Unique and unprecedented recombination mechanisms in class switching

RNA Polymerase Collision versus DNA Structural Distortion: Twists and Turns Can Cause Break Failure

The twisting of DNA due to the movement of RNA polymerases is the basis of numerous classic experiments in molecular biology. Recent mouse genetic models indicate that chromosomal breakage is common at sites of transcriptional turbulence. Two key studies on this point mapped breakpoints to sites of either convergent or divergent transcription but arrived at different conclusions as to which is more detrimental and why. The issue hinges on whether DNA strand separation is the basis for the chromosomal instability or collision of RNA polymerases.

PI3Kδ and primary immunodeficiencies

Primary immunodeficiencies are inherited disorders of the immune system, often caused by the mutation of genes required for lymphocyte development and activation. Recently, several studies have identified gain-of-function mutations in the phosphoinositide 3-kinase (PI3K) genes PIK3CD (which encodes p110δ) and PIK3R1 (which encodes p85α) that cause a combined immunodeficiency syndrome, referred to as activated PI3Kδ syndrome (APDS; also known as p110δ-activating mutation causing senescent T cells, lymphadenopathy and immunodeficiency (PASLI)). Paradoxically, both loss-of-function and gain-of-function mutations that affect these genes lead to immunosuppression, albeit via different mechanisms. Here, we review the roles of PI3Kδ in adaptive immunity, describe the clinical manifestations and mechanisms of disease in APDS and highlight new insights into PI3Kδ gleaned from these patients, as well as implications of these findings for clinical therapy.

Heterogeneity in the differentiation and function of memory B cells

Vaccines that induce neutralizing antibodies have led to the eradication of small pox and have severely reduced the prevalence of many other infections. However, even the most successful vaccines do not induce protective antibodies in all individuals, and can fail to induce lifelong immunity. A key to remedying these shortcomings may lie in a better understanding of long-lived memory B cells. Recent studies have revealed novel insights into the differentiation and function of these cells, and have shown that the memory B cell pool is much more heterogeneous than previously appreciated.

Immunoglobulin class-switch recombination deficiencies

Immunoglobulin class-switch recombination deficiencies (Ig-CSR-Ds) are rare primary immunodeficiencies characterized by defective switched isotype (IgG/IgA/IgE) production. Depending on the molecular defect in question, the Ig-CSR-D may be combined with an impairment in somatic hypermutation (SHM). Some of the mechanisms underlying Ig-CSR and SHM have been described by studying natural mutants in humans. This approach has revealed that T cell-B cell interaction (resulting in CD40-mediated signaling), intrinsic B-cell mechanisms (activation-induced cytidine deaminase-induced DNA damage), and complex DNA repair machineries (including uracil-N-glycosylase and mismatch repair pathways) are all involved in class-switch recombination and SHM. However, several of the mechanisms required for full antibody maturation have yet to be defined. Elucidation of the molecular defects underlying the diverse set of Ig-CSR-Ds is essential for understanding Ig diversification and has prompted better definition of the clinical spectrum of diseases and the development of increasingly accurate diagnostic and therapeutic approaches.

8,9-Epoxyeicosatrienoic acid inhibits antibody production of B lymphocytes in mice

Epoxyeicosatrienoic acids (EETs), synthesized from arachidonic acid by cytochrome P450 epoxygenases, are converted to dihydroxyeicosatrienoic acids by soluble epoxide hydrolase. EETs exert anti-inflammatory effects. However, the effect of EETs on humoral immunity is poorly understood. The present study is to investigate the potential role of EETs on B cell function and mechanisms. We examined the role of EETs on antibody production of splenic B cells from C57BL/6 and apolipoprotein E-deficient (ApoE−/−) mice by means of ELISA. Of the 4 EET regioisomers, 8,9-EET decreased basal and activation-induced B cell antibody secretion. As well, 8,9-EET significantly inhibited B-cell proliferation and survival, plasma cell differentiation and class-switch recombination. Western blot analysis revealed that lipopolysaccharide-induced nuclear translocation of NF-κB could be attenuated by 8,9-EET. Furthermore, germinal center formation was impaired by 8,9-EET in mice in vivo. 8,9-EET may inhibit B-cell function in vitro and in vivo, which suggests a new therapeutic strategy for diseases with excess B cell activation.

Protein kinase R is a novel mediator of CD40 signaling and plays a critical role in modulating immunoglobulin expression during respiratory syncytial virus infection

Effective immunoglobulin responses play a vital role in protection against most pathogens. However, the molecular mediators and mechanisms responsible for signaling and selective expression of immunoglobulin types remain to be elucidated. Previous studies in our laboratory have demonstrated that protein kinase R (PKR) plays a crucial role in IgE responses to double-stranded RNA (dsRNA) in vitro. In this study, we show that PKR plays a critical role in IgG expression both in vivo and in vitro. PKR(-/-) mice show significantly altered serum IgG levels during respiratory syncytial virus (RSV) infection. IgG2a expression is particularly sensitive to a lack of PKR and is below the detection level in mock- or RSV-infected PKR(-/-) mice. Interestingly, we show that upon activation by anti-CD40 and gamma interferon (IFN-γ), B cells from PKR(-/-) mice show diminished major histocompatibility complex class II (MHC II), CD80, and CD86 levels on the cell surface compared to wild-type (WT) mice. Our data also show that PKR is necessary for optimal expression of adhesion molecules, such as CD11a and ICAM-1, that are necessary for homotypic aggregation of B cells. Furthermore, in this report we demonstrate for the first time that upon CD40 ligation, PKR is rapidly phosphorylated and activated, indicating that PKR is an early and novel downstream mediator of CD40 signaling pathways.

Genetic and environmental regulation of inflammatory CVD biomarkers Lp-PLA2 and IgM anti-PC

OBJECTIVE

We set out to investigate the relative contribution of genetic and environmental effect on two inflammatory CVD biomarkers; lipoprotein-associated phospholipase A(2) (Lp-PLA(2)) and anti-phosphorylcholine IgM (anti-PC). Their relationships and possible co-regulation with other established CVD biomarkers are also examined.

METHODS

Lp-PLA(2) activity (N=1600) and anti-PC (N=2036) levels were measured in elderly Swedish twins. Correlation analyses and heritability estimation were conducted by structural equation modeling.

RESULTS

We attribute 0.37 of the variance of Lp-PLA(2) and 0.40 of anti-PC variance to genetic variance. In addition, a bivariate heritability of 0.33, 0.35 and 0.36 could be detected for levels of Lp-PLA(2) together with ApoB, total cholesterol and LDL, respectively. Anti-PC was only weakly related to other biomarkers of CVD, which may suggest a more independent role of anti-PC as a biomarker.

CONCLUSIONS

In this large sample, Lp-PLA(2) activity has lower heritability and higher environmental regulation than previously reported. Anti-PC levels are partly influenced by dominance genetics and appear to be regulated independently of more established CVD biomarkers.

Inherited defects of immunoglobulin class switch recombination

The investigation of an inherited primary immunodeficiency, the immunoglobulin class switch recombination deficiency, has allowed the delineation of complex molecular events that underlie antibody maturation in humans. The Activation-induced cytidine deaminase (AID)-deficiency, characterized by a defect in Class Switch Recombination (CSR) and somatic hypermutation, has revealed the master role of this molecule in the induction of DNA damage, the first step required for these two processes. The description that mutations in the gene encoding the Uracil-DNA glycosylase (UNG) lead to defective CSR has been essential for defining the DNA-editing activity of AID. Analysis of post meiotic segregation 2 (PMS2)-deficient patients gave evidence for the role of this mismatch repair enzyme in the generation of the DNA breaks that are required for CSR. Novel findings are awaited from the study ofyet-genetically undefined CSR-deficiencies, probably leading to the identification of AID cofactor(s) and/or proteins involved in CSR-induced DNA repair.

Genetic or pharmaceutical blockade of p110delta phosphoinositide 3-kinase enhances IgE production

BACKGROUND

Recent studies indicate that pharmaceutical blockade of phosphoinositide 3-kinase (PI3K) signaling enzymes might be effective in reducing allergic airway inflammation. Signals generated by the p110delta PI3K isoform play critical roles in signaling through antigen and cytokine receptors and were shown to be required for induction of type 2, but not type 1, cytokine responses.

OBJECTIVE

We sought to determine the effect of genetic or pharmaceutical inactivation of p110delta PI3K on induction of IgE responses.

METHODS

We determined the effect of p110delta inactivation on induction of systemic IgE responses and on the ability of purified B lymphocytes to undergo IgE isotype switch in vitro. IgG and IgE germline transcription, postswitch transcription, protein expression, and secretion were measured, as well as cell division and expression of activation-induced cytidine deaminase, an enzyme required for isotype switch.

RESULTS

Paradoxically, inactivation of p110delta PI3K led to markedly increased IgE responses, despite reduced production of other antibody isotypes. This result was seen by using genetic inactivation of p110delta inhibition with IC87114 compound or blockade with the broad-spectrum PI3K inhibitors PIK-90 and PI-103. Significant increases in IgG1/IgE double-positive cells were observed, indicating that inactivation of PI3K leads to uncontrolled sequential switching from IgG1 to IgE. Disruption of p110delta signaling results in increased germline transcription at the epsilon locus and increased activation-induced cytidine deaminase expression, suggesting deregulation at the level of the isotype switch process.

CONCLUSION

Blockade of PI3K signaling leads to markedly enhanced B-cell switch to IgE and increased IgE levels in vivo, despite reduced type 2 cytokine production.

Tocopherol transfer protein deficiency modifies nuclear receptor transcriptional networks in lungs: Modulation by cigarette smoke in vivo

Dietary factors and environmental pollutants initiate signaling cascades that converge on AhR:Nrf2:NF-kappaB transcription factor (TF) networks and, in turn, affect the health of the organism through its effects on the expression of numerous genes. Reactive oxygen metabolites (ROMs) have been hypothesized to be common mediators in these pathways. alpha-Tocopherol (AT) is a potent, lipophilic, scavenger of ROMs in vitro and has been hypothesized to be a major chain-breaking anti-oxidant in lipoproteins and biological membranes in vivo. The lung offers a vital organ to test the various postulated actions of AT in vivo. Lung AT concentrations can be manipulated by several methods that include dietary and genetic techniques. In this study we have used mice with severe AT deficiency inflicted at birth by the deletion of AT transfer protein (ATTP) which is abundantly expressed in the liver and regulates systemic concentrations of AT. Mice and humans deficient in ATTP are AT deficient. Female ATTP-deficient (ATTP-KO) mice and their congenic ATTP normal (WT) mice fed a diet containing 35 IU AT/kg diet were used to test our hypothesis. The mice (n=5/group) were exposed to either air or cigarette smoke (CS, total suspended particles 60 mg/m(3), 6h/day), a source of ROM, for 3 or 10 days. Post-exposure lung tissue was dissected, RNA extracted from each lung and it was pooled group-wise and processed for GeneChip analysis (Affymetrix 430A 2.0). Differential analysis of the transcriptomes ( approximately 16,000 mRNAs) identified CS sensitive genes that were modulated by lung AT-concentration. CS activated AhR driven genes such as cyp1b1 whose induction was augmented in CS-exposed, AT-deficient lungs. However, CS-induced expression of some of the Nrf2 driven genes was not potentiated in the AT-deficient lungs. Largest clusters of CS-AT sensitive genes were lymphocyte and leukocyte specific genes. These gene-clusters included those encoding cytokines and immunoglobulins, which were repressed by CS and were modulated by lung AT concentrations. Our genome-wide analysis suggests reciprocal regulation of xenobiotic and immune response genes by CS and a modulatory role of lung AT concentration on the expression of these clusters of genes. These data suggest that in vivo network of AT, AT-metabolites and ATTP affects the transcription of genes driven by AhR, Nrf2 and NF-kappaB, transcription factor networks that transduce cellular metabolic signals and orchestrate adaptive responses of lungs to inhaled environmental pollutants.

A primary immunodeficiency characterized by defective immunoglobulin class switch recombination and impaired DNA repair

Immunoglobulin class switch recombination (CSR) deficiencies are rare primary immunodeficiencies, characterized by a lack of switched isotype (IgG, IgA, or IgE) production, variably associated with abnormal somatic hypermutation (SHM). Deficiencies in CD40 ligand, CD40, activation-induced cytidine deaminase, and uracil-N-glycosylase may account for this syndrome. We previously described another Ig CSR deficiency condition, characterized by a defect in CSR downstream of the generation of double-stranded DNA breaks in switch (S) μ regions. Further analysis performed with the cells of five affected patients showed that the Ig CSR deficiency was associated with an abnormal formation of the S junctions characterized by microhomology and with increased cell radiosensitivity. In addition, SHM was skewed toward transitions at G/C residues. Overall, these findings suggest that a unique Ig CSR deficiency phenotype could be related to an as-yet-uncharacterized defect in a DNA repair pathway involved in both CSR and SHM events.

Pathophysiology of B‐Cell Intrinsic Immunoglobulin Class Switch Recombination Deficiencies

B-cell intrinsic immunoglobulin class switch recombination (Ig-CSR) deficiencies, previously termed hyper-IgM syndromes, are genetically determined conditions characterized by normal or elevated serum IgM levels and an absence or very low levels of IgG, IgA, and IgE. As a function of the molecular mechanism, the defective CSR is variably associated to a defect in the generation of somatic hypermutations (SHMs) in the Ig variable region. The study of Ig-CSR deficiencies contributed to a better delineation of the mechanisms underlying CSR and SHM, the major events of antigen-triggered antibody maturation. Four Ig-CSR deficiency phenotypes have been so far reported: the description of the activation-induced cytidine deaminase (AID) deficiency (Ig-CSR deficiency 1), caused by recessive mutations of AICDA gene, characterized by a defect in CSR and SHM, clearly established the role of AID in the induction of the Ig gene rearrangements underlying CSR and SHM. A CSR-specific function of AID has, however, been detected by the observation of a selective CSR defect caused by mutations affecting the C-terminus of AID. Ig-CSR deficiency 2 is the consequence of uracil-N-glycosylase (UNG) deficiency. Because UNG, a molecule of the base excision repair machinery, removes uracils from DNA and AID deaminates cytosines into uracils, that observation indicates that the AID-UNG pathway directly targets DNA of switch regions from the Ig heavy-chain locus to induce the CSR process. Ig-CSR deficiencies 3 and 4 are characterized by a selective CSR defect resulting from blocks at distinct steps of CSR. A further understanding of the CSR machinery is expected from their molecular definition.

Activation-induced cytidine deaminase: structure-function relationship as based on the study of mutants

Activation-induced cytidine deaminase (AID; gene symbol AICDA) is the key molecule required to induce immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM) of the variable regions of Ig genes. Its deficiency causes a form of hyper-IgM (HIGM) syndrome. The study of natural AID mutants associated with HIGM as well as engineered mutants led to the characterization of the active domains of the protein. AID, through its cytidine deaminase activity, induces a targeted DNA lesion as an early step required for both CSR and SHM. Besides its cytidine deaminase activity, AID plays a further essential role in CSR, likely by recruiting CSR-specific cofactors by its C-terminus. A similar binding of SHM-specific cofactors to the N-terminal part is suggested by the functional characteristics of N(ter) AID artificial mutants. These data require confirmation in vivo. Finally, AID acts as a homo-, di-, or multimeric complex. Together, these data strongly suggest that AID, a master molecule for antibody diversification, exerts its activity on CSR not only as a cytidine deaminase enzyme but also as a docking protein, recruiting specific cofactors to a multimeric complex.

Hyper-IgM syndromes

PURPOSE OF REVIEW

The recent elucidation of the molecular defects leading to hyper-IgM syndromes has provided considerable insight into the complex mechanisms that govern the antibody maturation in humans.

RECENT FINDINGS

The study of a large cohort of patients revealed unexpected clinical, immunological and genetic findings, which have significant implications on the molecular basis of immunoglobulin class switch recombination and somatic hypermutation, as shown for hypomorphic mutations in the nuclear factor-kappaB essential modulator (NEMO) gene and peculiar activation-induced cytidine deaminase defects that differently affect class switch recombination and somatic hypermutation. The description of the hyper-IgM condition due to mutations in the gene encoding uracil-N glycosylase has been essential for defining the DNA-editing activity of activation-induced cytidine deaminase. Novel findings are awaited from the study of the yet genetically undefined hyper-IgM syndromes, leading to the identification of activation-induced cytidine deaminase cofactors and proteins involved in class switch recombination-induced DNA repair. In the genetically characterized hyper-IgM syndromes, the precise identification of the molecular defect allows the evaluation of hyper-IgM complications, and thus aids assessment of prognosis and proper survey and treatment.

SUMMARY

The important contribution made by investigation of this condition improves our understanding of the physiology of the antibody response in humans.

Cotranscriptional processes and their influence on genome stability

Numerous studies support the idea that the complex process of gene expression is composed of multiple highly coordinated and integrated steps. While such an extensive coupling ensures the efficiency and accuracy of each step during the gene expression pathway, recent studies have suggested an evolutionarily conserved function for cotranscriptional processes in the maintenance of genome stability. Specifically, such processes prevent a detrimental effect of nascent transcripts on the integrity of the genome. Here we describe studies indicating that nascent transcripts can rehybridize with template DNA, and that this can lead to DNA strand breaks and rearrangements. We present an overview of the diverse mechanisms that different species employ to keep nascent RNA away from DNA during transcription. We also discuss possible mechanisms by which nascent transcripts impact genome stability, as well as the possibility that transcription-induced genomic instability may contribute to disease.

AID to overcome the limitations of genomic information by introducing somatic DNA alterations

The immune system has adopted somatic DNA alterations to overcome the limitations of the genomic information. Activation induced cytidine deaminase (AID) is an essential enzyme to regulate class switch recombination (CSR), somatic hypermutation (SHM) and gene conversion (GC) of the immunoglobulin gene. AID is known to be required for DNA cleavage of S regions in CSR and V regions in SHM. However, its molecular mechanism is a focus of extensive debate. RNA editing hypothesis postulates that AID edits yet unknown mRNA, to generate specific endonucleases for CSR and SHM. By contrast, DNA deamination hypothesis assumes that AID deaminates cytosine in DNA, followed by DNA cleavage by base excision repair enzymes. We summarize the basic knowledge for molecular mechanisms for CSR and SHM and then discuss the importance of AID not only in the immune regulation but also in the genome instability.

Immunoglobulin replacement therapy in primary antibody deficiency diseases--maximizing success

Antibody or humoral immunodeficiencies comprise the largest group of primary immunodeficiency diseases. Since the first description of patients with low gammaglobulin levels more than four decades ago, a great wealth of information has been accumulated. Especially in the last several years, the application of molecular and genetic techniques has unraveled many of these disorders, identifying disorders of B cell development, failure of class switch recombination and abnormalities of specific antibody production. Regardless of the underlying defect, the mainstay of therapy has been and remains immunoglobulin (Ig) replacement therapy, currently by intravenous infusion or subcutaneous injection. With advances in manufacturing, a number of products are not only safe for intravenous administration but doses can be increased to provide even more effective infection prophylaxis. However, manufacturing processes, methods of viral inactivation and removal and final composition differ widely among the available preparations. How these variables impact clinical outcome is not clear, but they have the potential to do so. As a result, careful selection of an intravenous immunoglobulin (IVIG), matching patient needs and risks to those risks associated with a specific IVIG, is necessary to optimize outcomes and maximize the success of Ig replacement therapy.

Hyper-immunoglobulin M syndromes caused by intrinsic B-lymphocyte defects

Hyper-immunoglobulin M (IgM) syndromes are primary immunodeficiencies characterized by normal or elevated serum IgM levels with the absence of other isotypes, pinpointing to a defect in the Ig class switch recombination (CSR). The delineation of hyper-IgM syndromes made it possible to better define the mechanisms underlying the two major events of antibody maturation in humans, CSR and introduction of somatic hypermutation (SHM) in the variable region of immunoglobulins. The description of the activation-induced cytidine deaminase (AID) deficiency, characterized by a defect in both CSR and SHM, demonstrated for the first time that this molecule acts as a master player in the antigen-induced Ig gene-modification events responsible for both CSR and SHM. However, deleterious mutations located in the C-terminus lead to a CSR defect without affecting SHM, providing evidence for a role of AID in CSR distinct from the cytidine deaminase activity, likely by binding to a specific CSR cofactor. Molecular causes of two other hyper-IgM conditions have not yet been defined. However, they may be caused by either a defect in AID targeting on S regions or a CSR-specific DNA-repair defect. The mechanism of action of AID remains somewhat debated, but the observation that uracil-DNA-glycosylase deficiency leads to a severe hyper-IgM syndrome strongly argues in favor of a DNA-editing activity of AID.

Transcription of Ig Germline Genes in Single Human B Cells and the Role of Cytokines in Isotype Determination

We have developed a critical test of the chromatin accessibility model of Ig isotype determination in which local unfolding of chromatin higher order structure (chromatin accessibility) in the region of specific germline genes in the H chain locus determines the Ab class to be expressed in the B cell. We show that multiple germline genes are constitutively transcribed in the majority of naive human B cells in a population. Thus, because chromatin in its higher order structure cannot be transcribed, the entire Ig H chain locus must be unfolded in naive B cells. We have also established that IL-4 and anti-CD40 act by enhancing transcription in the majority of cells, rather than by activating transcription in more of the cells. Transcriptional activity in the human H chain locus rules out the perturbation of chromatin higher order structure as a factor in isotype determination. We have also found that the levels of germline gene transcription cannot fully account for the levels of secretion of the different Ig isotypes, and that secretion of IgE, in particular, is suppressed relative to that of IgG.

Nucleic acid structures and enzymes in the immunoglobulin class switch recombination mechanism

Class switch recombination is the gene rearrangement process by which our B lymphocytes change from IgM production to IgG, IgA, or IgE. Unlike the well-characterized V(D)J recombination, the mechanism of class switch recombination has been largely enigmatic until very recent progress has begun to shed light on this gene rearrangement process. Progress has been made on the enzymes involved in leading to the DNA cleavage events and on identifying the unusual DNA structures that those enzymes recognize.

The biology of IGE and the basis of allergic disease

Allergic individuals exposed to minute quantities of allergen experience an immediate response. Immediate hypersensitivity reflects the permanent sensitization of mucosal mast cells by allergen-specific IgE antibodies bound to their high-affinity receptors (FcepsilonRI). A combination of factors contributes to such long-lasting sensitization of the mast cells. They include the homing of mast cells to mucosal tissues, the local synthesis of IgE, the induction of FcepsilonRI expression on mast cells by IgE, the consequent downregulation of FcgammaR (through an insufficiency of the common gamma-chains), and the exceptionally slow dissociation of IgE from FcepsilonRI. To understand the mechanism of the immediate hypersensitivity phenomenon, we need explanations of why IgE antibodies are synthesized in preference to IgG in mucosal tissues and why the IgE is so tenaciously retained on mast cell-surface receptors. There is now compelling evidence that the microenvironment of mucosal tissues of allergic disease favors class switching to IgE; and the exceptionally high affinity of IgE for FcepsilonRI can now be interpreted in terms of the recently determined crystal structures of IgE-FcepsilonRI and IgG-FcgammaR complexes. The rate of local IgE synthesis can easily compensate for the rate of the antibody dissociation from its receptors on mucosal mast cells. Effective mechanisms ensure that allergic reactions are confined to mucosal tissues, thereby minimizing the risk of systemic anaphylaxis.

The role of DNA breaks in genomic instability and tumorigenesis

DNA double-strand breaks (DSBs) represent dangerous chromosomal lesions that can lead to mutation, neoplastic transformation, or cell death. DSBs can occur by extrinsic insult from environmental sources or may occur intrinsically as a result of cellular metabolism or a genetic program. Mammalian cells possess potent and efficient mechanisms to repair DSBs, and thus complete normal development as well as mitigate oncogenic potential and prevent cell death. When DSB repair (DSBR) fails, chromosomal instability results and can be associated with tumor formation or progression. Studies of mice deficient in various components of the non-homologous end joining pathway of DSBR have revealed key roles in both the developmental program of B and T lymphocytes as well as in the maintenance of general genome stability. Here, we review the current thinking about DSBs and DSBR in chromosomal instability and tumorigenesis, and we highlight the implications for understanding the karyotypic features associated with human tumors.

Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation

Activation-induced cytidine deaminase (AID) is a protein required for B cells to undergo class switch recombination and somatic hypermutation (SHM)--two processes essential for producing high-affinity antibodies. Purified AID catalyses the deamination of C to U on single-stranded (ss)DNA. Here, we show in vitro that AID-catalysed C deaminations occur preferentially on 5' WRC sequences in accord with SHM spectra observed in vivo. Although about 98% of DNA clones suffer no mutations, most of the remaining mutated clones have 10-70 C to T transitions per clone. Therefore, AID carries out multiple C deaminations on individual DNA strands, rather than jumping from one strand to another. The avid binding of AID to ssDNA could result from its large net positive charge (+11) at pH 7.0, owing to a basic amino-terminal domain enriched in arginine and lysine. Furthermore, AID exhibits a 15-fold preference for C deamination on the non-transcribed DNA strand exposed by RNA polymerase than the transcribed strand protected as a RNA-DNA hybrid. These deamination results on ssDNA bear relevance to three characteristic features of SHM: preferential mutation at C sites within WRC hotspot sequences, the broad clonal mutagenic heterogeneity of antibody variable regions targeted for mutation, and the requirement for active transcription to obtain mutagenesis.

Visualization of the genesis and fate of isotype-switched B cells during a primary immune response

The life history of isotype-switched B cells is unclear, in part, because of an inability to detect rare antigen-specific B cells at early times during the immune response. To address this issue, a small population of B cells carrying targeted antibody transgenes capable of class switching was monitored in immunized mice. After contacting helper T cells, the first switched B cells appeared in follicles rather than in the red pulp, as was expected. Later, some of the switched B cells transiently occupied the red pulp and marginal zone, whereas others persisted in germinal centers (GCs). Antigen-experienced IgM B cells were rarely found in GCs, indicating that these cells switched rapidly after entering GCs or did not persist in this environment.

R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells

The mechanism responsible for immunoglobulin class switch recombination is unknown. Previous work has shown that class switch sequences have the unusual property of forming RNA-DNA hybrids when transcribed in vitro. Here we show that the RNA-DNA hybrid structure that forms in vitro is an R-loop with a displaced guanine (G)-rich strand that is single-stranded. This R-loop structure exists in vivo in B cells that have been stimulated to transcribe the gamma3 or the gamma2b switch region. The length of the R-loops can exceed 1 kilobase. We propose that this distinctive DNA structure is important in the class switch recombination mechanism

Regulation of B lymphocytes in health and disease. Meeting review

Signal transduction by the B cell receptor (BCR) is an absolute requirement for the selection and development of B lymphocytes at multiple checkpoints. Binding to antigen via the BCR is complemented by a co-stimulus delivered through accessory and co-stimulatory cell surface molecules that regulate the signalling threshold. In addition, identification of genes associated with immunodeficiency syndromes has highlighted the importance of genetic regulation, particularly in immunoglobulin class-switching and somatic hypermutation. A 1-day symposium organised by the Biochemical Society considered some of the recent advances in our understanding of the molecules and regulatory pathways involved in B lymphocyte activation, differentiation and survival and the health consequences when threshold settings malfunction.

Immunological disorders and DNA repair

Cellular DNA continuously incurs damage and a range of damage response mechanisms function to maintain genomic integrity in the face of this onslaught. During the development of the immune response, the cell utilises three defined processes, V(D)J recombination, class switch recombination and somatic hypermutation, to create genetic diversity in developing T and B cells. Curiously, the damage response mechanisms employed to maintain genomic stability in somatic cells have been exploited and adapted to help generate diversity during immune development. As a consequence of this overlap, there is mounting evidence that disorders attributable to impaired damage response mechanisms display associated immunodeficiency. Since double strand breaks (DSB) are created during at least two of the mechanisms used to create immunoglobulin diversity, namely V(D)J recombination and class switch recombination, it is not surprising that disorders associated with defects in the response to double strand breaks are those most associated with immunodeficiency. Here, we review the steps involved in the generation of genetic diversity during immune development with a focus on the damage response mechanisms employed and then consider human immunodeficiency disorders associated with impaired damage response mechanisms.

Molecular mechanism of class switch recombination: linkage with somatic hypermutation

Class switch recombination (CSR) and somatic hypermutation (SHM) have been considered to be mediated by different molecular mechanisms because both target DNAs and DNA modification products are quite distinct. However, involvement of activation-induced cytidine deaminase (AID) in both CSR and SHM has revealed that the two genetic alteration mechanisms are surprisingly similar. Accumulating data led us to propose the following scenario: AID is likely to be an RNA editing enzyme that modifies an unknown pre-mRNA to generate mRNA encoding a nicking endonuclease specific to the stem-loop structure. Transcription of the S and V regions, which contain palindromic sequences, leads to transient denaturation, forming the stem-loop structure that is cleaved by the AID-regulated endonuclease. Cleaved single-strand tails will be processed by error-prone DNA polymerase-mediated gap-filling or exonuclease-mediated resection. Mismatched bases will be corrected or fixed by mismatch repair enzymes. CSR ends are then ligated by the NHEJ system while SHM nicks are repaired by another ligation system.

Novel insights into class switch recombination

The discovery of activation-induced cytidine deaminase, a putative RNA editing enzyme essential for both class switch recombination and somatic hypermutation, marked the field of isotype switching studies in the year 2000. More recent work from the same group now highlights some essential mechanistic aspects of the switch recombination process. In particular, much has been learnt about the relationship between transcription and recombination and the transcriptional competence of intronic promoters on looped-out circular DNA uncoupled from the proximal and distal enhancers. These findings have far-reaching implications, particularly for studies of class switch recombination in tissues. Although these important advances do not directly relate to interleukin-4-dependent immunoglobulin E switching, the conceptual and experimental tools developed through these studies are certain to foster progress in the immunoglobulin E field.

Mechanism and control of class-switch recombination

Class-switch recombination (CSR) occurs by an unusual and intriguing mechanism that has not been clearly elucidated as yet. Currently, we know that this mechanism involves recombination between large and highly repetitive switch (S) regions, is targeted by S-region transcription and requires the activity of the newly discovered activation-induced deaminase (AID). In this review, we discuss the potential role of these factors in CSR, discuss potential relationships between CSR and somatic hypermutation, and speculate how CSR and related mechanisms might contribute to genomic instability.

Terminal defects of B lymphocyte differentiation

In humans several abnormalities can occur during terminal B cell differentiation, leading to primary humoral immunodeficiencies. A recent study provided evidence of a qualitative defect of the affinity antibody maturation in some patients affected with common variable immunodeficiency syndrome, the molecular basis of which remains unknown. Several genetic defects in class switch recombination leading to a hyper-IgM syndrome have recently been delineated. Besides the well-known role of CD40-CD40 ligand interaction, they definitively demonstrate the requirement of CD40-mediated nuclear factor kappa B activation and the essential role of a newly described molecule, the activation-induced cytidine deaminase, in B cell terminal differentiation.

Variable deletion and duplication at recombination junction ends: implication for staggered double-strand cleavage in class-switch recombination

Immunoglobulin class-switch recombination (CSR) gives rise to looped-out circular DNA of a cleaved S segment, which is lost eventually after cell divisions. To understand the molecular mechanism of S region cleavage during CSR, we constructed artificial CSR substrates in which inversion-type CSR takes place to retain the cleaved S segment. Sequencing analyses of recombinant clones of these substrates revealed that varying degrees of deletions and duplications exist at CSR breakpoints, suggesting the involvement of staggered cleavage of the S region in CSR. In addition, mutations frequently found near junctions showed a similar profile of base replacement to Ig somatic hypermutation. These findings suggest that single-strand tails of staggered cleavage may be repaired by error-prone DNA synthesis.

Class switch recombination signals induce lymphocyte-derived Spo11 expression and Spo11 antisense oligonucleotide inhibits class switching

Recently, we showed that mouse Spo11 is induced in normal mu(+) B cells by class switch recombination (CSR) stimuli, by RT-PCR using primers based on the reported cDNA sequence of testis-derived Spo11 (test-Spo11) cDNA. In the present study, we first determined the cDNA sequence of lymphocyte-derived Spo11 (lym-Spo11). The 5' upstream portion had an as yet unreported sequence but the remaining part from exons 2 to 12 and the subsequent 3'UTR was completely identical to that of test-Spo11. RT-PCR analysis indicated that lymphocytes express lym-Spo11 but not test-Spo11. Second, we showed that lym-Spo11 is strongly induced (above eightfold) in the IgA CSR system of LPS-stimulated mu(+)B cells in the presence of all-trans retinoic acid and IL-4. Finally, we examined whether lym-Spo11 antisense S-oligonucleotide (AS) can inhibit CSR reactions in three in vitro CSR systems, IgA,IgG1, and IgE. Lym-Spo11 AS or the sense oligonucleotide was added to the cultures at the start, and total RNA was extracted after 4 days. IgA, IgG1, and IgE mRNAs (J(H)C(H)) and mature germline C(H) transcripts (I(H)C(H)) were quantitatively assayed by RT-PCR. AS inhibited J(H)C(H) expression dose-dependently. In all three systems, the maximum inhibition by 20 microM AS was in the range of 60 to 90%. Interestingly, I(H)C(H) was also inhibited by AS to a similar extent as J(H)C(H). These results suggested that lym-Spo11 plays an important role in the initiation step of CSR.

Ku protein in human T and B lymphocytes: full length functional form and signs of degradation

DNA-dependent protein kinase (DNA-PK) has been shown to take part in cell cycle regulatory signal transduction and in the repair of X-ray-induced DNA double-strand breaks. Functional DNA-PK is furthermore needed for the generation of antigen specificity during lymphocyte maturation. The Ku86 subunit of DNA-PK has been reported to exist in human B lymphocytes in a truncated form capable of binding to broken DNA but lacking the ability to activate the kinase function of DNA-PK. In the present work the Ku70 and Ku86 dimer proteins in T and B lymphocytes from human blood donors were analysed by immunoblotting and were observed apparently to be of full length. Also, nuclear protein extracted from B and non-B lymphocytes displayed DNA-dependent kinase activity. However, a minor fraction of Ku86 in lymphocytes was observed to be truncated with a molecular mass of approx. 70 kDa.

Palindromic but not G-rich sequences are targets of class switch recombination

In order to understand the specificity of sequences or structures recognized by a recombinase involved in class switch recombination (CSR), we examined the relative CSR efficiency of various switch sequences in artificial CSR constructs that undergo CSR in CH12F3-2 murine B lymphoma line. Since CSR recombination is not specific to switch regions of different isotypes or orientation of S sequences, we examined the efficiency of S sequences of non-mammalian species and artificial sequences which lack several characters of mammal switch sequences: chicken S(mu), Xenopus S(mu), telomere, multiple cloning site (MCS) and unrelated negative control sequence. CSR occurred in chicken S(mu) and MCS with significantly higher efficiency than the negative control. A common character of these two sequences is that they are rich in palindrome and stem-loop structures. However, telomeres, which are G-rich and repetitive but not palindromic, could not serve as switch sequences at all. The AT-rich Xenopus S(mu) sequence was inefficient but capable of CSR. CSR breakpoint distribution suggests that the cleavage may take place preferentially in the proximity of the junctions (neck) between the loop and stem in the secondary structure of the single-stranded S sequence, which can be formed by palindromic sequences. The results suggest that the secondary structure of S-region sequences which is transiently formed during transcription may be necessary for recognition by class switch recombinase.

The RAG proteins in V(D)J recombination: more than just a nuclease

V(D)J recombination is the process that generates the diversity among T cell receptors and is one of three mechanisms that contribute to the diversity of antibodies in the vertebrate immune system. The mechanism requires precise cutting of the DNA at segment boundaries followed by rejoining of particular pairs of the resulting termini. The imprecision of aspects of the joining reaction contributes significantly to increasing the variability of the resulting functional genes. Signal sequences target DNA recombination and must participate in a highly ordered protein-DNA complex in order to limit recombination to appropriate partners. Two proteins, RAG1 and RAG2, together form the nuclease that cleaves the DNA at the border of the signal sequences. Additional roles of these proteins in organizing the reaction complex for subsequent steps are explored.

The mu switch region tandem repeats are important, but not required, for antibody class switch recombination

Class switch DNA recombinations change the constant (C) region of the antibody heavy (H) chain expressed by a B cell and thereby change the antibody effector function. Unusual tandemly repeated sequence elements located upstream of H chain gene exons have long been thought to be important in the targeting and/or mechanism of the switch recombination process. We have deleted the entire switch tandem repeat element (S(mu)) from the murine (mu) H chain gene. We find that the S(mu) tandem repeats are not required for class switching in the mouse immunoglobulin H-chain locus, although the efficiency of switching is clearly reduced. Our data demonstrate that sequences outside of the S(mu) tandem repeats must be capable of directing the class switch mechanism. The maintenance of the highly repeated S(mu) element during evolution appears to reflect selection for a highly efficient switching process rather than selection for a required sequence element.

Mutations in activation-induced cytidine deaminase in patients with hyper IgM syndrome

Recent studies have shown that mutations in a newly described RNA editing enzyme, activation-induced cytidine deaminase (AID), can cause an autosomal recessive form of hyper IgM syndrome. To determine the relative frequency of mutations in AID, we evaluated a group of 27 patients with hyper IgM syndrome who did not have defects in CD40 ligand and 23 patients with common variable immunodeficiency. Three different mutations in AID were identified in 18 patients with hyper IgM syndrome, including 14 French Canadians, 2 Lumbee Indians, and a brother and sister from Okinawa. No mutations were found in the remaining 32 patients. In the group of patients with hyper IgM syndrome, the patients with mutations in AID were older at the age of diagnosis, were more likely to have positive isohemagglutinins, and were less likely to have anemia, neutropenia, or thrombocytopenia. Lymphoid hyperplasia was seen in patients with hyper IgM syndrome and normal AID as well as the patients with hyper IgM syndrome and defects in AID.

Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2)

The activation-induced cytidine deaminase (AID) gene, specifically expressed in germinal center B cells in mice, is a member of the cytidine deaminase family. We herein report mutations in the human counterpart of AID in patients with the autosomal recessive form of hyper-IgM syndrome (HIGM2). Three major abnormalities characterize AID deficiency: (1) the absence of immunoglobulin class switch recombination, (2) the lack of immunoglobulin somatic hypermutations, and (3) lymph node hyperplasia caused by the presence of giant germinal centers. The phenotype observed in HIGM2 patients (and in AID-/- mice) demonstrates the absolute requirement for AID in several crucial steps of B cell terminal differentiation necessary for efficient antibody responses.

Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme

Induced overexpression of AID in CH12F3-2 B lymphoma cells augmented class switching from IgM to IgA without cytokine stimulation. AID deficiency caused a complete defect in class switching and showed a hyper-IgM phenotype with enlarged germinal centers containing strongly activated B cells before or after immunization. AID-/- spleen cells stimulated in vitro with LPS and cytokines failed to undergo class switch recombination although they expressed germline transcripts. Immunization of AID-/- chimera with 4-hydroxy-3-nitrophenylacetyl (NP) chicken gamma-globulin induced neither accumulation of mutations in the NP-specific variable region gene nor class switching. These results suggest that AID may be involved in regulation or catalysis of the DNA modification step of both class switching and somatic hypermutation.