Illegitimate RAG-mediated recombination events are involved in IKZF1 Δ3-6 deletion in BCR-ABL1 lymphoblastic leukaemia

Clin Exp Immunol. 2016 Sep;185(3):320-31. doi: 10.1111/cei.12812. Epub 2016 Jul 28.

Abstract

Breakpoint cluster region-Abelson murine leukaemia viral oncogene homologue 1 (BCR-ABL1), encoded by the Philadelphia (Ph) chromosome, is the characteristic of chronic myeloid leukaemia (CML) and a subset of acute lymphoblastic leukaemia (ALL). We demonstrated that expression of the Ik6 transcript, which lacked exons 3-6, was observed exclusively in BCR-ABL1(+) B ALL and lymphoid blast crisis CML (BC-CML) patients harbouring the IKZF1 Δ3-6 deletion. To confirm the hypothesis that illegitimate recombination activating gene protein (RAG)-mediated recombination events are involved in IKZF1 Δ3-6 deletion in BCR-ABL1 lymphoblastic leukaemia, we first demonstrated that the expression rates of RAG1 and RAG2, collectively called RAG, were higher in ALL and BC-CML (lymphoid). Notably, analysis of relationships among RAG, BCR-ABL1 and Ikaros 6 (Ik6) showed that Ik6 can be generated only if RAG and BCR-ABL1 are co-existing. The sequencing data showed that the deleted segments of introns 2 and 6 contained cryptic recombination signal sequences (cRSSs) and frequently had non-template nucleotides inserted between breakpoints. Furthermore, we used chromatin immunoprecipitation (ChIP) technology and demonstrated that the sequences directly flanking IKZF1 Δ3-6 deletion breakpoints have significantly higher levels of histone H3 lysine 4 trimethylation (H3K4me3) modifications. Overall, RAG expression, good-quality cRSS and a specific chromatin modification, H3K4me3, satisfy the conditions of RAG's off-target effects on IKZF1. Our work provides evidence for RAG-mediated IKZF1 Δ3-6 deletion. Our results raise the prospect that RAG is a valuable biomarker in disease surveillance. Dissecting the contribution of RAG should not only provide valuable mechanistic insights, but will also lead to a new therapeutic direction.

Keywords: ALL; BCR-ABL1; CML; Ik6; RAG.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Biomarkers, Tumor / blood
  • Biomarkers, Tumor / genetics
  • DNA-Binding Proteins / blood
  • DNA-Binding Proteins / genetics
  • Female
  • Gene Deletion*
  • Genes, abl / genetics*
  • Homeodomain Proteins / blood
  • Homeodomain Proteins / genetics
  • Humans
  • Ikaros Transcription Factor / genetics*
  • Immunoprecipitation
  • Male
  • Middle Aged
  • Nuclear Proteins / blood
  • Nuclear Proteins / genetics
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma / genetics*
  • Recombination, Genetic*
  • Young Adult

Substances

  • Biomarkers, Tumor
  • DNA-Binding Proteins
  • Homeodomain Proteins
  • IKZF1 protein, human
  • Ikaros 6 protein, human
  • Nuclear Proteins
  • RAG2 protein, human
  • RAG-1 protein
  • Ikaros Transcription Factor