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Background  Abnormalities of 11q23 involving the  MLL  gene are found in approximately 10% of human leukemias. To date, nearly 100 different chromosome bands have been described in rearrangements involving 11q23 and 64 fusion genes have been cloned and characterized at the molecular level. In this work we present the identification of a novel  MLL  fusion partner in a pediatric patient with  de novo  biphenotypic acute leukemia.    Methods  Cytogenetics, fluorescence in situ hybridization (FISH), molecular studies (RT-PCR and LDI-PCR), and bioinformatic sequence analysis were used to characterize the  CT45A2  gene as novel  MLL  fusion partner in pediatric acute leukemia.    Results  Fluorescence  in situ  hybridization of bone marrow G-banded metaphases demonstrated a cryptic insertion of 11q23 in Xq26.3 involving the  MLL  gene. Breakpoint fusion analysis revealed that a DNA fragment of 653 kb from 11q23, containing  MLL  exons 1-9 in addition to 16 other 11q23 genes, was inserted into the upstream region of the  CT45A2  gene located at Xq26.3. In addition, a deletion at Xq26.3 encompassing the 3' region of the  DDX26B  gene (exons 9-16) and the entire  CT45A1  gene was identified. RNA analysis revealed the presence of a novel  MLL-CT45A2  fusion transcript in which the first 9 exons of the  MLL  gene were fused in-frame to exon 2 of the  CT45A2  gene, resulting in a spliced  MLL  fusion transcript with an intact open reading frame. The resulting chimeric transcript predicts a fusion protein where the N-terminus of MLL is fused to the entire open reading frame of CT45A2. Finally, we demonstrate that all breakpoint regions are rich in long repetitive motifs, namely LINE/L1 and SINE/Alu sequences, but all breakpoints were exclusively identified outside these repetitive DNA sequences.    Conclusion  We have identified  CT45A2  as a novel spliced  MLL  fusion partner in a pediatric patient with  de novo  biphenotypic acute leukemia, as a result of a cryptic insertion of 11q23 in Xq26.3. Since  CT45A2  is the first Cancer/Testis antigen family gene found fused with  MLL  in acute leukemia, future studies addressing its biologic relevance for leukemogenesis are warranted.

A novel spliced fusion of MLL with CT45A2in a pediatric biphenotypic acute leukemia