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.

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Epigenetic tethering of AID to the donor switch region during immunoglobulin class switch recombination

Journal of Experimental Medicine ◽

10.1084/jem.20110118 ◽

2011 ◽

Vol 208 (8) ◽

pp. 1649-1660 ◽

Cited By ~ 82

Author(s):

Beena Patricia Jeevan-Raj ◽

Isabelle Robert ◽

Vincent Heyer ◽

Adeline Page ◽

Jing H. Wang ◽

...

Keyword(s):

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Class Switch Recombination ◽

Epigenetic Modifications ◽

Dna Breaks ◽

Switch Region ◽

Heterochromatin Protein 1 ◽

Immunoglobulin Class ◽

Class Switch

Immunoglobulin class switch recombination (CSR) is initiated by double-stranded DNA breaks (DSBs) in switch regions triggered by activation-induced cytidine deaminase (AID). Although CSR correlates with epigenetic modifications at the IgH locus, the relationship between these modifications and AID remains unknown. In this study, we show that during CSR, AID forms a complex with KAP1 (KRAB domain–associated protein 1) and HP1 (heterochromatin protein 1) that is tethered to the donor switch region (Sμ) bearing H3K9me3 (trimethylated histone H3 at lysine 9) in vivo. Furthermore, in vivo disruption of this complex results in impaired AID recruitment to Sμ, inefficient DSB formation, and a concomitant defect in CSR but not in somatic hypermutation. We propose that KAP1 and HP1 tether AID to H3K9me3 residues at the donor switch region, thus providing a mechanism linking AID to epigenetic modifications during CSR.

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Regulation of class switch recombination and somatic mutation by AID phosphorylation

Journal of Experimental Medicine ◽

10.1084/jem.20081319 ◽

2008 ◽

Vol 205 (11) ◽

pp. 2585-2594 ◽

Cited By ~ 97

Author(s):

Kevin M. McBride ◽

Anna Gazumyan ◽

Eileen M. Woo ◽

Tanja A. Schwickert ◽

Brian T. Chait ◽

...

Keyword(s):

Somatic Mutation ◽

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Point Mutations ◽

Class Switch Recombination ◽

Variable Region ◽

Dna Breaks ◽

Class Switching ◽

Class Switch

Activation-induced cytidine deaminase (AID) is a mutator enzyme that initiates somatic mutation and class switch recombination in B lymphocytes by introducing uracil:guanine mismatches into DNA. Repair pathways process these mismatches to produce point mutations in the Ig variable region or double-stranded DNA breaks in the switch region DNA. However, AID can also produce off-target DNA damage, including mutations in oncogenes. Therefore, stringent regulation of AID is required for maintaining genomic stability during maturation of the antibody response. It has been proposed that AID phosphorylation at serine 38 (S38) regulates its activity, but this has not been tested in vivo. Using a combination of mass spectrometry and immunochemical approaches, we found that in addition to S38, AID is also phosphorylated at position threonine 140 (T140). Mutation of either S38 or T140 to alanine does not impact catalytic activity, but interferes with class switching and somatic hypermutation in vivo. This effect is particularly pronounced in haploinsufficient mice where AID levels are limited. Although S38 is equally important for both processes, T140 phosphorylation preferentially affects somatic mutation, suggesting that posttranslational modification might contribute to the choice between hypermutation and class switching.

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Parp1 facilitates alternative NHEJ, whereas Parp2 suppresses IgH/c-myc translocations during immunoglobulin class switch recombination

Journal of Experimental Medicine ◽

10.1084/jem.20082468 ◽

2009 ◽

Vol 206 (5) ◽

pp. 1047-1056 ◽

Cited By ~ 121

Author(s):

Isabelle Robert ◽

Françoise Dantzer ◽

Bernardo Reina-San-Martin

Keyword(s):

Dna Damage ◽

Cytidine Deaminase ◽

Class Switch Recombination ◽

Dependent Manner ◽

Dna Breaks ◽

End Joining ◽

Immunoglobulin Class ◽

Class Switch ◽

Switch Regions ◽

Alternative Nhej

Immunoglobulin class switch recombination (CSR) is initiated by DNA breaks triggered by activation-induced cytidine deaminase (AID). These breaks activate DNA damage response proteins to promote appropriate repair and long-range recombination. Aberrant processing of these breaks, however, results in decreased CSR and/or increased frequency of illegitimate recombination between the immunoglobulin heavy chain locus and oncogenes like c-myc. Here, we have examined the contribution of the DNA damage sensors Parp1 and Parp2 in the resolution of AID-induced DNA breaks during CSR. We find that although Parp enzymatic activity is induced in an AID-dependent manner during CSR, neither Parp1 nor Parp2 are required for CSR. We find however, that Parp1 favors repair of switch regions through a microhomology-mediated pathway and that Parp2 actively suppresses IgH/c-myc translocations. Thus, we define Parp1 as facilitating alternative end-joining and Parp2 as a novel translocation suppressor during CSR.

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Genetic loss of the ubiquitin ligase RNF126, an AID interacting partner and modifier, affects strand targeting during somatic hypermutation of antibody genes

10.1101/469775 ◽

2018 ◽

Author(s):

Nicholas Economos ◽

Rebecca K Delker ◽

Pete Stavropoulos ◽

F. Nina Papavasiliou

Keyword(s):

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Point Mutations ◽

Variable Region ◽

Dna Breaks ◽

Switch Region ◽

Post Translational Modifications ◽

Class Switch ◽

Double Stranded Dna ◽

Activation Induced Cytidine Deaminase

AbstractActivation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) in B lymphocytes by catalyzing the introduction of deoxyuracil: deoxyguanine mismatches into the DNA of the transcribed Ig locus. Repair pathways then process these mismatches to produce point mutations in the Ig variable region or double-stranded DNA breaks in the switch region followed by deletional recombination. It has been suggested that post-translational modifications on AID mediate a number of these different decisions, ranging from global targeting (Ig vs the genome), local targeting (variable vs switch region; transcribed vs non-transcribed strand) as well as process-appropriate DNA repair. Here we demonstrate that absence of RNF126, an E3 ligase shown to mono-ubiquitylate AID, results in a specific strand targeting defect in SHM, producing substantial G>C bias; strickingly, loss of RNF126 was also associated with tandem indels within the variable region (JH4 intron) but only a slight increase in the types of chromosomal translocations that are characteristic of deregulated AID. Conversely, these findings suggest that mono-ubiquitination of AID, likely in situ, is necessary for the proper removal of the protein from the non-transcribed strand, thus producing both optimal patterns of SHM and also limiting the number of indels within the target locus.

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Hyper-IgM syndromes: a model for studying the regulation of class switch recombination and somatic hypermutation generation

Biochemical Society Transactions ◽

10.1042/bst0300815 ◽

2002 ◽

Vol 30 (4) ◽

pp. 815-818 ◽

Cited By ~ 28

Author(s):

A. Durandy

Keyword(s):

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Class Switch Recombination ◽

Humoral Response ◽

Cd40 Ligand ◽

Class Switch ◽

Hyper Igm Syndrome ◽

Hyper Igm ◽

Nuclear Factor Kb

Several genetic defects in class switch recombination, which lead to a hyper-IgM syndrome, have been described recently in humans. In addition to the well known role of CD40-ligand-CD40 interaction, these pathologies demonstrate definitively the requirement of CD40-mediated nuclear factor kB activation and the essential role of a recently described molecule, the activationinduced cytidine deaminase in an efficient humoral response, which includes class switch recombination and the production of high-affinity antibodies.

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Molecular analysis of a large cohort of patients with the hyper immunoglobulin M (IgM) syndrome

Blood ◽

10.1182/blood-2003-12-4420 ◽

2005 ◽

Vol 105 (5) ◽

pp. 1881-1890 ◽

Cited By ~ 139

Author(s):

Wen-I Lee ◽

Troy R. Torgerson ◽

Michael J. Schumacher ◽

Leman Yel ◽

Qili Zhu ◽

...

Keyword(s):

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Cd40 Ligand ◽

Immunoglobulin M ◽

Uracil Dna Glycosylase ◽

Molecular Defects ◽

Class Switch ◽

Activation Induced Cytidine Deaminase ◽

Cd40 Activation ◽

Common Variable

AbstractThe hyper immunoglobulin M (IgM) syndrome (HIGM), characterized by recurrent infections, low serum IgG and IgA, normal or elevated IgM, and defective class switch recombination and somatic hypermutation, is a heterogenous disorder with at least 5 distinct molecular defects, including mutations of the genes coding for the CD40 ligand (CD40L) and IKK-gamma (NEMO) genes, both X-linked; and mutations of CD40, activation-induced cytidine deaminase (AICDA), and uracil-DNA glycosylase (UNG), associated with autosomal recessive HIGM syndromes. To investigate the molecular basis of HIGM, we determined the prevalence of mutations affecting these 5 genes in a cohort of 140 patients (130 males and 10 females). Those patients without a molecular diagnosis were subsequently evaluated for mutations of the following genes: inducible CO-stimulator molecule (ICOS), ICOS ligand (ICOSL), and if male, Bruton tyrosine kinase (Btk) and SLAM-associated protein (SAP/SH2D1A). We found mutations of CD40L in 98 males; AICDA in 4 patients (3 males, 1 female); UNG in one adult male; and Btk in 3 boys. Of the remaining 25 males, one infant with hypohidrotic ectodermal dysplasia had a mutation of NEMO. None of the remaining 33 patients (24 males/9 females) had mutations affecting CD40, ICOS, ICOSL, or SH2D1, and are best classified as common variable immune deficiency (CVID), although other genes, including some not yet identified, may be responsible.

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Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination

F1000Research ◽

10.12688/f1000research.13247.1 ◽

2018 ◽

Vol 7 ◽

pp. 458 ◽

Cited By ~ 3

Author(s):

Laura Nicolas ◽

Montserrat Cols ◽

Jee Eun Choi ◽

Jayanta Chaudhuri ◽

Bao Vuong

Keyword(s):

Regulatory Networks ◽

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Class Switch Recombination ◽

Affinity Maturation ◽

Genomic Integrity ◽

Dna Double Strand Breaks ◽

Dna Breaks ◽

Directed Mutation ◽

Class Switch

Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity.

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Human PMS2 deficiency is associated with impaired immunoglobulin class switch recombination

Journal of Experimental Medicine ◽

10.1084/jem.20080789 ◽

2008 ◽

Vol 205 (11) ◽

pp. 2465-2472 ◽

Cited By ~ 110

Author(s):

Sophie Péron ◽

Ayse Metin ◽

Pauline Gardès ◽

Marie-Alexandra Alyanakian ◽

Eamonn Sheridan ◽

...

Keyword(s):

Somatic Hypermutation ◽

Cytidine Deaminase ◽

Class Switch Recombination ◽

Dna Breaks ◽

Gene Encoding ◽

Class Switch ◽

Double Strand Dna Breaks ◽

Switch Regions

Immunoglobulin (Ig) class switch recombination (CSR) deficiencies are rare primary immunodeficiencies characterized by the lack of switched isotype (IgG/IgA/IgE) production. In some cases, CSR deficiencies can be associated with abnormal somatic hypermutation. Analysis of CSR deficiencies has helped reveal the key functions of CSR-triggering molecules, i.e., CD40L, CD40, and effector molecules such as activation-induced cytidine deaminase and uracil N-glycosylase. We report a new form of B cell–intrinsic CSR deficiency found in three patients with deleterious, homozygous mutations in the gene encoding the PMS2 component of the mismatch repair machinery. CSR was found partially defective in vivo and markedly impaired in vitro. It is characterized by the defective occurrence of double-strand DNA breaks (DSBs) in switch regions and abnormal formation of switch junctions. This observation strongly suggests a role for PMS2 in CSR-induced DSB generation.

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