title: Characterization of genomic breakpoints in MLL and CBP in leukemia patients with t(11;16).
abstract: The recurring chromosome translocation t(11;16)(q23;p13) is detected in leukemia patients, virtually all of whom have received previous chemotherapy with topoisomerase (topo) II inhibitors. In the t(11;16), 3' CBP, on 16p13, is fused to 5' MLL, on 11q23, resulting in an MLL-CBP fusion gene that plays an important role in leukemogenesis. In this study, we cloned genomic breakpoints of the MLL and CBP genes in the t(11;16) in the SN-1 cell line and in five patients with therapy-related leukemia, all of whom had received topo II inhibitors for previous tumors. In all patients except one, both the genomic MLL-CBP and the reciprocal fusions were cloned. Genomic breakpoints in MLL occurred in the 8.3-kb breakpoint cluster region in all patients, whereas the breakpoints in CBP clustered in an 8.2-kb region of intron 3 in four patients. Genomic breakpoints in MLL occurred in intron 11 near the topo II cleavage site in the SN-1 cell line and in one patient, and they were close to LINE repetitive sequences in two other patients. In the remaining two patients, genomic breakpoints were in intron 9 in Alu repeats. Genomic breakpoints in CBP occurred in and around Alu repeats in one and two patients, respectively. In two patients, the breaks were near LINE repetitive sequences, suggesting that repetitive DNA sequences may play a role. No specific recombination motifs were identified at or near the breakpoint junctions. No topo II cleavage sites were detected in introns 2 and 3 of CBP. However, there were deletions and duplications at the breakpoints in both MLL and CBP and microhomologies or nontemplated nucleotides at most of the genomic fusion junctions, suggesting that a nonhomologous end-joining repair mechanism was involved in the t(11;16).
authors.affiliation: Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois 60637, USA.
authors.forename: Yanming
authors.initials: Y
authors.lastname: Zhang
authors.forename: Nancy
authors.initials: N
authors.lastname: Zeleznik-Le
authors.forename: Neelmini
authors.initials: N
authors.lastname: Emmanuel
authors.forename: Nimanthi
authors.initials: N
authors.lastname: Jayathilaka
authors.forename: Jianjun
authors.initials: J
authors.lastname: Chen
authors.forename: Pamela
authors.initials: P
authors.lastname: Strissel
authors.forename: Reiner
authors.initials: R
authors.lastname: Strick
authors.forename: Loretta
authors.initials: L
authors.lastname: Li
authors.forename: Mary Beth
authors.initials: MB
authors.lastname: Neilly
authors.forename: Tomohiko
authors.initials: T
authors.lastname: Taki
authors.forename: Yasuhide
authors.initials: Y
authors.lastname: Hayashi
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Kaneko
authors.forename: Brigitte
authors.initials: B
authors.lastname: Schlegelberger
authors.forename: Janet D
authors.initials: JD
authors.lastname: Rowley
mesh_terms: D000368:Aged; D001483:Base Sequence; D045744:Cell Line, Tumor; D002648:Child; D002675:Child, Preschool; D002880:Chromosomes, Human, Pair 11; D002885:Chromosomes, Human, Pair 16; D019295:Computational Biology; D004247:DNA / Q000737:chemistry; D017931:DNA Primers / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000235:genetics*; D005260:Female; D016678:Genome; D011495:Histone-Lysine N-Methyltransferase; D006801:Humans; D007438:Introns; D015470:Leukemia, Myeloid, Acute / Q000235:genetics*; D008297:Male; D008957:Models, Genetic; D008969:Molecular Sequence Data; D051788:Myeloid-Lymphoid Leukemia Protein; D009687:Nuclear Proteins / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011519:Proto-Oncogenes / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014178:Translocation, Genetic
chemical_list: D017931:DNA Primers; D004268:DNA-Binding Proteins; C497422:KMT2A protein, human; D009687:Nuclear Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D051788:Myeloid-Lymphoid Leukemia Protein; D004247:DNA; D011495:Histone-Lysine N-Methyltransferase