XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination

IJspeert, Hanna; Rozmus, Jacob; Schwarz, Klaus; Warren, René L.; Zessen, David van; Holt, Robert A.; Pico-Knijnenburg, Ingrid; Simons, Erik J.; Jerchel, Isabel S.; Wawer, Angela; Lorenz, Myriam Ricarda; Patıroğlu, Türkan; Akar, Himmet Haluk; Leite, Ricardo A.; Verkaik, Nicole S.; Stubbs, Andrew; Gent, Dik C. van; Dongen, Jacques J. M. van; Burg, Mirjam van der

doi:10.1182/blood-2016-02-701029

Cited by 33 publications

(32 citation statements)

References 57 publications

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“…Although this swing does not impact the A-KBM binding site nor the DNA binding domain, it exposes a large groove between the vWA and the ring domain of Ku80 that may non-exclusively reinforce XRCC4-LIG4 and/or XLF interaction with Ku or attract yet unknown components. Interestingly, XLF deficiency impacts on the activity of the Ku partner terminal deoxynucleotidyl transferase during V(D)J recombination 52 . Mutagenesis studies on the conserved positions that delineated the unmasked surface of this groove will help to define precisely the role of this swing in the NHEJ reaction.…”

Section: Discussionmentioning

confidence: 99%

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining

Nemoz

Ropars

Frit

et al. 2018

Nat Struct Mol Biol

111

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The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to ends of DNA double-strand breaks and recruits several factors of the Non-Homologous End Joining (NHEJ) pathway through molecular mechanisms that remain unclear. Here, we describe the crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBMs motifs bind on remote sites of Ku80 α/β domain. The X-KBM occupies an internal pocket formed after an unprecedented large outward rotation of the Ku80 α/β domain. We reveal independent recruitment at laser-irradiated sites of the APLF-interacting protein XRCC4 and of XLF through the respective binding of A- and X-KBMs to Ku80. Finally, we show that mutations on the X-KBM and A KBM binding sites in Ku80 compromises efficiency and accuracy of end-joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchorage points necessary to build the NHEJ intricate interactions network.

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Section: Discussionmentioning

confidence: 99%

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining

Nemoz

Ropars

Frit

et al. 2018

Nat Struct Mol Biol

111

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“…IJspeert et al . analysed the BCR heavy and light chain repertoire of XLF‐deficient patients and found a marked decrease in the number of N nucleotide additions in patients compared with HC, resulting in significantly shorter CDR3 regions.…”

Section: Use Of Bcr Repertoire Sequencing In Patients With Pidmentioning

confidence: 99%

“…Similar to LIG4 deficiency, XRCC4-like factor (XLF) deficiency is a rare form of autosomal-recessive disorder characterized by microcephaly, growth retardation, sensitivity to ionizing radiation and combined immunodeficiency of variable severity. 58 IJspeert et al 59 analysed the BCR heavy and light chain repertoire of XLF-deficient patients and found a marked decrease in the number of N nucleotide additions in patients compared with HC, resulting in significantly shorter CDR3 regions. The BCR repertoire of XLF patients showed a diverse use of VDJ genes, suggesting an intact combinational diversity in these patients.…”

Section: Combined Immunodeficienciesmentioning

confidence: 99%

B‐cell receptor repertoire sequencing in patients with primary immunodeficiency: a review

et al. 2017

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SummaryThe advent of next-generation sequencing (NGS) now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent throughout phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies. It is somewhat surprising that BCR repertoires, even from severe clinical phenotypes, often show only mild abnormalities and that diversity or immunoglobulin gene segment usage is generally preserved to some extent. Despite the great variety of wet laboratory and analytical methods that were used in the different studies, several findings are common to most investigated PIDs, such as the increased usage of gene segments that are associated with self-reactivity. These findings suggest that BCR repertoire characteristics may be used to assess the functionality of the B-cell compartment irrespective of the underlying defect. With the use of NGS approaches, there is now the opportunity to apply BCR repertoire sequencing to multiple patients and explore the PID BCR repertoire in more detail. Ultimately, using BCR repertoire sequencing in translational research could aid the management of PID patients by improving diagnosis, estimating functionality of the immune system and improving assessment of prognosis.

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“…ARTEMIS deficiency results in increased numbers of palindromic nucleotides, which are caused by defective opening of the hairpins formed on the coding ends of the junctions. XLF, XRCC4, and LIG4 form the ligation complex and genetic defects in these genes result in decreased number of nontemplated nucleotides (12,13,29,30). Diversity of the repertoire.…”

Section: Applications Of Argalaxymentioning

confidence: 99%

“…Peripheral blood was used from one ARTEMIS-deficient patient (ARTEMIS-13) (10), one UNG-deficient patient (UNG-2) (11), six XLFdeficient patients (XLF-1, XLF-5, XLF6-1, XLF6-2, and XLFP1, XLFP2) (12), four XRCC4-deficient patients (XRCC4-1, XRCC4-2, XRCC4-3, and XRCC4-4) (13), three LIG4-deficient patients (Ligase-IV-5, Ligase-IV-6, and Ligase-IV-7) (13), one NBS-deficient patient (NBS-4) (14), patients AT3 and AT4 (15) with ataxia telangiectasia (AT), and one patient suffering from chronic lymphocytic leukemia. Samples were obtained according to the guidelines of the Medical Ethics Committees of the Erasmus MC.…”

Section: Patient Samplesmentioning

confidence: 99%

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

IJspeert

Schouwenburg

Zessen

et al. 2017

The Journal of Immunology

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Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.

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XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination

Cited by 33 publications

References 57 publications

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining

B‐cell receptor repertoire sequencing in patients with primary immunodeficiency: a review

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

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