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Molecular characterization of the MLL-SEPT6 fusion gene in acute myeloid leukemia: identification of novel fusion transcripts and cloning of genomic breakpoint junctions

¹ Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
² Section for Cancer Cytogenetics, Department of Medical Genetics, Radiumhospitalet-Rikshospitalet Medical Center, Oslo, Norway
³ Department of Pediatrics, Portuguese Oncology Institute, Porto, Portugal
⁴ Department of Pediatrics, Radiumhospitalet-Rikshospitalet Medical Center, Oslo, Norway
⁵ Department of Pediatrics, St Olav University Hospital, Trondheim, Norway
⁶ Faculty Division, The Norwegian Radium Hospital, Medical Faculty, University of Oslo, Norway
⁷ Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal

Correspondence: Manuel R. Teixeira, Department of Genetics, Portuguese Oncology Institute, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal. E-mail:mteixeir{at}ipoporto.min-saude.pt

One of the MLL fusion partners in leukemia is the SEPT6 gene, which belongs to the evolutionarily conserved family of genes of septins. In this work we aimed to characterize at both the RNA and DNA levels three acute myeloid leukemias with cytogenetic evidence of a rearrangement between 11q23 and Xq24. Molecular analysis led to the identification of several MLL-SEPT6 fusion transcripts in all cases, including a novel MLL-SEPT6 rearrangement (MLL exon 6 fused with SEPT6 exon 2). Genomic DNA breakpoints were found inside or near Alu or LINE repeats in the MLL breakpoint cluster region, whereas the breakpoint junctions in the SEPT6 intron 1 mapped to the vicinity of GC-rich low-complexity repeats, Alu repeats, and a topoisomerase II consensus cleavage site. These data suggest that a non-homologous end-joining repair mechanism may be involved in the generation of MLL-SEPT6 rearrangements in acute myeloid leukemia.

Key words: MLL-SEPT6, fusion oncogene, fusion transcript, genomic breakpoint, acute myeloid leukemia.