title: Rearrangements of the MLL gene are influenced by DNA secondary structure, potentially mediated by topoisomerase II binding.
abstract: The location of MLL translocation breakpoints within therapy-related acute myeloid leukemia linked to drugs targeting Topoisomerase II and infant acute leukemia (IAL) are biased toward the intron 11-exon 12 region of MLL, although lacking a comprehensive explanation. To address this, blood samples were taken from breast cancer and lymphoma patients receiving Topoisomerase II inhibitor therapy. Inverse PCR analysis was used to interrogate the exon 12 region of MLL for rearrangements. Eleven of 19 observed translocations showed breakpoint junctions restricted to a single 5 bp location within exon 12. A similarly restricted distribution (11/20 breakpoint junctions) was observed in TK6 cells exposed to either estrogen (linked to IAL) or anti-CD95 antibody. The translocation hotspot was at the 5' edge of a 10-bp tract matched with a perfect palindrome, 101 bp distant. A high stringency Topoisomerase II consensus sequence binding site was noted at the geometric midpoint of the palindromes. Ligation-mediated PCR to screen TK6 cells exposed to anti-CD95 antibody showed 14/37 (38%) of DNA breaks adjacent to the 5' palindrome and 10/37 (27%) at the 3' partner. We propose a model whereby Topoisomerase II facilitates the organization of nuclease-sensitive secondary structures, stabilized by palindrome association, which are prone to rearrangement.
authors.affiliation: Department of Radiation Oncology, UC Davis Cancer Center, Sacramento, CA 95817, USA.
authors.forename: Hongan
authors.initials: H
authors.lastname: Le
authors.forename: Sheetal
authors.initials: S
authors.lastname: Singh
authors.forename: Shyh-Jen
authors.initials: SJ
authors.lastname: Shih
authors.forename: Nga
authors.initials: N
authors.lastname: Du
authors.forename: Sabine
authors.initials: S
authors.lastname: Schnyder
authors.forename: Grace A
authors.initials: GA
authors.lastname: Loredo
authors.forename: Christine
authors.initials: C
authors.lastname: Bien
authors.forename: Laura
authors.initials: L
authors.lastname: Michaelis
authors.forename: Amir
authors.initials: A
authors.lastname: Toor
authors.forename: Manuel O
authors.initials: MO
authors.lastname: Diaz
authors.forename: Andrew T
authors.initials: AT
authors.lastname: Vaughan
mesh_terms: D000328:Adult; D000368:Aged; D001483:Base Sequence; D001943:Breast Neoplasms / Q000188:drug therapy / Q000201:enzymology / Q000235:genetics; D002460:Cell Line; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D005260:Female; D015321:Gene Rearrangement; D011495:Histone-Lysine N-Methyltransferase; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics; D008223:Lymphoma / Q000188:drug therapy / Q000201:enzymology / Q000235:genetics; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D051788:Myeloid-Lymphoid Leukemia Protein / Q000235:genetics*; D016609:Neoplasms, Second Primary / Q000235:genetics; D009690:Nucleic Acid Conformation; D059005:Topoisomerase II Inhibitors; D014178:Translocation, Genetic
chemical_list: C497422:KMT2A protein, human; D059005:Topoisomerase II Inhibitors; D051788:Myeloid-Lymphoid Leukemia Protein; D004247:DNA; D011495:Histone-Lysine N-Methyltransferase; D004250:DNA Topoisomerases, Type II