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).

Common chromatin structures at breakpoint cluster regions may lead to chromosomal translocations found in chronic and acute leukemias

“…For both infant and therapy-related leukemia patients a significant bias accumulation for breakpoint distribution has been demonstrated in the telomeric region of the MLL BCR, 5¢ of the topo II cleavage site (Domer et al 1995;Strissel et al 1998b;Reichel et al 2001;Langer et al 2003;Zhang et al 2004) supporting a similar mechanism of DNA breakage. To explain the enrichment of patient breakpoints in the MLL telomeric region, the limiting factors may be the topo II inhibitor dose, the number of topo II molecules in the region and the finding of a strong topo II site co-localizing within a SAR.…”

The BRCA1/2 pathway prevents hematologic cancers in addition to breast and ovarian cancers

“…In some leukemias, the make-up of a fusion protein may bear witness to other abnormal repairs [e.g. [17]]. Error-tolerant repair may also leave other signs such as in the acute myeloid leukemias, where there may be evidence of abnormal gene fusions, duplications, inversions, deletions or reciprocal translocations [18].…”

Roles of DNA topoisomerase II isozymes in chemotherapy and secondary malignancies

“…VP-16-induced t-AML is frequently associated with balanced translocations between the mixed lineage leukemia (MLL) gene on chromosome 11q23 and Ͼ50 partner genes (the MLL gene is also known as ALL-1, hTRX, or HRX) (4)(5)(6)(7). These rearrangements, as well as those found in infant leukemia, cluster within a well characterized 8.3-kb breakpoint cluster region (bcr) (8)(9)(10)(11)(12)(13)(14)(15)(16). The bcr of MLL is AT-rich and contains Alu sequences, putative recognition sites of Top2-mediated DNA cleavage, and chromosome scaffold/matrix attachment regions (SAR/MAR) (5,(8)(9)(10)(11)(12)(13)(14)(15)(16)(17).…”

“…These rearrangements, as well as those found in infant leukemia, cluster within a well characterized 8.3-kb breakpoint cluster region (bcr) (8)(9)(10)(11)(12)(13)(14)(15)(16). The bcr of MLL is AT-rich and contains Alu sequences, putative recognition sites of Top2-mediated DNA cleavage, and chromosome scaffold/matrix attachment regions (SAR/MAR) (5,(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). There is substantial evidence that chromosome 11q23 translocations in t-AML and infant leukemia are a consequence of drug-induced formation of double-strand breaks (DSBs) (6)(7)(8)(9).…”