title: Neoplastic MiR-17~92 deregulation at a DNA fragility motif (SIDD).
abstract: Chromosomal or mutational activation of BCL6 (at 3q27) typifies diffuse large B-cell lymphoma (DLBCL) which in the germinal center subtype may be accompanied by focal amplification of chromosome band 13q31 effecting upregulation of miR-17~92. Using long distance inverse-polymerase chain reaction, we mapped and sequenced six breakpoints of a complex BCL6 rearrangement t(3;13)(q27;q31)t(12;13)(p11;q31) in DLBCL cells, which places miR-17~92 antisense within the resulting ITPR2-BCL6 chimeric fusion gene rearrangement. MiR-17~92 members were upregulated ~15-fold over controls in a copy number independent manner consistent with structural deregulation. MIR17HG and ITPR2-BCL6 were, despite their close configuration, independently expressed, discounting antisense regulation. MIR17HG in t(3;13)t(12;13) cells proved highly responsive to treatment with histone deacetylase inhibitors implicating epigenetic deregulation, consistent with which increased histone-H3 acetylation was detected by chromatin immunoprecipitation near the upstream MIR17HG breakpoint. Remarkably, 5/6 DNA breaks in the t(3;13)t(12;13) precisely cut at stress-induced DNA duplex destabilization (SIDD) peaks reminiscent of chromosomal fragile sites, while the sixth lay 150 bp distant. Extended SIDD profiling showed that additional oncomiRs also map to SIDD peaks. Fluorescence in situ hybridization analysis showed that 11 of 52 (21%) leukemia-lymphoma (L-L) cell lines with 13q31 involvement bore structural rearrangements at/near MIR17HG associated with upregulation. As well as fueling genome instability, SIDD peaks mark regulatory nuclear-scaffold matrix attachment regions open to nucleosomal acetylation. Collectively, our data indict a specific DNA instability motif (SIDD) in chromosome rearrangement, specifically alterations activating miR-17~92 epigenetically via promoter hyperacetylation, and supply a model for the clustering of oncomiRs near cancer breakpoints.
authors.affiliation: Department of Human and Animal Cell Cultures, DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7b, 38124 Braunschweig, Germany. bjoern.schneider@med.uni-rostock.de
authors.forename: Björn
authors.initials: B
authors.lastname: Schneider
authors.forename: Stefan
authors.initials: S
authors.lastname: Nagel
authors.forename: Stefan
authors.initials: S
authors.lastname: Ehrentraut
authors.forename: Maren
authors.initials: M
authors.lastname: Kaufmann
authors.forename: Corinna
authors.initials: C
authors.lastname: Meyer
authors.forename: Robert
authors.initials: R
authors.lastname: Geffers
authors.forename: Hans G
authors.initials: HG
authors.lastname: Drexler
authors.forename: Roderick A F
authors.initials: RA
authors.lastname: MacLeod
mesh_terms: D000107:Acetylation; D047369:Chromatin Immunoprecipitation; D002871:Chromosome Banding; D056905:Chromosome Breakpoints; D043283:Chromosome Fragile Sites / Q000235:genetics; D004247:DNA / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D053496:Inositol 1,4,5-Trisphosphate Receptors / Q000235:genetics; D016403:Lymphoma, Large B-Cell, Diffuse / Q000235:genetics* / Q000473:pathology; D035683:MicroRNAs / Q000235:genetics*; D009363:Neoplasm Proteins / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D051560:Proto-Oncogene Proteins c-bcl-6; D062085:RNA, Long Noncoding; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D014178:Translocation, Genetic
chemical_list: C084103:BCL6 protein, human; D004268:DNA-Binding Proteins; D006657:Histones; C506927:ITPR2 protein, human; D053496:Inositol 1,4,5-Trisphosphate Receptors; C568997:MIR17HG, human; D035683:MicroRNAs; D009363:Neoplasm Proteins; D015514:Oncogene Proteins, Fusion; D051560:Proto-Oncogene Proteins c-bcl-6; D062085:RNA, Long Noncoding; D004247:DNA