XLF deficiency results in reduced N-nucleotide addition during V(D)J recombination.
Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and performed immune phenotyping and antigen receptor repertoire analysis of immunoglobulin (Ig) and T-cell receptor (TR) rearrangements, using next-generation sequencing in 6 patients. The results were compared with XRCC4 and LIG4 deficiency. Both Ig and TR rearrangements showed a significant decrease in the number of nontemplated (N) nucleotides inserted by terminal deoxynucleotidyl transferase, which resulted in a decrease of 2 to 3 amino acids in the CDR3. Such a reduction in the number of N-nucleotides has a great effect on the junctional diversity, and thereby on the total diversity of the Ig and TR repertoire. This shows that XLF has an important role during V(D)J recombination in creating diversity of the repertoire by stimulating N-nucleotide insertion.
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Hanna
H
IJspeert
Child & Family Research Institute, BC Children's Hospital, Vancouver, BC, Canada;
Jacob
J
Rozmus
Institute for Transfusion Medicine, Ulm University, Ulm, Germany; Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg-Hessen, Ulm, Germany;
Klaus
K
Schwarz
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada;
René L
RL
Warren
Department of Bioinformatics, and.
David
D
van Zessen
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada;
Robert A
RA
Holt
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Ingrid
I
Pico-Knijnenburg
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Erik
E
Simons
Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Isabel
I
Jerchel
Pediatric Hematology/Oncology, Childrens Hospital, TU Munich, Munich, Germany; and.
Angela
A
Wawer
Institute for Transfusion Medicine, Ulm University, Ulm, Germany;
Myriam
M
Lorenz
Department of Pediatric Immunology, Erciyes University School of Medicine, Kayseri, Turkey.
Turkan
T
Patıroğlu
Department of Pediatric Immunology, Erciyes University School of Medicine, Kayseri, Turkey.
Himmet Haluk
HH
Akar
Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Ricardo
R
Leite
Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Nicole S
NS
Verkaik
Department of Bioinformatics, and.
Andrew P
AP
Stubbs
Department of Molecular Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Dik C
0000-0003-1473-8148
DC
van Gent
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Jacques J M
0000-0001-7686-0021
JJ
van Dongen
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands;
Mirjam
0000-0002-1510-3104
M
van der Burg
D000818:Animals; D000941:Antigens / Q000378:metabolism; D022801:Complementarity Determining Regions / Q000235:genetics; D004253:DNA Nucleotidylexotransferase / Q000378:metabolism; D045643:DNA Repair Enzymes / Q000172:deficiency* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000172:deficiency* / Q000378:metabolism; D015321:Gene Rearrangement / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics; D051379:Mice; D009711:Nucleotides / Q000378:metabolism*; D011839:Radiation, Ionizing; D011948:Receptors, Antigen, T-Cell / Q000235:genetics; D060152:V(D)J Recombination / Q000235:genetics*
D000941:Antigens; D022801:Complementarity Determining Regions; D004268:DNA-Binding Proteins; D007136:Immunoglobulins; C508551:NHEJ1 protein, human; D009711:Nucleotides; D011948:Receptors, Antigen, T-Cell; C519508:XLF protein, mouse; D004253:DNA Nucleotidylexotransferase; D045643:DNA Repair Enzymes