeway

Immunology_Janeway. Cytokines can be detected by their activity in biological assays of cell growth, where the cytokines serve either as growth factors or as growth inhibitors. A more specific assay is a modification of ELISA known as a capture or sandwich ELISA (see Section A-4). In this assay, the cytokine is characterized by its ability to act as a 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-22).


Immunology_Janeway

Immunology_Janeway. Sandwich ELISA and ELISPOT avoid a major problem of cytokine bioassays, namely, 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 then identify and count them by FACS (see Section A-23).


Immunology_Janeway

Immunology_Janeway. 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 the reverse transcriptase–polymerase chain reaction (RT–PCR). Reverse transcriptase is an enzyme used by certain RNA viruses, such as HIV, to convert an RNA genome into a DNA copy, or cDNA. In RT–PCR, mRNA is isolated from cells and cDNA copies are made in vitro using reverse transcriptase. The desired cDNA is then selectively amplified by PCR by 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 will thus give


Immunology_Janeway

Immunology_Janeway. 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 will 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.


Immunology_Janeway

A-30 Transfer of protective immunity.

Immunology_Janeway. A-30 Transfer of protective immunity.


Immunology_Janeway

Immunology_Janeway. Protective immunity to a pathogen may involve humoral immunity, cell-mediated immunity, or both. For studies in experimental animals such as 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). 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 (Fig. A.40). 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, to distinguish it from active immunization with antigen,


Immunology_Janeway

Immunology_Janeway. so long as the transferred antibodies remain active in the recipient’s body. This type of transfer is therefore called passive immunization, to distinguish it from active immunization with antigen, which can provide lasting immunity. A disadvantage of passive


Immunology_Janeway

Immunology_Janeway. Fig. A.40 In vivo assay for the presence of protective immunity after vaccination in animals. Mice are injected with the test vaccine, such as a heat-killed pathogen, or a control such as saline solution. Different groups are then challenged with lethal or pathogenic doses of the test pathogen or with an unrelated pathogen as a specificity control (not shown). Unimmunized animals die or become severely infected (left panel). Successful vaccination is seen as specific protection of immunized mice against infection with the test pathogen. This is called active immunity, and the process is called active immunization (middle panel). If this immune protection can be transferred to a normal syngeneic recipient with serum from an immune donor, then immunity is mediated by antibodies; such immunity is called humoral immunity and the process is called passive immunization (right panel). If immunity can be transferred only by infusing lymphoid cells from the immune donor into a normal syngeneic


Immunology_Janeway

Immunology_Janeway. is called humoral immunity and the process is called passive immunization (right panel). If immunity can be transferred only by infusing lymphoid cells from the immune donor into a normal syngeneic recipient, then the immunity is called cell-mediated immunity and the transfer process is called adoptive transfer or adoptive immunization (not shown). Passive immunity is short-lived, because antibody is eventually catabolized, but adoptively transferred immunity is mediated by immune cells, which can survive and provide longer-lasting immunity.


Immunology_Janeway

Immunology_Janeway. immunization is that 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 14-5) or, if the recipient becomes allergic to the foreign serum, to anaphylaxis (see Section 14-10).


Immunology_Janeway

Immunology_Janeway. 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 cellmediated 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-31 Adoptive transfer of lymphocytes.


Immunology_Janeway

Immunology_Janeway. A-31 Adoptive transfer of lymphocytes. Ionizing radiation from X-ray or gamma-ray sources kills lymphoid and other immune cells at doses that spare the other tissues of the body. This makes it possible to eliminate immune function in a recipient animal before CD45.1 CD45.2 After transfer into CD45.2 recipient, CD45.1 cells can be identifed by ˜ow cytometry Cells isolated from one congenic mouse line express CD45.1


Immunology_Janeway

Immunology_Janeway. CD45.1 CD45.2 After transfer into CD45.2 recipient, CD45.1 cells can be identifed by ˜ow cytometry Cells isolated from one congenic mouse line express CD45.1 Fig. A.41 Adoptive transfer of congenically marked cells. Hematopoietic cells can be transferred between genetically identical (or nearly identical) mice. The transferred cells, usually a minority population in the recipient, are identified based on expression of an allelic variant of an abundant cell-surface receptor. One common receptor used for this purpose is CD45, which has two alleles that can be distinguished by allele-specific antibodies. When cells from a CD45.1+ mouse are transferred into mice of the identical strain (save for their expression of CD45.2), the donor-cell population can easily be identified by antibody staining followed by flow cytometry or immunofluorescence microscopy.


Immunology_Janeway

Immunology_Janeway. 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.


Immunology_Janeway

Immunology_Janeway. One common use of adoptive transfer assays takes advantage of the availability of T-cell receptor or B-cell receptor transgenic mice (see Section A-34). In this case, the adoptively transferred lymphocytes are a homogeneous population with a fixed antigen specificity. These cells can be transferred into unmanipulated recipient animals of the same inbred strain without the need to deplete the host immune system, and their ability to respond to immunization or challenge by infection can be monitored. One advantage of this experimental strategy is that relatively small numbers of antigen-specific T cells or B cells can be transferred; after dilution by the recipient’s lymphocyte population, the responses of these cells can be examined in the environment of a normal immune response carried out by the host’s immune system. Commonly, the transferred cells are ‘marked’ with an allelic variant of an abundant cell-surface receptor, such as CD45 (Fig. A.41). When the donor lymphocytes express


Immunology_Janeway

Immunology_Janeway. by the host’s immune system. Commonly, the transferred cells are ‘marked’ with an allelic variant of an abundant cell-surface receptor, such as CD45 (Fig. A.41). When the donor lymphocytes express one allelic variant of CD45 and the recipient cells express a different variant, the transferred cells can easily be distinguished from the host cells by staining with an antibody that binds to one variant of CD45, but not the other. When two strains of mice are genetically identical with the exception of a single gene, they are said to be congenic. In the example above, the donor strain and the recipient strain are referred to as ‘CD45 congenics’; it should be noted, however, that in the case where one strain is a T-cell receptor or B-cell receptor transgenic line, this terminology is not completely accurate, as the presence of the transgenic DNA as a genetic difference is conveniently ignored. Such adoptive transfer studies are a cornerstone in the study of the intact immune system. They


Immunology_Janeway

Immunology_Janeway. accurate, as the presence of the transgenic DNA as a genetic difference is conveniently ignored. Such adoptive transfer studies are a cornerstone in the study of the intact immune system. They have provided a rapid and convenient means of determining the effects of many gene deficiencies, such as those in cell-surface receptors, transcription factors, cytokines, and cell survival/cell death genes, on the ability of T cells or B cells to mount protective immune responses.


Immunology_Janeway

A-32 Hematopoietic stem-cell transfers.

Immunology_Janeway. A-32 Hematopoietic stem-cell transfers.


Immunology_Janeway

Immunology_Janeway. All cells of hematopoietic origin can be eliminated by treatment with high doses of γ radiation or 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 immune-cell lineages, 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 humans, bone marrow is the main source of hematopoietic stem cells, but they


Immunology_Janeway

Immunology_Janeway. accidents, or to eradicate the bone marrow and replace it with normal marrow in the treatment of certain cancers. In humans, bone marrow is the main source of hematopoietic stem cells, but they are increasingly 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 (see Chapter 15).


Immunology_Janeway

Immunology_Janeway. A-33 In vivo administration of antibodies. Antibodies administered to intact experimental animals, or to humans, provide a potent means of manipulating the immune system. Depending on the target molecule recognized by the antibody, and the intrinsic properties of each antibody, in vivo antibody administration can either inhibit the function of the target molecule or, in some cases, lead to the elimination of a cell population that expresses the target molecule.


Immunology_Janeway

Immunology_Janeway. In animal models, antibodies targeting an individual cytokine have been used to inhibit that cytokine’s function during an otherwise intact immune response. Experiments of this type provided some of the first evidence that the cytokine IL-12 provides an important signal in polarizing CD4+ T cells into the TH1 lineage following infection with an intracellular protozoan. This approach has also been used with great success in humans. One of the most common treatments for the inflammatory autoimmune disease rheumatoid arthritis (see Chapter 16) is the administration of an antibody that binds to the cytokine TNF-α; in this case, the inhibition of TNF-α activity provides patients with relief from the symptoms of joint inflammation. The great utility of this antibody therapy has led to the development of related strategies for inhibiting cytokine actions in vivo. One successful approach has been to create a hybrid protein that has the ligand-binding domain of the cytokine’s receptor fused to


Immunology_Janeway

Immunology_Janeway. of related strategies for inhibiting cytokine actions in vivo. One successful approach has been to create a hybrid protein that has the ligand-binding domain of the cytokine’s receptor fused to the constant-region domains (Fc) of an antibody heavy chain (Fig. A.42). This Fc-fusion protein acquires the stability and long half-life of an antibody, but has the binding properties of the cytokine receptor. When given in vivo, the Fc-fusion protein binds to the cytokine, thereby interfering with the cytokine’s ability to stimulate its receptor on immune cells. As an example, the Fc-fusion protein containing the TNF-receptor ligand-binding domain has also been used as an effective treatment for patients with rheumatoid arthritis.


Immunology_Janeway

Immunology_Janeway. Antibody administration can also be used to augment the immune response by interfering with T-cell surface receptors, such as CTLA-4 or PD-1. When engaged by their ligands, these receptors normally function to downregulate the immune response. From experiments in mice, antibodies that bind to and inhibit these receptors have been found to enhance immune responses to tumors, leading in some cases to tumor eradication. Currently, these strategies are being tested in humans for a variety of tumor types, and the initial results have shown great promise.


Immunology_Janeway

Immunology_Janeway. In vivo administration of antibodies can also be used to deplete specific cell populations. The efficiency with which a given antibody functions for in vivo depletion is quite variable, as the mechanism relies on a process known as antibodydependent cellmediated cytotoxicity (ADCC) (see Section 10-23 and Fig. 10.36). When a cell is coated with antibodies, it becomes a target of natural killer (NK) cells that express the Fc receptor known as CD16 or FcγRIII. The cross-linking of FcγRIII induces the NK cell to kill the antibody-coated target cell. While FcγRIII is a receptor for IgG, it does not bind with equal affinity to all IgG subtypes; thus the efficiency of ADCC after administration of a given antibody is determined by its ability to cross-link FcγRIII and induce NK cell killing. Common uses for this technique include the depletion of CD4+ T cells with an antibody to CD4, or the depletion of CD8+ T cells with an antibody to CD8. In human patients undergoing organ transplantation,


Immunology_Janeway

Immunology_Janeway. uses for this technique include the depletion of CD4+ T cells with an antibody to CD4, or the depletion of CD8+ T cells with an antibody to CD8. In human patients undergoing organ transplantation, T cells are transiently depleted by administering an antibody to the CD3 component of the T-cell receptor complex. This produces a severe, but temporary, state of immunosuppression during the early stages of post-transplantation. As with all in vivo antibody depletion regimens, the depleted cell population gradually returns as cells of that subset are replenished by ongoing lymphocyte development.


Immunology_Janeway

Immunology_Janeway. Fig. A.42 In vivo administration of antibodies is an effective therapeutic. The cytokine TNF-α contributes to chronic inflammation in a range of conditions, including rheumatoid arthritis, by binding to and triggering signaling of the TNF receptor (TNFR). To treat these conditions, a fusion protein consisting of the constant-region domains of human IgG1 is fused to the extracellular portion of the TNFR, creating a therapeutic known as etanercept. When administered to patients, this fusion protein is effective at binding TNF-α and preventing it from triggering TNFR signaling, thereby reducing inflammation.


Immunology_Janeway

Immunology_Janeway. Fig. A.43 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 are then implanted into pseudopregnant female mice. The resulting offspring are screened for the presence of the transgene in their cells, and positive mice are used as founders that transmit the transgene to their offspring, establishing a line of transgenic mice that carry one or more extra genes. The function of the Eα gene used here is tested by breeding the transgene into C57BL/6 mice that carry an inactivating mutation in their endogenous Eα gene. A-34 Transgenic mice.


Immunology_Janeway

Immunology_Janeway. A-34 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 makes 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.43).


Immunology_Janeway

Immunology_Janeway. 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 overexpression or its 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 8, and in providing a source of primary T and B lymphocytes of known antigen specificity for adoptive transfer studies (see Section A-31). This utility is largely due to the fact that expression of the transgene-encoded T-cell and B-cell receptors preempts the rearrangement and expression of the endogenous antigen receptor genes during T-cell and B-cell development, respectively, thereby generating homogeneous populations of cells bearing a unique antigen receptor of known specificity.


Immunology_Janeway

Immunology_Janeway. A-35 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 the 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 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 that, on implantation into a blastocyst, can give rise to all cell lineages in a chimeric mouse.


Immunology_Janeway

Immunology_Janeway. 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 (neor). 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


Immunology_Janeway

Immunology_Janeway. 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


Immunology_Janeway

Immunology_Janeway. 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).


Immunology_Janeway

Immunology_Janeway. DNA is introduced into cell Target gene interrupted by insertion of neomycin-resistance gene (neor) neorDNA fails to integrate Cell is killed by ganciclovir DNA integrates at random site on genome. Cell expresses both neorand HSV-tk Cell expresses neomycin resistance but not HSV-tk, so is not killed by either G418 or ganciclovir Homologous recombination replaces wild-type ˜2 -microglobulin gene with interrupted copy Cell is killed by G418 (a neomycin analog)


Immunology_Janeway

Immunology_Janeway. To knock out a gene in vivo, it is necessary only to disrupt one copy of the cellular gene in an ES cell. These ES cells are then 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 to homozygosity of the mutant gene 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


Immunology_Janeway

Immunology_Janeway. Fig. 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 is usually integrated, often in several copies. However, extrachromosomal DNA can also undergo homologous recombination with the cellular copy of the gene, in which case only the central, homologous region is incorporated into cellular DNA. Inserting a selectable marker gene such as resistance to neomycin (neor) into the coding region of a gene does not prevent homologous recombination, and it achieves two goals. First, any cell that has integrated the injected DNA is protected from the neomycin-like antibiotic G418. Second, when the gene recombines with homologous cellular DNA, the neor gene disrupts the coding sequence of the modified cellular gene. Homologous recombinants can be discriminated from random insertions if the


Immunology_Janeway

Immunology_Janeway. the gene recombines with homologous cellular DNA, the neor gene disrupts the coding sequence of the modified cellular gene. Homologous recombinants can be discriminated from random insertions if the gene encoding herpes simplex virus thymidine kinase (HSV-tk) is placed at one or both ends of the DNA construct, which is often known as a ‘targeting construct’ because it targets the cellular gene. In random DNA integrations, HSV-tk is retained. HSV-tk renders the cell sensitive to the antiviral agent ganciclovir. However, as HSV-tk is not homologous to the target DNA, it is lost from homologous recombinants. Thus, cells that have undergone homologous recombination are uniquely resistant to both G418 and ganciclovir, and survive in a mixture of the two antibiotics. The presence of the disrupted gene has to be confirmed by Southern blotting or by PCR using primers in the neor gene and in cellular DNA lying outside the region used in the targeting construct. By using two different


Immunology_Janeway

Immunology_Janeway. disrupted gene has to be confirmed by Southern blotting or by PCR using primers in the neor gene and in cellular DNA lying outside the region used in the targeting construct. By using two different resistance genes, one can disrupt the two cellular copies of a gene, making a deletion mutant (not shown).


Immunology_Janeway

Immunology_Janeway. Fig. 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 performed as described in Fig. A.44. In this example, the gene encoding β2-microglobulin in ES cells is disrupted by homologous recombination with a targeting construct. Only a single copy of the gene needs to be disrupted. ES cells in which homologous recombination has taken place are injected into mouse blastocysts. If the mutant ES cells give rise to germ cells in the resulting chimeric mice (striped in the figure), the mutant gene can be transferred to their offspring. By breeding the mutant gene to homozygosity, offspring can be tested to determine if a mutant phenotype is generated. In this case, the homozygous mutant mice lack MHC class I molecules on their cells, because MHC class I molecules have to pair with β2-microglobulin for surface expression. The


Immunology_Janeway

Immunology_Janeway. is generated. In this case, the homozygous mutant mice lack MHC class I molecules on their cells, because MHC class I molecules have to pair with β2-microglobulin for surface expression. The β2-microglobulin-deficient mice can then be bred with mice transgenic for subtler mutants of the deleted gene, allowing the effect of such mutants to be tested in vivo.


Immunology_Janeway

Immunology_Janeway. 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. The manipulation of the mouse genome by gene knockout and transgenesis has revolutionized 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. 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.


Immunology_Janeway

Immunology_Janeway. 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. To study the function of such a gene, tissue-specific or developmentally regulated gene deletion can be employed. This strategy makes use of 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 flanking just a single exon, are introduced by homologous recombination (Fig. A.46). Usually, the introduction


Immunology_Janeway

Immunology_Janeway. or at certain times in development. First, loxP sites flanking a gene, or perhaps flanking just a single exon, are introduced by homologous recombination (Fig. A.46). Usually, the introduction of these sequences into flanking or intronic DNA does not disrupt the normal function of the gene. Next, mice containing such loxP mutant genes are mated with mice made transgenic for Cre recombinase that has been placed 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 extremely powerful genetic technique was used to demonstrate the importance of B-cell receptors in B-cell survival.


Immunology_Janeway

Immunology_Janeway. Recently, a new technology has been developed for inducing specific gene disruptions in mice; it is known as the CRISPR/Cas9 system. This technique is adapted from a bacterial system that uses an RNA-based strategy to generate double-stranded DNA breaks in the genomes of invading pathogens or plasmids, a form of bacterial immunity. The Cas9 gene encodes an endonuclease; this has been modified for use in eukaryotic cells by incorporating a nuclear localization signal into the protein-coding sequence of the enzyme. To target mutations to a particular gene, a synthetic guide RNA is produced that incorporates a short sequence (~20 nucleotides) homologous to the gene Animals containing the loxP sites are made transgenic for the Cre protein, expressed from a tissue-specifc promoter only in certain cells, e.g., lymphocytes When expressed, the Cre protein excises the DNA between the loxP sites, deleting the gene only in specifc cell types


Immunology_Janeway

Immunology_Janeway. Fig. A.46 The P1 bacteriophage recombination system times during development (center panel). In the cells in which the Cre can be used to eliminate genes in particular cell lineages. protein is expressed, it recognizes the loxP sequences and excises The P1 bacteriophage protein Cre excises DNA that is bounded the DNA lying between them (right panel). Thus, individual genes can by recombination signal sequences called loxP sequences. be deleted only in certain cell types or only at certain times. In this These sequences can be introduced at either end of a gene by way, genes that are essential for the normal development of a mouse homologous recombination (left panel). Animals carrying genes can be analyzed for their function in the developed animal and/or in flanked by loxP can also be made transgenic for the gene encoding specific cell types. Genes are shown as boxes, RNA as squiggles, the Cre protein, which is placed under the control of a tissue-specific and proteins as colored


Immunology_Janeway

Immunology_Janeway. made transgenic for the gene encoding specific cell types. Genes are shown as boxes, RNA as squiggles, the Cre protein, which is placed under the control of a tissue-specific and proteins as colored balls. promoter so that it is expressed only in certain cells or only at certain being targeted along with sequences that bind the Cas9 enzyme. The guide RNA recruits Cas9 to the genomic location, where the endonuclease will produce a double-stranded DNA break (Fig. A.47). When this break is repaired


Immunology_Janeway

Immunology_Janeway. Fig. A.47 Genetic engineering using the bacterial CRISPR/ Cas9 system. Genetic engineering can be targeted to a specific gene locus in cells by using two components, the bacterial Cas9 enzyme and a guide RNA (left panel). The guide RNA is a single-stranded RNA that contains two regions of sequence in tandem, the first with homology to the gene being targeted and a second recognized by the Cas9 enzyme. The guide RNA targets the enzyme to the homologous genomic region, promoting double-stranded DNA cleavage by the Cas9 endonuclease 3–4 nucleotides upstream of the protospacer adjacent motif (PAM) sequence (right panel). The PAM sequence required by the Cas9 endonuclease is the dinucleotide GG (CC on the other strand). When the double-stranded DNA break is repaired by the nonhomologous end-joining pathway, small deletions and/or point mutations are introduced into the target gene, often leading to loss of gene function. To induce a specific sequence replacement in the target gene, cells


Immunology_Janeway

Immunology_Janeway. pathway, small deletions and/or point mutations are introduced into the target gene, often leading to loss of gene function. To induce a specific sequence replacement in the target gene, cells are provided with a template DNA, in addition to Cas9 and the guide RNA. This template is a double-stranded DNA sequence homologous to the target gene, but containing specific nucleotide changes. In the presence of this template, cells will repair the Cas9-mediated double-stranded cleavage using homologous recombination, rather than nonhomologous end-joining, thereby replacing the original sequence with the sequence provided in the template DNA.


Immunology_Janeway

Immunology_Janeway. by the nonhomologous end-joining DNA repair pathway, small insertions or deletions are commonly introduced, leading to a disruption of the original sequence.


Immunology_Janeway

Immunology_Janeway. This powerful technique can be used to generate homozygous gene deficiencies in cultured cells and cell lines, but importantly, it can also be used as a single-step means of generating homozygous mutant mice. For this latter purpose, RNA molecules encoding Cas9 are mixed with guide RNAs and injected into single-cell mouse zygotes, using the same technique as that used to generate transgenic mouse lines (see Fig. A.43). Due to the efficiency of the CRISPR/Cas9 system, these embryos frequently harbor mutations on both alleles of the targeted gene. Thus, after transplantation of the embryos into foster mothers, the pups born from these embryos are already homozygous for the targeted gene, without the need for lengthy mouse breeding. A refinement of this technique has been developed that allows specific nucleotide changes to be introduced into the targeted gene, rather than the random changes resulting from nonhomologous end-joining. This is accomplished by introducing a DNA


Immunology_Janeway

Immunology_Janeway. that allows specific nucleotide changes to be introduced into the targeted gene, rather than the random changes resulting from nonhomologous end-joining. This is accomplished by introducing a DNA oligonucleotide into the fertilized mouse zygotes along with the Cas9 and guide RNAs. The oligonucleotide contains the desired nucleotide changes flanked by sequences homologous to the targeted gene. When this oligonucleotide is present, the double-strand DNA break introduced by Cas9 is preferentially repaired by a homology-directed process that replaces the damaged DNA with the sequences from the oligonucleotide (see Fig. A.47).


Immunology_Janeway

Immunology_Janeway. A-36 Knockdown of gene expression by RNA interference (RNAi).


Immunology_Janeway

Immunology_Janeway. In some cases, the function of a gene can be assessed by reducing, or even eliminating, the expression of that gene in specific cells. This can be accomplished by harnessing a system known as RNA interference, or RNAi, that is present in many eukaryotic cell types. When small double-stranded RNA molecules (referred to as small interfering RNAs, or siRNAs) are introduced into cells, the two RNA strands will be separated and one will bind to an enzyme complex known as RISC (RNA-induced silencing complex). The bound siRNA targets the RISC complex to the mRNA to which it has homology, leading either to translation arrest or to degradation of the mRNA, and thus to silencing of the gene (Fig. A.48). For cells that are not easily transfected with siRNA molecules directly, such as primary lymphocytes and myeloid cells, gene silencing can be implemented by using recombinant viruses. In this case, genes encoding small hairpin RNAs (shRNAs) are introduced into viral vectors that can be packaged


Immunology_Janeway

Immunology_Janeway. and myeloid cells, gene silencing can be implemented by using recombinant viruses. In this case, genes encoding small hairpin RNAs (shRNAs) are introduced into viral vectors that can be packaged into infectious viral particles. The shRNAs encode small RNAs that form a double-stranded hairpin structure; these hairpins are processed by enzymes in the cell to generate the siRNAs needed for gene silencing (see Fig. A.48). Since many primary hematopoietic cell types are readily transduced with recombinant viruses, such as retroviruses and lentiviruses, shRNAs can be effectively used to silence genes in these cell types.


Immunology_Janeway

Immunology_Janeway. Fig. A.48 Knockdown of gene expression using the RNAi pathway. Small double-stranded RNA molecules with homology to an mRNA transcript will target the mRNA for degradation or translation arrest. This pathway is initiated by expression of a short hairpin RNA (shRNA), which can be produced from an expression vector that is introduced into cells, or by the direct transfection of cells with small double-stranded RNA molecules called siRNA. shRNA molecules are processed by the enzyme Dicer to generate siRNA duplexes. The siRNA duplexes bind to the RISC complex, which separates the two RNA strands, retaining the noncoding strand of the siRNA. This noncoding strand targets the siRNA–RISC complex to the mRNA, leading to mRNA degradation or translation termination. Compiled by Daniel DiToro, Carson Moseley, and Jeff Singer, University of Alabama at Birmingham. Data based on CD designations made at the 9th Workshop on Human Leukocyte Differentiation Antigens.


Immunology_Janeway

Immunology_Janeway. Compiled by Daniel DiToro, Carson Moseley, and Jeff Singer, University of Alabama at Birmingham. Data based on CD designations made at the 9th Workshop on Human Leukocyte Differentiation Antigens. * May function as dimers Compiled by Robert Schreiber, Washington University School of Medicine, St Louis, and Daniel DiToro, Carson Moseley, and Jeff Singer, University of Alabama at Birmingham. Chromosome locations are for humans. Chemokines for which there is no human homolog are listed with the mouse chromosome. † ELR refers to the three amino acids that precede the first cysteine residue of the CXC motif. If these amino acids are Glu-Leu-Arg (i.e. ELR+), then the chemokine is chemotactic for neutrophils; if they are not (ELR–) then the chemokine is chemotactic for lymphocytes Compiled by Joost Oppenheim, National Cancer Institute, NIH. Emil von Behring (1854–1917) discovered antitoxin antibodies with Shibasaburo Kitasato.


Immunology_Janeway

Immunology_Janeway. Compiled by Joost Oppenheim, National Cancer Institute, NIH. Emil von Behring (1854–1917) discovered antitoxin antibodies with Shibasaburo Kitasato. Baruj Benacerraf (1920–2011) discovered immune response genes and collaborated in the first demonstration of MHC restriction. Bruce Beutler (1957–) discovered the role of the Toll-like receptor in innate immunity in mice. Jules Bordet (1870–1961) discovered complement as a heat-labile component in normal serum that would enhance the antimicrobial potency of specific antibodies. Ogden C. Bruton (1908–2003) documented the first description of an immunodeficiency disease describing the failure of a male child to produce antibody. Because inheritance of this condition is X-linked and is characterized by the absence of immunoglobulin in the serum (agammaglobulinemia), it was called Bruton’s X-linked agammaglobulinemia.


Immunology_Janeway

Immunology_Janeway. Frank MacFarlane Burnet (1899–1985) proposed the first generally accepted clonal selection hypothesis of adaptive immunity. Robin Coombs (1921–2006) first developed anti-immunoglobulin antibodies to detect the antibodies that cause hemolytic disease of the newborn. The test for this disease is still called the Coombs test. Jean Dausset (1916–2009) was an early pioneer in the study of the human major histocompatibility complex or HLA. Peter Doherty (1940–) and Rolf Zinkernagel (1944–) showed that antigen recognition by T cells is MHC-restricted, thereby establishing the biological role of the proteins encoded by the major histocompatibility complex and leading to an understanding of antigen processing and its importance in the recognition of antigen by T cells. Gerald Edelman (1929–2014) made crucial discoveries about the structure of immunoglobulins, including the first complete sequence of an antibody molecule.


Immunology_Janeway

Immunology_Janeway. Gerald Edelman (1929–2014) made crucial discoveries about the structure of immunoglobulins, including the first complete sequence of an antibody molecule. Paul Ehrlich (1854–1915) was an early champion of humoral theories of immunity, and proposed a famous side-chain theory of antibody formation that bears a striking resemblance to current thinking about surface receptors. James Gowans (1924–) discovered that adaptive immunity is mediated by lymphocytes, focusing the attention of immunologists on these small cells. Jules Hoffman (1941–) discovered the role of the Toll-like receptor in innate immunity in Drosophila melanogaster. Michael Heidelberger (1888–1991) developed the quantitative precipitin assay, ushering in the era of quantitative immunochemistry.


Immunology_Janeway

Immunology_Janeway. Michael Heidelberger (1888–1991) developed the quantitative precipitin assay, ushering in the era of quantitative immunochemistry. Charles A. Janeway, Jr. (1945–2003) recognized the importance of co-stimulation for initiating adaptive immune responses. He predicted the existence of receptors of the innate immune system that would recognize pathogen-associated molecular patterns and would signal activation of the adaptive immune system. His laboratory discovered the first mammalian Toll-like receptor that had this function. He was also the principal original author of this textbook. Edward Jenner (1749–1823) described the successful protection of humans against smallpox infection by vaccination with cowpox or vaccinia virus. This founded the field of immunology.


Immunology_Janeway

Immunology_Janeway. Edward Jenner (1749–1823) described the successful protection of humans against smallpox infection by vaccination with cowpox or vaccinia virus. This founded the field of immunology. Niels Jerne (1911–1994) developed the hemolytic plaque assay and several important immunological theories, including an early version of clonal selection, a prediction that lymphocyte receptors would be inherently biased to MHC recognition, and the idiotype network. Shibasaburo Kitasato (1852–1931) discovered antibodies in collaboration with Emil von Behring. Robert Koch (1843–1910) defined the criteria needed to characterize an infectious disease, known as Koch’s postulates. Georges Kler (1946–1995) pioneered monoclonal antibody production from hybrid antibody-forming cells with César Milstein. Karl Landsteiner (1868–1943) discovered the ABO blood group antigens. He also carried out detailed studies of the specificity of antibody binding using haptens as model antigens.


Immunology_Janeway

Immunology_Janeway. Karl Landsteiner (1868–1943) discovered the ABO blood group antigens. He also carried out detailed studies of the specificity of antibody binding using haptens as model antigens. Peter Medawar (1915–1987) used skin grafts to show that tolerance is an acquired characteristic of lymphoid cells, a key feature of clonal selection theory. Èlie Metchnikoff (1845–1916) was the first champion of cellular immunology, focusing his studies on the central role of phagocytes in host defense. César Milstein (1927–2002) pioneered monoclonal antibody production with Georges Köhler. Ray Owen (1915–2014) discovered that genetically different twin calves with a common placenta, thus sharing placental blood circulation, were immunologically tolerant to one another’s tissues. Louis Pasteur (1822–1895) was a French microbiologist and immunologist who validated the concept of immunization first studied by Jenner. He prepared vaccines against chicken cholera and rabies.


Immunology_Janeway

Immunology_Janeway. Louis Pasteur (1822–1895) was a French microbiologist and immunologist who validated the concept of immunization first studied by Jenner. He prepared vaccines against chicken cholera and rabies. Rodney Porter (1917–1985) worked out the polypeptide structure of the antibody molecule, laying the groundwork for its analysis by protein sequencing. Ignác Semmelweis (1818–1865) German-Hungarian physician who first determined a connection between hospital hygiene and an infectious disease, puerperal fever, and consequently introduced antisepsis into medical practice. George Snell (1903–1996) worked out the genetics of the murine major histocompatibility complex and generated the congenic strains needed for its biological analysis, laying the groundwork for our current understanding of the role of the MHC in T-cell biology.


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Immunology_Janeway. Tomio Tada (1934–2010) first formulated the concept of the regulation of the immune response by ‘suppressor T cells’ in the 1970s, from indirect experimental evidence. The existence of such cells could not be verified at the time and the concept became discredited, but Tada was vindicated when researchers in the 1980s identified the cells now called ‘regulatory T cells.’ Susumu Tonegawa (1939–) discovered the somatic recombination of immunological receptor genes that underlies the generation of diversity in human and murine antibodies and T-cell receptors. Jg Tschopp (1951-2011) contributed to the delineation of the complement system and T-cell cytolytic mechanisms, and made seminal contributions to the fields of apoptosis and innate immunity, in particular by discovering the inflammasome. Don C. Wiley (1944–2001) solved the first crystal structure of an MHC I protein, providing a startling insight into how T cells recognize their antigen in the in the context of MHC molecules.


Immunology_Janeway

Immunology_Janeway. Don C. Wiley (1944–2001) solved the first crystal structure of an MHC I protein, providing a startling insight into how T cells recognize their antigen in the in the context of MHC molecules. Fig. 1.1 reproduced courtesy of Yale University, Harvey Cushing/John Hay Whitney Medical Library. Fig. 1.4 second panel from Tilney, L.G., Portnoy, D.A.: Actin filaments and the growth, movement, and spread of the intracellular bacterial parasite, Listeria monocytogenes. J. Cell. Biol. 1989, 109:1597–1608. With permission from Rockefeller University Press. Fig. 1.24 photographs from Mowat, A., Viney, J.: The anatomical basis of intestinal immunity. Immunol. Rev. 1997, 156:145–166. Fig. 1.34 photographs from Kaplan, G., et al.: Efficacy of a cell-mediated reaction to the purified protein derivative of tuberculin in the disposal of Mycobacterium leprae from human skin. PNAS 1988, 85:5210–5214.


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Immunology_Janeway. Chapter 2 Fig. 2.7 top panel from Button, B., et al.: A periciliary brush promotes the lung health by separating the mucus layer from airway epithelia. Science 2012, 337:937–941. With permission from AAAS. Fig. 2.12 micrograph adapted from Mukherjee, S., et al.: Antibacterial membrane attack by a pore-forming intestinal C-type lectin. Nature 2014, 505:103–107. Fig. 2.35 photographs reproduced with permission from Bhakdi, S., et al.: Functions and relevance of the terminal complement sequence. Blut 1990, 60:309–318. © 1990 Springer-Verlag.


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Immunology_Janeway. Functions and relevance of the terminal complement sequence. Blut 1990, 60:309–318. © 1990 Springer-Verlag. Chapter 3 Fig. 3.12 structure reprinted with permission from Jin, M.S., et al.: Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a triacylated lipopeptide. Cell 2007, 130:1071–82. © 2007 with permission from Elsevier. Fig. 3.13 structure reprinted with permission from Macmillan Publishers Ltd. Park, B.S., et al.: The structural basis of lipopolysaccharide recognition by the TLR4-MD-2 complex. Nature 2009, 458:1191–1195. Fig. 3.34 model structure reprinted with permission from Macmillan Publishers Ltd. Emsley, J., et al.: Structure of pentameric human serum amyloid P component. Nature 1994, 367: 338–345.


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Immunology_Janeway. Chapter 4 Fig. 4.5 photograph from Green, N.M.: Electron microscopy of the immunoglobulins. Adv. Immunol. 1969, 11:1–30. © 1969 with permission from Elsevier. Fig. 4.15 and Fig. 4.24 model structures from Garcia, K.C., et al.: An αβ T cell receptor structure at 2.5 Å and its orientation in the TCR-MHC complex. Science 1996, 274:209–219. Reprinted with permission from AAAS.


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Immunology_Janeway. Fig. 6.6 reprinted with permission from Macmillan Publishers Ltd. Whitby, F.G., et al.: Structural basis for the activation of 20S proteasomes by 11S regulators. Nature 2000, 408:115–120. Fig. 6.7 bottom panel from Velarde, G., et al.: Three-dimensional structure of transporter associated with antigen processing (TAP) obtained by single particle image analysis. J. Biol. Chem. 2001 276:46054–46063. © 2001 ASBMB. Fig. 6.22 structures from Mitaksov, V.E., & Fremont, D.: Structural definition of the H-2Kd peptide-binding motif. J. Biol. Chem. 2006, 281:10618–10625. © 2006 American Society of Biochemistry and Molecular Biology. Fig. 6.25 molecular model reprinted with permission from Macmillan Publishers Ltd. Fields, B.A., et al.: Crystal structure of a T-cell receptor β-chain complexed with a superantigen. Nature 1996, 384:188–192.


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Immunology_Janeway. Fig. 8.19 photographs reprinted with permission from Macmillan Publishers Ltd. Surh, C. D., Sprent, J.: T-cell apoptosis detected in situ during positive and negative selection in the thymus. Nature 1994, 372:100–103. Fig. 9.12 ﬂuorescent micrographs reprinted with permission from Macmillan Publishers Ltd. Pierre, P., Turley, S.J., et al.: Development regulation of MHC class II transport in mouse dendritic cells. Nature 1997, 388:787–792. Fig. 9.38 panel c from Henkart, P.A., & Martz, E. (eds): Second International Workshop on Cell Mediated Cytotoxicity. © 1985 Kluwer/Plenum Publishers. With kind permission of Springer Science and Business Media.


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Immunology_Janeway. Chapter 10 Fig. 10.17 left panel from Szakal, A.K., et al.: Isolated follicular dendritic cells: cytochemical antigen localization, Nomarski, SEM, and TEM morphology. J. Immunol. 1985, 134:1349–1359. © 1985 The American Association of Immunologists. Fig. 10.17 center and right panels from Szakal, A.K., et al.: Microanatomy of lymphoid tissue during humoral immune responses: structure function relationships. Ann. Rev. Immunol. 1989, 7:91–109. © 1989 Annual Reviews www.annualreviews.org. Chapter 12


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Immunology_Janeway. Fig. 12.4 adapted by permission from Macmillan Publishers Ltd. Dethlefsen, L., McFall-Ngai, M., Relman, D.A.: An ecological and evolutionary perspective on human–microbe mutualism and disease. Nature 2007, 449:811–818. © 2007. Fig. 12.10 bottom left micrograph from Niess, J.H., et al.: CX3CR1mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science 2005, 307:254–258. Reprinted with permission from AAAS. Fig. 12.10 bottom center micrograph from McDole, J.R., et al.: Goblet cells deliver luminal antigen to CD103+ DCs in the small intestine. Nature 2012, 483: 345–9. With permission from Macmillan Publishers Ltd. Fig. 12.10 bottom right micrograph from Farache, J., et al.: Luminal bacteria recruit CD103+ dendritic cells into the intestinal epithelium to sample bacterial antigens for presentation. Immunity 2013, 38: 581–95. With permission from Elsevier.


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Immunology_Janeway. Chapter 13 Fig. 13.20 top left photograph from Kaplan, G., Cohn, Z.A.:The immunobiology of leprosy. Int. Rev. Exp. Pathol. 1986, 28:45–78. © 1986 with permission from Elsevier. Fig. 13.37 based on data from Palella, F.J., et al.: Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators. N. Engl. J. Med. 1998, 338:853–860. Fig. 13.40 adapted by permission from Macmillan Publishers Ltd. Wei, X., et al.: Viral dynamics in human immunodeficiency virus type 1 infection. Nature 1995, 373:117–122.


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Immunology_Janeway. Chapter 14 Fig. 14.5 top photograph from Sprecher, E., et al.: Deleterious mutations in SPINK5 in a patient with congenital ichthyosiform erythroderma: molecular testing as a helpful diagnostic tool for Netherton syndrome. Clin. Exp. Dermatol. 2004, 29:513–517. Fig. 14.14 photographs from Finotto, S., et al: Development of spontaneous airway changes consistent with human asthma in mice lacking T-bet. Science 2002, 295:336–338. Reprinted with permission from AAAS. Fig. 14.24 left photograph from Mowat, A.M., Viney, J.L.: The anatomical basis of intestinal immunity. Immunol. Rev. 1997 156:145–166. Chapter 16 Fig. 16.16 photographs are reprinted from Herberman, R., & Callewaert, D. (eds): Mechanisms of Cytotoxicity by Natural Killer Cells, © 1985 with permission from Elsevier. -omab Suffix applied to fully murine monoclonal antibodies used for human therapies. -umab Suffix applied to fully human monoclonal antibodies used for human therapies.


Immunology_Janeway

Immunology_Janeway. -omab Suffix applied to fully murine monoclonal antibodies used for human therapies. -umab Suffix applied to fully human monoclonal antibodies used for human therapies. -ximab Suffix applied to chimeric (i.e., mouse/human) monoclonal antibodies used for human therapies. -zumab Suffix applied to humanized monoclonal antibodies used for human therapies. 12/23 rule Phenomenon wherein two gene segments of an immunoglobulin or T-cell receptor can be joined only if one recognition signal sequence has a 12-base-pair spacer and the other has a 23-basepair spacer. α:β heterodimer The dimer of one α and one β chain that makes up the antigen-recognition portion of an α:β T-cell receptor. α:β T-cell receptors See T-cell receptor. α4:β1 integrin (VLA-4, CD49d/CD29) See integrins. Properties of individual CD antigens can be found in Appendix II. α-defensins A class of antimicrobial peptides produced by neutrophils and the Paneth cells of the intestine.


Immunology_Janeway

Immunology_Janeway. α-defensins A class of antimicrobial peptides produced by neutrophils and the Paneth cells of the intestine. α-galactoceramide (α-GalCer) An immunogenic glycolipid originally extracted from marine sponges but actually produced by various bacteria that is a ligand presented by CD1 to invariant NKT (iNKT) cells. 2B4 A receptor belonging to the signaling lymphocyte activation molecule (SLAM) family expressed by NK cells, which binds to CD48, another SLAM receptor. These signal through SAP and Fyn to promote survival and proliferation. 19S regulatory caps Multisubunit component of the proteasome that functions to capture ubiquitinated proteins for degradation in the catalytic core. 20S catalytic core Multisubunit component of proteasome responsible for protein degradation. abatacept An Fc fusion protein containing the CTLA-4 extracellular domain used in treating rheumatoid arthritis that blocks co-stimulation of T cells by binding B7 molecules.


Immunology_Janeway

Immunology_Janeway. abatacept An Fc fusion protein containing the CTLA-4 extracellular domain used in treating rheumatoid arthritis that blocks co-stimulation of T cells by binding B7 molecules. accelerated rejection The more rapid rejection of a second graft after rejection of the first graft. It was one of the pieces of evidence that showed that graft rejection was due to an adaptive immune response. accessory effector cells Cells that aid in an adaptive immune response but are not involved in specific antigen recognition. They include phagocytes, neutrophils, mast cells, and NK cells. acellular pertussis vaccines A formulation of pertussis used for vaccination containing chemically inactivated antigens, including pertussis toxoid. acquired immune deficiency syndrome (AIDS) A disease caused by infection with the human immunodeficiency virus (HIV-1). AIDS occurs when an infected patient has lost most of his or her CD4 T cells, so that infections with opportunistic pathogens occur.


Immunology_Janeway

Immunology_Janeway. activating receptors On NK cells, a receptor whose stimulation results in activation of the cell’s cytotoxic activity. activation-induced cell death A process by which autoreactive T cells are induced to die if they complete thymic maturation and migrate to the periphery. activation-induced cytidine deaminase (AID) Enzyme that initiates somatic hypermutation and isotype switching by deaminating DNA directly at cytosine in immunoglobulin V regions or switch regions. Loss of AID activity in patients leads to loss of both activities, causing hyper IgM and lack of affinity maturation. activator protein 1 (AP-1) A transcription factor formed as one of the outcomes of intracellular signaling by antigen receptors of lymphocytes. active immunization Immunization with antigen to provoke adaptive immunity.


Immunology_Janeway

Immunology_Janeway. active immunization Immunization with antigen to provoke adaptive immunity. acute desensitization An immunotherapeutic technique for rapidly inducing temporary tolerance to, for example, an essential drug such as insulin or penicillin in a person who is allergic to it. Also called rapid desensitization. When performed properly, can produce symptoms of mild to moderate anaphylaxis. acute phase In reference to HIV infection, the period that occurs soon after a person becomes infected. It is characterized by an inﬂuenza-like illness, abundant virus in the blood, and a decrease in the number of circulating CD4 T cells. acute-phase proteins Proteins with innate immune function whose production is increased in the presence of an infection (the acute-phase response). They circulate in the blood and participate in early phases of host defense against infection. An example is mannose-binding lectin.


Immunology_Janeway

Immunology_Janeway. acute-phase response A change in the proteins present in the blood that occurs during the early phases of an infection. It includes the production of acute-phase proteins, many of which are produced in the liver. acute rejection The rejection of a tissue or organ graft from a genetically unrelated donor that occurs within 10–13 days of transplantation unless prevented by immunosuppressant treatment. adaptive immunity Immunity to infection conferred by an adaptive immune response. adaptors Nonenzymatic proteins that form physical links between members of a signaling pathway, particularly between a receptor and other signaling proteins. They recruit members of the signaling pathway into functional protein complexes. ADCC See antibody-dependent cell-mediated cytotoxicity. adenoids Paired mucosa-associated lymphoid tissues located in the nasal cavity.


Immunology_Janeway

Immunology_Janeway. ADCC See antibody-dependent cell-mediated cytotoxicity. adenoids Paired mucosa-associated lymphoid tissues located in the nasal cavity. adenosine deaminase (ADA) deficiency An inherited defect characterized by nonproduction of the enzyme adenosine deaminase, which leads to the accumulation of toxic purine nucleosides and nucleotides in cells, resulting in the death of most developing lymphocytes within the thymus. It is a cause of severe combined immunodeficiency. adhesins Cell-surface proteins on bacteria that enable them to bind to the surfaces of host cells. adipose differentiation related protein A protein that functions in the maintenance and storage of neutral lipid droplets in many types of cells. adjuvant Any substance that enhances the immune response to an antigen with which it is mixed.


Immunology_Janeway

Immunology_Janeway. adjuvant Any substance that enhances the immune response to an antigen with which it is mixed. afferent lymphatic vessels Vessels of the lymphatic system that drain extracellular ﬂuid from the tissues and carry antigen, macrophages, and dendritic cells from sites of infection to lymph nodes or other peripheral lymphoid organs. affinity The strength of binding of one molecule to another at a single site, such as the binding of a monovalent Fab fragment of antibody to a monovalent antigen. Cf. avidity. affinity hypothesis Hypothesis that proposes how the choice between negative selection and positive selection of T cells in the thymus is made, according to the strength of self-peptide:MHC binding by the T-cell receptor. Low-affinity interactions rescue the cell from death by neglect, leading to positive selection; high-affinity interactions induce apoptosis and thus negative selection.


Immunology_Janeway

Immunology_Janeway. affinity maturation The increase in affinity for their specific antigen of the antibodies produced as an adaptive immune response progresses. This phenomenon is particularly prominent in secondary and subsequent immunizations. agammaglobulinemia An absence of antibodies in the blood. See also X-linked agammaglobulinemia (XLA). age-related macular degeneration A leading cause of blindness in the elderly, for which some single-nucleotide polymorphisms (SNPs) in the factor H genes confer an increased risk. agnathan paired receptors resembling Ag receptors (APARs) Multigene family of genes containing immunoglobulin domains present in hagfish and lamprey, that possibly represent ancestral predecessors of mammalian antigen receptors. agnathans A class of vertebrate comprising jawless fish lacking adaptive immunity based on the RAG-mediated V(D)J recombination, but possessing a distinct system of adaptive immunity based on somatically assembled VLRs.


Immunology_Janeway

Immunology_Janeway. agonist selection A process by which T cells are positively selected in the thymus by their interaction with relatively high-affinity ligands. AID See activation-induced cytidine deaminase. AIDS See acquired immune deficiency syndrome. AIM2 (absent in melanoma 2) A member of PYHIN subfamily of NLR (NOD-like receptor) family containing an N-terminal HIN domain. It activates caspase 1 in response to viral double-stranded DNA. AIRE Gene encoding a protein (autoimmune regulator) that is involved in the expression of numerous genes by thymic medullary epithelial cells, enabling developing T cells to be exposed to self proteins characteristic of other tissues, thereby promoting tolerance to these proteins. Deficiency of AIRE leads to an autoimmune disease, APECED.


Immunology_Janeway

Immunology_Janeway. airway hyperreactivity, hyperresponsiveness The condition in which the airways are pathologically sensitive to both immunological (allergens) and nonimmunological stimuli, such as cold air, smoke, or perfumes. This hyperreactivity usually is present in chronic asthma. airway tissue remodeling A thickening of the airway walls that occurs in chronic asthma due to hyperplasia and hypertrophy of the smooth muscle layer and mucus glands, with the eventual development of fibrosis. Often results in an irreversible decrease of lung function. Akt Serine/threonine kinase activated downstream of PI3 kinase with numerous downstream targets involved in cell growth and survival, including activation of the mTOR pathways. alefacept Recombinant CD58–IgG1 fusion protein that blocks CD2 binding by CD58 used in treatment for psoriasis. alemtuzumab Antibody to CD52 used for lymphocyte depletion, such as for T-cell depletion during bone marrow allografts used in treating chronic myeloid leukemia.


Immunology_Janeway

Immunology_Janeway. alemtuzumab Antibody to CD52 used for lymphocyte depletion, such as for T-cell depletion during bone marrow allografts used in treating chronic myeloid leukemia. allele A variant form of a gene; many genes occur in several (or more) different forms within the general population. See also heterozygous, homozygous, polymorphism. allelic exclusion In a heterozygous individual, the expression of only one of the two alternative alleles of a particular gene. In immunology, the term describes the restricted expression of the individual chains of the antigen receptor genes, such that each individual lymphocyte produces immunoglobulin or T-cell receptors of a single antigen specificity. allergen Any antigen that elicits an allergic reaction.


Immunology_Janeway

Immunology_Janeway. allergen Any antigen that elicits an allergic reaction. allergen desensitization An immunotherapeutic technique that aims either to change an allergic immune response to a symptom-free non-allergic response, or to develop immunologic tolerance to an allergen that has been causing unpleasant clinical symptoms. The procedure involves exposing an allergic individual to increasing doses of allergen. allergic asthma An allergic reaction to inhaled antigen, which causes constriction of the bronchi, increased production of airway mucus, and difficulty in breathing. allergic conjunctivitis An allergic reaction involving the conjunctiva of the eye that occurs in sensitized individuals exposed to airborne allergens. It is usually manifested together with nasal allergy symptoms as allergic rhinoconjunctivitis or hay fever.


Immunology_Janeway

Immunology_Janeway. allergic contact dermatitis A largely T-cell-mediated immunological hypersensitivity reaction manifested by a skin rash at the site of contact with the allergen. Often the stimulus is a chemical agent, for example urushiol oil from the leaves of the poison ivy plant, which can haptenate normal host molecules to render them allergenic. allergic reaction A specific response to an innocuous environmental antigen, or allergen, that is caused by sensitized B or T cells. Allergic reactions can be caused by various mechanisms, but the most common is the binding of allergen to IgE bound to mast cells, which causes the cells to release histamine and other biologically active molecules that cause the signs and symptoms of asthma, hay fever, and other common allergic responses. allergic rhinitis An allergic reaction in the nasal mucosa that causes excess mucus production, nasal itching, and sneezing.


Immunology_Janeway

Immunology_Janeway. allergic rhinitis An allergic reaction in the nasal mucosa that causes excess mucus production, nasal itching, and sneezing. allergy The state in which a symptomatic immune reaction is made to a normally innocuous environmental antigen. It involves the interaction between the antigen and antibody or primed T cells produced by earlier exposure to the same antigen. alloantibodies Antibodies produced against antigens from a genetically nonidentical member of the same species. alloantigens Antigens from another genetically nonidentical member of the same species. allogeneic Describes two individuals or two mouse strains that differ at genes in the MHC. The term can also be used for allelic differences at other loci. allograft A transplant of tissue from an allogeneic (genetically nonidentical) donor of the same species. Such grafts are invariably rejected unless the recipient is immunosuppressed.


Immunology_Janeway

Immunology_Janeway. allograft A transplant of tissue from an allogeneic (genetically nonidentical) donor of the same species. Such grafts are invariably rejected unless the recipient is immunosuppressed. allograft rejection The immunologically mediated rejection of grafted tissues or organs from a genetically nonidentical donor. It is due chieﬂy to recognition of nonself MHC molecules on the graft. alloreactivity The recognition by T cells of MHC molecules other than self. Such responses are also called alloreactions or alloreactive responses. altered peptide ligands (APLs) Peptides in which amino acid substitutions have been made in T-cell receptor contact positions that affect their binding to the receptor. alternative pathway A form of complement activation that is initiated by spontaneous hydrolysis of C3 and which uses factor B and factor D to form the unique C3 convertase C3bBb. alternatively activated macrophages See M2 macrophages.


Immunology_Janeway

Immunology_Janeway. alternatively activated macrophages See M2 macrophages. alum Inorganic aluminum salts (for example aluminum phosphate and aluminum hydroxide); they act as adjuvants when mixed with antigens and are one of the few adjuvants permitted for use in humans. amphipathic Describes molecules that have a positively charged (or hydrophilic) region separated from a hydrophobic region. anakinra A recombinant IL-1 receptor antagonist (IL-1RA) used to block IL-1 receptor activation and used in treating rheumatoid arthritis. anaphylactic shock See anaphylaxis. anaphylatoxins Pro-inﬂammatory complement fragments C5a and C3a released by cleavage during complement activation. They are recognized by specific receptors, and recruit ﬂuid and inﬂammatory cells to the site of their release.


Immunology_Janeway

Immunology_Janeway. anaphylaxis A rapid-onset and systemic allergic reaction to antigen, for example to insect venom injected directly into the bloodstream, or to foods such as peanuts. Severe systemic reactions can be potentially fatal due to circulatory collapse and suffocation from tracheal swelling. It usually results from antigens binding to IgE bound by Fcε receptors on mast cells, leading to systemic release of inﬂammatory mediators. anchor residues Specific amino acid residues in antigenic peptides that determine peptide binding specificity to MHC class I molecules. Anchor residues for MHC class II molecules exist but are less obvious than for MHC class I. anergy A state of nonresponsiveness to antigen. People are said to be anergic when they cannot mount delayed-type hypersensitivity reactions to a test antigen, whereas T cells and B cells are said to be anergic when they cannot respond to their specific antigen under optimal conditions of stimulation.


Immunology_Janeway

Immunology_Janeway. ankylosing spondylitis Inﬂammatory disease of the spine leading to vertebral fusion strongly associated with HLA-B27. antibody A protein that binds specifically to a particular substance—called its antigen. Each antibody molecule has a unique structure that enables it to bind specifically to its corresponding antigen, but all antibodies have the same overall structure and are known collectively as immunoglobulins. Antibodies are produced by differentiated B cells (plasma cells) in response to infection or immunization, and bind to and neutralize pathogens or prepare them for uptake and destruction by phagocytes. antibody combining site See antigen-binding site. antibody-dependent cell-mediated cytotoxicity (ADCC) The killing of antibody-coated target cells by cells with Fc receptors that recognize the constant region of the bound antibody. Most ADCC is mediated by NK cells that have the Fc receptor FcγRIII on their surface.


Immunology_Janeway

Immunology_Janeway. antibody-directed enzyme/pro-drug therapy (ADEPT) Treatment in which an antibody is linked to an enzyme that metabolizes a nontoxic pro-drug to the active cytotoxic drug. antibody repertoire The total variety of antibodies in the body of an individual. antigen Any molecule that can bind specifically to an antibody or generate peptide fragments that are recognized by a T-cell receptor. antigen-binding site The site at the tip of each arm of an antibody that makes physical contact with the antigen and binds it noncovalently. The antigen specificity of the site is determined by its shape and the amino acids present. antigenic determinant That portion of an antigenic molecule that is bound by the antigen-binding site of a given antibody or antigen receptor; it is also known as an epitope.


Immunology_Janeway

Immunology_Janeway. antigenic determinant That portion of an antigenic molecule that is bound by the antigen-binding site of a given antibody or antigen receptor; it is also known as an epitope. antigenic drift The process by which inﬂuenza virus varies genetically in minor ways from year to year. Point mutations in viral genes cause small differences in the structure of the viral surface antigens. antigenic shift A radical change in the surface antigens of inﬂuenza virus, caused by reassortment of their segmented genome with that of another inﬂuenza virus, often from an animal. antigenic variation Alterations in surface antigens that occur in some pathogens (such as African trypanosomes) from one generation to another, which allows them to evade preexisting antibodies. antigen presentation The display of antigen on the surface of a cell in the form of peptide fragments bound to MHC molecules. T cells recognize antigen when it is presented in this way.


Immunology_Janeway

Immunology_Janeway. antigen presentation The display of antigen on the surface of a cell in the form of peptide fragments bound to MHC molecules. T cells recognize antigen when it is presented in this way. antigen-presenting cells (APCs) Highly specialized cells that can process antigens and display their peptide fragments on the cell surface together with other, co-stimulatory, proteins required for activating naive T cells. The main antigen-presenting cells for naive T cells are dendritic cells, macrophages, and B cells. antigen processing The intracellular degradation of foreign proteins into peptides that can bind to MHC molecules for presentation to T cells. All protein antigens must be processed into peptides before they can be presented by MHC molecules. antigen receptor The cell-surface receptor by which lymphocytes recognize antigen. Each individual lymphocyte bears receptors of a single antigen specificity.


Immunology_Janeway

Immunology_Janeway. antigen receptor The cell-surface receptor by which lymphocytes recognize antigen. Each individual lymphocyte bears receptors of a single antigen specificity. anti-lymphocyte globulin Antiserum raised in another species against human T cells. It is used in the temporary suppression of immune responses in transplantation. antimicrobial enzymes Enzymes that kill microorganisms by their actions. An example is lysozyme, which digests bacterial cell walls. antimicrobial peptides, antimicrobial proteins Amphipathic peptides or proteins secreted by epithelial cells and phagocytes that kill a variety of microbes nonspecifically, mainly by disrupting cell membranes. Antimicrobial peptides in humans include the defensins, the cathelicidins, the histatins, and RegIIIγ.


Immunology_Janeway

Immunology_Janeway. antiserum The ﬂuid component of clotted blood from an immune individual that contains antibodies against the antigen used for immunization. An antiserum contains a mixture of different antibodies that all bind the antigen, but which each have a different structure, their own epitope on the antigen, and their own set of cross-reactions. This heterogeneity makes each antiserum unique. antivenin Antibody raised against the venom of a poisonous snake or other organism and which can be used as an immediate treatment for the bite to neutralize the venom. aorta-gonad-mesonephros (AGM) An embryonic region in which hematopoietic cells arise during development. AP-1 A heterodimeric transcription factor formed as one of the outcomes of intracellular signaling via the antigen receptors of lymphocytes and the TLRs of cells of innate immunity. Most often, contains one Fos-family member and one Jun-family member. AP-1 mainly activates the expression of genes for cytokines and chemokines.


Immunology_Janeway

Immunology_Janeway. APECED See autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. An RNA editing enzyme that deaminates cytidine to uracil in certain mRNAs, such as apolipoprotein B, and which is related to the enzyme AID involved in somatic hypermutation and isotype switching. apoptosis A form of cell death common in the immune system, in which the cell activates an internal death program. It is characterized by nuclear DNA degradation, nuclear degeneration and condensation, and the rapid phagocytosis of cell remains. Proliferating lymphocytes experience high rates of apoptosis during their development and during immune responses. apoptosome A large, multimeric protein structure that forms in the process of apoptosis when cytochrome c is released from mitochondria and binds Apaf-1. A heptamer of cytochrome c-Apaf-1 heterodimers assembles into wheel-like structure that binds and activates procaspase-9, an initiator caspase, to initiate the caspase cascade.


Immunology_Janeway

Immunology_Janeway. appendix A gut-associated lymphoid tissue located at the beginning of the colon. APRIL A TNF family cytokine related to BAFF that binds the receptors TACI and BCMA on B cells to promote survival and regulate differentiation. apurinic/apyrimidinic endonuclease 1 (APE1) A DNA repair endonuclease involved in class switch recombination. Artemis An endonuclease involved in the gene rearrangements that generate functional immunoglobulin and T-cell receptor genes. Arthus reaction A local skin reaction that occurs when a sensitized individual with IgG antibodies against a particular antigen is challenged by injection of the antigen into the dermis. Immune complexes of the antigen with IgG antibodies in the extracellular spaces in the dermis activate complement and phagocytic cells to produce a local inﬂammatory response.


Immunology_Janeway

Immunology_Janeway. aryl hydrocarbon receptor (AhR) A basic helix-loop-helix transcription factor that is activated by various aromatic ligands including, famously, dioxin. It functions in the normal activity of several types of immune cells including some ILCs and IELs. ASC (PYCARD) An adaptor protein containing pyrin and CARD domains involved in activating caspase 1 in the inﬂammasome. asymptomatic phase In reference to HIV infection, period in which the infection is being partly held in check and no symptoms occur; it may last for many years. ataxia telangiectasia (ATM) A disease characterized by a staggering gait and multiple disorganized blood vessels, and often accompanied by clinical immunodeficiency. It is caused by defects in the ATM protein, which is involved in DNA repair pathways that are also used in V(D)J recombination and class-switch recombination.


Immunology_Janeway

Immunology_Janeway. atopic march The clinical observation that it is common for children with atopic eczema to later develop allergic rhinitis and/or asthma. atopy A genetically based increased tendency to produce IgE-mediated allergic reactions against innocuous substances. ATP-binding cassette (ABC) A large family of proteins containing a particular domain for nucleotide-binding that includes many transporters, such as TAP1 and TAP2, but also various NOD members. attenuation The process by which human or animal pathogens are modified by growth in culture so that they can grow in their host and induce immunity without producing serious clinical disease. atypical hemolytic uremic syndrome A condition characterized by damage to platelets and red blood cells and inﬂammation of the kidneys that is caused by uncontrolled complement activation in individuals with inherited deficiencies in complement regulatory proteins. autoantibodies Antibodies specific for self antigens.


Immunology_Janeway

Immunology_Janeway. autoantibodies Antibodies specific for self antigens. autoantigens A self antigen to which the immune system makes a response. autocrine Describes a cytokine or other biologically active molecule acting on the cell that produces it. autograft A graft of tissue from one site to another on the same individual. autoimmune disease Disease in which the pathology is caused by adaptive immune responses to self antigens. autoimmune hemolytic anemia A pathological condition with low levels of red blood cells (anemia), which is caused by autoantibodies that bind red blood cell surface antigens and target the red blood cell for destruction. autoimmune lymphoproliferative syndrome (ALPS) An inherited syndrome in which a defect in the Fas gene leads to a failure in normal apoptosis, causing unregulated immune responses, including autoimmune responses.


Immunology_Janeway

Immunology_Janeway. autoimmune polyendocrinopathy–candidiasis–ectodermal dystrophy (APECED) A disease characterized by a loss of tolerance to self antigens, caused by a breakdown of negative selection in the thymus. It is due to defects in the gene AIRE, which encodes a transcriptional regulatory protein that enables many self antigens to be expressed by thymic medullary epithelial cells. Also called autoimmune polyglandular syndrome type I. autoimmune thrombocytopenic purpura An autoimmune disease in which antibodies against platelets are made. Antibody binding to platelets causes them to be taken up by cells with Fc receptors and complement receptors, resulting in a decrease in platelet count that leads to purpura (bleeding). autoimmunity Adaptive immunity specific for self antigens. autoinflammatory diseases Diseases due to unregulated inﬂammation in the absence of infection; they can have a variety of causes, including inherited genetic defects.


Immunology_Janeway

Immunology_Janeway. autoinflammatory diseases Diseases due to unregulated inﬂammation in the absence of infection; they can have a variety of causes, including inherited genetic defects. autophagosome A double bilayer membrane structure that functions in macroautophagy by engulfing cytoplasmic contents and fusing with lysosomes. autophagy The digestion and breakdown by a cell of its own organelles and proteins in lysosomes. It may be one route by which cytosolic proteins can be processed for presentation on MHC class II molecules. avidity The sum total of the strength of binding of two molecules or cells to one another at multiple sites. It is distinct from affinity, which is the strength of binding of one site on a molecule to its ligand. avoidance Mechanisms that prevent a host's exposure to microbes, such as anatomic barriers or particular behaviors.


Immunology_Janeway

Immunology_Janeway. avoidance Mechanisms that prevent a host's exposure to microbes, such as anatomic barriers or particular behaviors. azathioprine A powerful cytotoxic drug that is converted to its active form in vivo, which then kills rapidly proliferating cells, including proliferating lymphocytes; it is used as an immunosuppressant to treat autoimmune disease and in transplantation. B-1 B cells A class of atypical, self-renewing B cells (also known as CD5 B cells) found mainly in the peritoneal and pleural cavities in adults and considered part of the innate rather than the adaptive immune system. They have a much less diverse antigen-receptor repertoire than conventional B cells and are the major source of natural antibody.


Immunology_Janeway

Immunology_Janeway. B7 molecules, B7.1 and B7.2 Cell-surface proteins on specialized antigen-presenting cells such as dendritic cells, which are the major co-stimulatory molecules for T cells. B7.1 (CD80) and B7.2 (CD86) are closely related members of the immunoglobulin superfamily and both bind to the CD28 and CTLA-4 proteins on T cells. β1i (LMP2), β2i (MECL-1), β5i (LMP7) Alternative proteasome subunits that replace the constitutive catalytic subunits β1, β2, and β5 that are induced by interferons and produce the immunoproteasome. β5t Alternative proteasome subunit expressed by thymic epithelial cells that substitutes for β5 to produce the thymoproteasome involved in generating peptides encountered by thymocytes during development. β-defensins Antimicrobial peptides made by virtually all multicellular organisms. In mammals they are produced by the epithelia of the respiratory and urogenital tracts, skin, and tongue.


Immunology_Janeway

Immunology_Janeway. β-defensins Antimicrobial peptides made by virtually all multicellular organisms. In mammals they are produced by the epithelia of the respiratory and urogenital tracts, skin, and tongue. β sandwich A secondary protein structure composed of two β sheets that fold such that one lies over the other, as in an immunoglobulin fold. β sheets A secondary protein structure composed of β strands stabilized by noncovalent interactions between backbone amide and carbonyl groups. In ‘parallel’ β sheets, the adjacent strands run in the same direction; in ‘antiparallel’ β sheets, adjacent strands run in opposite directions. Immunoglobulin domains are made up of two antiparallel β sheets arranged in the form of a β barrel. β strands A secondary protein structure in which the polypeptide backbone of several consecutive amino acids is arranged in a ﬂat, or planar, conformation, and often illustrated as an arrow.


Immunology_Janeway

Immunology_Janeway. β strands A secondary protein structure in which the polypeptide backbone of several consecutive amino acids is arranged in a ﬂat, or planar, conformation, and often illustrated as an arrow. β2-microglobulin The light chain of the MHC class I proteins, encoded outside the MHC. It binds noncovalently to the heavy or α chain. B and T lymphocyte attenuator (BTLA) An inhibitory CD28-related receptor expressed by B and T lymphocytes that interacts with the herpes virus entry molecule (HVEM), a member of the TNF receptor family. bacteria A vast kingdom of unicellular prokaryotic microorganisms, some species of which cause infectious diseases in humans and animals, while others make up most of the body’s commensal microbiota. Disease-causing bacteria may live in the extracellular spaces, or inside cells in vesicles or in the cytosol. BAFF B-cell activating factor belonging to the TNF family that binds the receptors BAFF-R and TACI to promote B cell survival.


Immunology_Janeway

Immunology_Janeway. BAFF B-cell activating factor belonging to the TNF family that binds the receptors BAFF-R and TACI to promote B cell survival. BAFF-R Receptor for BAFF that can activate canonical and non-canonical NF-κB signaling and promote survival of B cells. bare lymphocyte syndrome See MHC class I deficiency, MHC class II deficiency. base-excision repair Type of DNA repair that can lead to mutation and that is involved in somatic hypermutation and class switching in B cells. basiliximab Antibody to human CD25 used to block IL-2 receptor signaling in T cells for treatment of rejection in renal transplantation. basophils Type of white blood cell containing granules that stain with basic dyes. It is thought to have a function similar to mast cells. BATF3 A transcription factor expressed in dendritic cells belonging to the AP1 family, which includes many other factors such as c-Jun and Fos.


Immunology_Janeway

Immunology_Janeway. BATF3 A transcription factor expressed in dendritic cells belonging to the AP1 family, which includes many other factors such as c-Jun and Fos. B cells, B lymphocytes One of the two types of antigen-specific lymphocytes responsible for adaptive immune responses, the other being the T cells. The function of B cells is to produce antibodies. B cells are divided into two classes. Conventional B cells have highly diverse antigen receptors and are generated in the bone marrow throughout life, emerging to populate the blood and lymphoid tissues. B-1 cells have much less diverse antigen receptors and form a population of self-renewing B cells in the peritoneal and pleural cavities.


Immunology_Janeway

Immunology_Janeway. B-cell antigen receptor, B-cell receptor (BCR) The cell-surface receptor on B cells for specific antigen. It is composed of a transmembrane immunoglobulin molecule (which recognizes antigen) associated with the invariant Igα and Igβ chains (which have a signaling function). On activation by antigen, B cells differentiate into plasma cells producing antibody molecules of the same antigen specificity as this receptor. B-cell co-receptor A transmembrane signaling receptor on the B-cell surface composed of the proteins CD19, CD81, and CD21 (complement receptor 2), which binds complement fragments on bacterial antigens also bound by the B-cell receptor. Co-ligation of this complex with the B-cell receptor increases responsiveness to antigen about 100-fold.


Immunology_Janeway

Immunology_Janeway. B-cell co-receptor complex A transmembrane signaling receptor on the B-cell surface composed of the proteins CD19, CD81, and CD21 (complement receptor 2), which binds complement fragments on bacterial antigens also bound by the B-cell receptor. Co-ligation of this complex with the B-cell receptor increases responsiveness to antigen about 100-fold. B-cell mitogens Any substance that nonspecifically causes B cells to proliferate. Bcl-2 family Family of intracellular proteins that includes members that promote apoptosis (Bax, Bak, and Bok) and members that inhibit apoptosis (Bcl-2, Bcl-W, and Bcl-XL). Bcl-6 A transcriptional repressor that opposes differentiation of B cells into plasma cells. BCMA Receptor of the TNFR superfamily that binds APRIL. Bcr–Abl tyrosine kinase Constitutively active tyrosine kinase fusion protein caused by a chromosomal translocation—the Philadelphia chromosome— between Bcr with the Abl tyrosine kinase genes associated with chronic myeloid leukemia.


Immunology_Janeway

Immunology_Janeway. BDCA-2 (blood dendritic cell antigen 2) A C-type lectin expressed selectively as a receptor on the surface of human plasmacytoid dendritic cells. Berlin patient A man with HIV who was treated in Berlin with a hematopoietic stem cell (HSC) transplant from a donor deficient in a co-receptor for the virus (CCR5) for an unrelated illness (leukemia). He is thought to be cured of HIV infection, and is one of the only known patients in which the virus is thought to be completely eliminated, a so-called ‘sterilizing’ cure. biologics therapy Medical treatments comprising natural proteins such as antibodies and cytokines, and antisera or whole cells. Blau syndrome An inherited granulomatous disease caused by gain-offunction mutations in the NOD2 gene. BLIMP-1 A transcriptional repressor that promotes B-cell differentiation into plasma cells and suppresses proliferation, and further class switching and affinity maturation. BLNK B-cell linker protein. See SLP-65.


Immunology_Janeway

Immunology_Janeway. BLNK B-cell linker protein. See SLP-65. bone marrow The tissue where all the cellular elements of the blood—red blood cells, white blood cells, and platelets—are initially generated from hematopoietic stem cells. The bone marrow is also the site of further B-cell development in mammals and the source of stem cells that give rise to T cells on migration to the thymus. Thus, bone marrow transplantation can restore all the cellular elements of the blood, including the cells required for adaptive immune responses. booster immunization See secondary immunization. bradykinin A vasoactive peptide that is produced as a result of tissue damage and acts as an inﬂammatory mediator. broadly neutralizing antibodies Antibodies that block viral infection by multiple strains. In reference to HIV, these are antibodies that block binding of the virus to CD4 and/or chemokine co-receptors.


Immunology_Janeway

Immunology_Janeway. bronchus-associated lymphoid tissue (BALT) Organized lymphoid tissue found in the bronchi in some animals. Adult humans do not normally have such organized lymphoid tissue in the respiratory tract, but it may be present in some infants and children. Bruton’s tyrosine kinase (Btk) A Tec-family tyrosine kinase important in B-cell receptor signaling. Btk is mutated in the human immunodeficiency disease X-linked agammaglobulinemia. Bruton’s X-linked agammaglobulinemia See X-linked agammaglobulinemia. bursa of Fabricius Lymphoid organ associated with the gut that is the site of B-cell development in chickens. butyrate A short chain fatty acid produced abundantly by anaerobic digestion of carbohydrates in the intestine by commensals that can inﬂuence host cells in several ways, acting as an energy source for enterocytes and as an inhibitor of histone deacetylases.