title: Illegitimate RAG-mediated recombination events are involved in IKZF1 Δ3-6 deletion in BCR-ABL1 lymphoblastic leukaemia.
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.
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: Y
authors.initials: Y
authors.lastname: Dong
authors.affiliation: Department of Hematology, Xi'an Central Hospital.
authors.forename: F
authors.initials: F
authors.lastname: Liu
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: C
authors.initials: C
authors.lastname: Wu
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: S
authors.initials: S
authors.lastname: Li
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: X
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: P
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: J
authors.initials: J
authors.lastname: Jiao
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: X
authors.initials: X
authors.lastname: Yu
authors.affiliation: Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center.|Ministry of Education of China, Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University).
authors.forename: Y
authors.initials: Y
authors.lastname: Ji
authors.affiliation: Department of Hematology, the First Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, China.
authors.forename: M
authors.initials: M
authors.lastname: Zhang
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics; D004268:DNA-Binding Proteins / Q000097:blood / Q000235:genetics; D005260:Female; D017353:Gene Deletion; D016313:Genes, abl / Q000235:genetics*; D018398:Homeodomain Proteins / Q000097:blood / Q000235:genetics; D006801:Humans; D051740:Ikaros Transcription Factor / Q000235:genetics*; D047468:Immunoprecipitation; D008297:Male; D008875:Middle Aged; D009687:Nuclear Proteins / Q000097:blood / Q000235:genetics; D054198:Precursor Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics*; D011995:Recombination, Genetic; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; C497239:IKZF1 protein, human; C586512:Ikaros 6 protein, human; D009687:Nuclear Proteins; C499311:RAG2 protein, human; C064658:RAG-1 protein; D051740:Ikaros Transcription Factor
keywords: ALL; BCR-ABL1; CML; Ik6; RAG