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*  The Activation-induced Deaminase Functions in a Postcleavage Step of the Somatic Hypermutation Process | JEM
The immune system generates diversity by using three distinct mechanisms of genetic alteration. V(D)J recombination, CSR, and SHM. Mechanistically, all three processes can be divided into at least three phases: targeting/recognition, DNA cleavage, and repair (18). In all three cases, transcription is thought to play a key role in targeting of a nuclease to the Ig locus. The cleavage step is thought to result in the production of a DNA DSB, though the creation of the DSB might not be the initial event. In V(D)J recombination for instance, the initial event is the nicking of one strand by the RAG recombinase, followed by hairpin formation and resolution into a blunt DSB (24). It is not known whether the CSR nuclease initially inflicts a single or double-strand break but there is some evidence to suggest that the final product of cleavage is a DSB (25). Finally, there is data to indicate that SHM also involves the creation of a DNA DSB, though that may not necessarily be the first step of the ...
  http://jem.rupress.org/content/195/9/1193.full
*  Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase | Adenosine Kinase...
Affinity maturation and class switching of antibodies requires activation-induced cytidine deaminase (AID)-dependent hypermutation of Ig V(D)J rearrangements and Ig S areas, respectively, in activated B cells. in DT40 cells elevated the pace of AID-induced BMS-754807 gene conversion as much as 5-collapse. Furthermore, DNA-PKcs-deficiency appeared to reduce point mutation. The data provide strong evidence that double-strand DNA ends capable of recruiting the DNA-dependent protein kinase complex are important intermediates in Ig V gene conversion. Author Summary To generate highly specific antibodies in response to an immune challenge, the antibody genes in triggered B cells mutate at a very high rate over a period of several days. The enzyme that initiates antibody gene mutation is definitely activation-induced cytidine deaminase (AID), the 1st protein recognized to directly edit DNA genomes BMS-754807 in vivo. AID induces point mutation of ...
  http://cutelevision.org/affinity-maturation-and-class-switching-of-antibodies-requires-activation-induced-cytidine-deaminase/
*  Somatic hypermutation analysis in follicular lymphoma provides evidence suggesting bidirectional cell migration between lymph...
In follicular lymphoma, somatic hypermutation of the immunoglobulin heavy chain genes facilitates the identification of different lymphoma cell clones, and the construction of genealogical trees. To analyze the dissemination of lymphoma cells, and the role of the bone marrow for disease progression, we simultaneously analyzed the somatic hypermutation patterns of lymph node and bone marrow specimens of three patients at onset and relapse. Immunoglobulin heavy chain genes were amplified by polymerase chain reaction, cloned and sequenced. Mutational pedigrees were constructed in a hierarchical order. Where direct transition of one mutation pattern into that of successor clones was not feasible, hypothetical predecessor clones were created, and a probability measurement calculation was introduced. Eighty-five sequenced clones were generated. The average mutation rates were 13,45% for the lymph nodes, and 9,78% ...
  http://www.haematologica.org/content/early/2013/03/28/haematol.2012.074252
*  Quantitative RT-PCR analysis of activation-induced cytidine deaminase expression in tissue samples from mantle cell lymphoma...
Quantitative RT-PCR analysis of activation-induced cytidine deaminase expression in tissue samples from mantle cell lymphoma and B-cell chronic lymphocytic leukemia patients ...
  http://repository.ubn.ru.nl/handle/2066/48420
*  DNA polymerase η is an A-T mutator in somatic hypermutation of immunoglobulin variable genes : Sussex Research Online
To determine whether DNA polymerase plays a role in the hypermutation of immunoglobulin variable genes, we examined the frequency and pattern of substitutions in variable VH6 genes from the peripheral blood lymphocytes of three patients with xeroderma pigmentosum variant disease, whose polymerase had genetic defects. The frequency of mutation was normal but the types of base changes were different: there was a decrease in mutations at A and T and a concomitant rise in mutations at G and C. We propose that more than one polymerase contributes to hypermutation and that if one is absent, others compensate. The data indicate that polymerase is involved in generating errors that occur predominantly at A and T and that another polymerase(s) may preferentially generate errors opposite G and C.. ...
  http://sro.sussex.ac.uk/29430/
*  Somatic hypermutation and B-cell lymphoma | Philosophical Transactions of the Royal Society B: Biological Sciences
During the B-cell response to T-cell-dependent antigens, the B cells undergo a rapid proliferative phase in the germinal centre. This is accompanied by the introduction of mutations into the immunoglobulin (Ig) variable region (V) genes. The B cells are then selected according to the affinity of the encoded immunoglobulin for antigen, resulting in affinity maturation of the response. Analysis of mutations in IgV genes has given insight into the history of individual B cells and their malignancies.. In most cases, analysis of mutations confirms classifications of B-cell lineage designated by studies of cellular morphology and surface antigen expression. However, of particular interest is the subdivision of groups of malignancies by analysis of somatic hypermutation. It is now apparent that there are two subsets of chronic lymphocytic leukaemia (CLL), one with a low load of mutations and poor prognosis, and one with a heavy ...
  http://rstb.royalsocietypublishing.org/content/356/1405/73
*  "Genome-Wide Characterization of the Effects of Nucleic Acid Modifying " by Eric Luke Fritz
Activation-induced cytidine deaminase (AID) is essential for two processes of immunoglobulin diversification in germinal center B cells: somatic hypermutation (SHM), in which mutations are introduced into immunoglobulin (Ig) genes, and class-switch recombination (CSR), in which genomic constant regions are recombined to encode antibodies of different isotypes. Both of these processes require AID-catalyzed C-to-U lesions at the Ig loci, which are resolved to generate point mutations or double-stranded DNA breaks in the cases of SHM and CSR, respectively. Despite over a decade of intense study, a number of open issues remain surrounding AID. The diversity of findings regarding AID's role in DNA demethylation raises the question of the scope of its involvement in this process. Additionally, while it is clear that AID-mediated damage occurs, the effects of this damage on the average B cell have not been characterized. Finally, ...
  http://digitalcommons.rockefeller.edu/student_theses_and_dissertations/215/
*  Regulation and Dysregulation of Antibody Diversification - Matthew Strout
Activation-Induced cytidine deaminase (AID) is expressed in germinal center B cells and is required for somatic hypermutation (SHM) and class switch recombinati...
  http://grantome.com/grant/NIH/K08-CA140718-05
*  dU Oligo Modifications from Gene Link
Deoxyuridine (dU) is a pyrimidine deoxyribonucleoside, and a derivative of the nucleoside uridine, with the only difference being that, in dU, a hydrogen (-H) group is substituted for uridine s OH group located at the 2 -position of the ribose. dU is generated in cellular DNA as a deamination product of dC (deoxycytidine), with the deamination process catalyzed by the enzyme AID (activation-induced cytidine deaminase) (1). AID is a B cell-specific gene that is necessary for antibody gene diversification via class-switch recombination and somatic hypermutation (2, 3). The dC-to-dU conversion(s) by AID occurs in the IgG locus, with various gene diversification pathways arising from the different DNA repair mechanisms used by B-cells to repair the dU lesion (1).. dC-to-dU conversion via cytidine deamination is also implicated in innate immunity to retroviruses. Here deamination of dC is mediated by the enzyme APOBEC3G, which is present in T cells, acting on the ...
  http://www.genelink.com/newsite/products/mod_detail.asp?modid=74
*  Regulation of activation-induced cytidine deaminase DNA deamination activity in B-cells by Ser38 phosphorylation | Biochemical...
To address the physiological significance of AID phosphorylation at Ser38, analysis of a mouse model (in which AIDS38A is expressed at physiological levels utilizing its endogenous control elements) was required. Two recent studies reported the generation and analysis of mice expressing only the AIDS38A mutant protein, which occurred at levels quite comparable with those of wild-type mAID expression in activated B-cells, from their endogenous AID alleles [45,51]. In addition, one of these studies also demonstrated that the AIDS38A protein expressed from the endogenous AID allele failed to associate with RPA in vivo [51]. Both studies found that mice homozygous for the AIDS38A (AIDS38A/S38A) mutation have quite severe CSR defects, demonstrating clearly that the apparently normal levels of CSR reported for this mutant form of AID by others [49] probably resulted from overexpression of the mutant protein as proposed in [47].. Activation of AIDS38A/S38A B-cells with αCD40 and IL-4 (interleukin 4) ...
  http://www.biochemsoctrans.org/content/37/3/561
*  AICDA antibody | pab0246-P | Covalab - Covalab Biotechnology
Activation-induced cytidine deaminase (AICDA) antibody | Q9GZX7 | Activation-induced cytidine deaminase (AICDA), Cytidine aminohydrolase, AID
  https://www.covalab.com/activation-induced-cytidine-deaminase-aicda-antibody-5.html
*  Signal regulated localisation of a mutagenic protein complex at the Igh locus
Our system to produce antibodies is critical for our survival against numerous infections, but it causes also many tumors. B-lymphocytes can modify their immunoglobulin (Ig) genes to generate specific antibodies with a new isotype and enhanced affinity against an antigen. Activation-induced cytidine deaminase (AID) is the key mutagenic enzyme that initiates these processes by deaminating cytosine to uracil. How somatic hypermutation (SH) and class switch recombination (CSR) are targeted is key to understanding the defect DNA integrity in lymphomas and also in other tumors where inflammatory signals aberrantly induces AID. The trans-acting factors mediating specific targeting of AID and thereby SH and CSR have remained elusive. Here we show that mutant E2A with defect inhibition by the Ca2+sensor protein calmodulin results in reduced B cell receptor- (BCR-), IL4-plus CD40 ligand-stimulated CSR to IgE and instead aberrant CSR. AID ...
  http://umu.diva-portal.org/smash/record.jsf?pid=diva2:868396
*  Anti-DNA Polymerase theta antibody (ab80906) | Abcam
Rabbit polyclonal DNA Polymerase theta antibody validated for WB, ELISA, ICC/IF and tested in Human. Referenced in 4 publications and 1 independent review…
  http://www.abcam.com/dna-polymerase-theta-antibody-ab80906.html
*  Profiling the pattern of human immunoglobulin SHM and CSR in B memory cells via high-throughput sequencing (62.11) | The...
One of the defining features of the adaptive immune system is that it adapts its response during an infection to improve its recognition of the pathogen. The adaptive feature is best embodied in the genetic alteration mechanism of somatic hypermutation (SHM) and class-switch recombination (CSR) as they are only activated to increase recognition to a previously encountered pathogen. Due to the limited number of sequence data, the hypermutation pattern such as mutation rate, and the distribution of mutation spots remains poorly understood. Using the combination of arm-PCR and high-throughput sequencing, we have determined about one million cDNA sequences of human immunoglobulin genes in B memory cells isolated from the peripheral blood from two subjects at various time points after administration of the 2009-2010 flu vaccine. We identified the location of the hypermutations, the distribution of mutation rate, ...
  http://www.jimmunol.org/content/186/1_Supplement/62.11
*  Switch recombination and somatic hypermutation are controlled by the heavy chain 3′ enhancer region | JEM
Several lines of work suggest that the 3′ enhancer region would control CSR. Chromatin interactions between heavy chain genes and HS1,2 suggest functional interactions (Wuerffel et al., 2007). Deletions or replacements of individual hypersensitive regions (Cogné et al., 1994; Manis et al., 1998; Seidl et al., 1999) implicate the 3′ regulatory locus in CSR. Additionally, insertions of foreign sequence in the locus also affect CSR, possibly by disrupting interactions between enhancer elements (Seidl et al., 1999). However, any conclusions are complicated by the fact that clean deletion of single elements reveals only a minimal phenotype (Manis et al., 1998; Seidl et al., 1999; Vincent-Fabert et al., 2009). Deletion of both HS3B and HS4 (Pinaud et al., 2001) from the germline demonstrates a role in CSR to some heavy chain genes. To pursue the role of the 3′ enhancer region, over the last 10 yr, several laboratories have attempted to delete all four elements from the mouse germline, but for ...
  http://jem.rupress.org/content/206/12/2613
*  REG-γ associates with and modulates the abundance of nuclear activation-induced deaminase | JEM
Reduced AID degradation in REG-γ−/− mice might also be expected to lead to a more general increase in genomic instability. However, REG-γ−/− mice on a normal background do not show any marked increase in tumor incidence, possibly reflecting p53 and other checkpoints (Jankovic et al., 2010). Only a small increase in the frequency of c-myc-IgH translocations was detected in cultured B cells from REG-γ-deficient (as opposed to REG-γ-proficient) mice in which AID overexpression had been induced by retroviral transduction (Fig. S3), possibly reflecting the ubiquitin-dependent degradation of such overexpressed AID (Fig. 3 D). Thus, although the results suggest that the dramatically increased class-switching in REG-γ-deficient mice is likely to be at least in part a direct consequence of the increased AID abundance, we cannot exclude the possibility that there is an additional contribution from some as yet unidentified effect of REG-γ deficiency (e.g., a perturbation of AID's ...
  http://jem.rupress.org/content/208/12/2385
*  V-region mutation in vitro, in vivo, and in silico reveal the importance of the enzymatic properties of AID and the sequence...
The somatic hyper mutation of Ig variable regions requires the activity of activation-induced cytidine deaminase (AID) which has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) motif hot spots in in vivo and in vitro assays. In this study, AECC investigators Bergman and Scharff compared mutation profiles of in vitro assays for the 3' flanking intron of VhJ558-Jh4 region to previously reported in vivo profiles for the same region in the Msh2(-/-)Ung(-/-) mice that lack base excision and mismatch repair. They found that the in vitro and in vivo mutation profiles were highly correlated for the top (nontranscribed) strand, while for the bottom (transcribed) strand the correlation is far lower. Using an in silico model of AID activity to elucidate the relative importance of motif targeting in vivo they found that the mutation process entails substantial complexity beyond motif targeting, a large part of which is captured in vitro. To elucidate the contribution of the ...
  http://www.einstein.yu.edu/centers/cancer/selected-achievements.aspx?id=33671
*  Cytidine Deaminase
Prof. McGuigan from Cardiff School of Pharmacy, UK along with Prof. Jan Balzarini of Rega Instutute for Medical Research, Belgium have reported an innovative approach to overcome the cancer Resistance mechanism using the pro-tide technology of their's. They prepared various Nucleotide Phosphoramidates of the known anticancer drug Gemcitabine and were able to find a molecule that was resistant to cytidine deaminase-mediated […]. » Read more ...
  http://www.rcmishra.com/tag/cytidine-deaminase/
*  Electrochemical direct detection of DNA deamination catalyzed by APOBEC3G.
APOBEC3G catalyzes deamination of cytosines in HIV-1 genome, and restricts the HIV-1 infection. Here, we propose a picomole-scale assay for the detection of DNA deamination catalyzed by APOBEC3G. Our results show the suitability of the developed meth
  http://www.biomedsearch.com/nih/Electrochemical-direct-detection-DNA-deamination/23145435.html
*  UPENN Biomedical Graduate Studies | Rahul M. Kohli
From the host immune perspective, the generation of genomic diversity is used as both a defensive and an offensive weapon. Host mutator enzymes such as Activation-Induced Cytidine Deaminase (AID) seed diversity in the adaptive immune system by introducing targeted mutations into the immunoglobulin locus that result in antibody maturation. Related deaminases of the innate immune system can directly attack retroviral threats by garbling the pathogen genome through mutation, as accomplished by the deaminase APOBEC3G, which restricts infection with HIV. Immune mutator enzymes, however, also pose a risk to the host, as overexpression or dysregulation have been associated with oncogenesis ...
  http://www.med.upenn.edu/apps/faculty/index.php/g20000220/p6341532
*  The Extracellular Membrane-Proximal Domain of Human Membrane IgE Controls Apoptotic Signaling of the B Cell Receptor in the...
B lymphocytes respond to Ags through engagement of the BCR by direct binding to the mIg. As a consequence, depending on the differentiation status of the B cells, the strength and duration of the interaction, presence or absence of costimulatory or inhibitory signals, cells are induced to proliferate and differentiate into plasma cells, or anergy or apoptosis is induced (28). In particular, mature B cells and memory B cells switched to IgA, IgG or IgE isotypes are recruited into germinal centers, where active somatic hypermutation leading to affinity maturation takes place. In this process, a large number of cells also fail to successfully engage Ag and die by apoptosis (15). The mechanism by which the BCR delivers apoptotic signaling is far from being clear (29, 30). Different regulation of BCR signaling through the B cell coreceptor CD22 was reported to be dependent on the distinct cytoplasmic tails (μ and γ) of the mIg isotypes (31). Also, for the ε-isotype, signal ...
  http://www.jimmunol.org/content/177/6/3597.full
*  Plus it
Inflammation predisposes to tumorigenesis in various organs by potentiating a susceptibility to genetic aberrations. The mechanism underlying the enhanced genetic instability through chronic inflammation, however, is not clear. Here we demonstrated that TNF-α stimulation induced transcriptional downregulation of MSH2, a member of the mismatch repair family, via nuclear factor-κB-dependent miR-21 expression in hepatocytes. Liver cancers developed in ALB-MSH2-/-AID+, ALB-MSH2-/-, and ALB-AID+ mice in which MSH2 is deficient and/or activation-induced cytidine deaminase (AICDA) is expressed in cells with albumin-producing hepatocytes. The mutation signatures in the tumors developed in these models, especially ALB-MSH2-/-AID+ mice, closely resembled those of human hepatocellular carcinoma. Our findings demonstrated that inflammation-mediated dysregulation of MSH2 may be a mechanism of genetic alterations during hepatocarcinogenesis. ...
  http://cancerres.aacrjournals.org/content/early/2016/06/03/0008-5472.CAN-15-2926
*  Development of an anti-HIV vaccine eliciting broadly neutralizing antibodies | AIDS Research and Therapy | Full Text
It has been reported that, during chronic infection, potent and cross-reactive bNAbs that are capable of neutralizing heterologous viruses of diverse subtypes develop in a small portion of HIV-1 infected individuals [28-31]. The effective humoral responses are slow, with NAbs to the initial viral strain appearing after ~12 weeks, and broad NAbs (in 10-30% of individuals) after 2-4 years [30, 32-34]. The development of bNAbs was shown to correlate with high plasma viremia and could result from evolving antigen exposure over many years that has allowed sufficient somatic hypermutation in the B-cell receptors (BCRs) and focuses the B-cell response to the conserved neutralization sites on Env [30]. Therefore, delayed bNAb response might be attributed to the slow, antigen-dependent affinity maturation process. Abs typically accumulate mutations in the complementarity determining region (CDR) loops, i.e. the typical antigen contact region [35]. Whereas most human Abs that have ...
  https://aidsrestherapy.biomedcentral.com/articles/10.1186/s12981-017-0178-3
*  RCSB PDB - Launch Viewer for 1YXS
1YXS: Crystal structures of proto-oncogene kinase Pim1: a target of aberrant somatic hypermutations in diffuse large cell lymphoma.
  http://www.rcsb.org/pdb/explore/viewerLaunch.do?viewerType=SV&structureId=1YXS&unit=bio&unit_id=1