SUMMARY In this study, we show that evolutionarily conserved chromosome loop anchors bound by CTCF and cohesin are vulnerable to DNA double strand breaks (DSBs) mediated by topoisomerase 2B (TOP2B). Polymorphisms in the genome that redistribute CTCF/cohesin occupancy rewire DNA cleavage sites to novel loop anchors. While transcription- and replication-coupled genomic rearrangements have been well documented, we demonstrate that DSBs formed at loop anchors are largely transcription-, replication-, and cell type- independent. DSBs are continuously formed throughout interphase, are enriched on both sides of strong topological domain borders, and frequently occur at breakpoint clusters commonly translocated in cancer. Thus, loop anchors serve as fragile sites that generate DSBs and chromosomal rearrangements.

Structural chromosomal rearrangements of the Nucleoporin 98 gene (NUP98), primarily balanced translocations and inversions, are associated with a wide array of hematopoietic malignancies. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. NUP98 gene fusions typically encode a fusion protein that retains the amino terminus of NUP98; in this context, it is important to note that several recent studies have demonstrated that the amino-terminal portion of NUP98 exhibits transcription activation potential. Approximately half of the NUP98 fusion partners encode homeodomain proteins, and at least 5 NUP98 fusions involve known histone-modifying genes. Several of the NUP98 fusions, including NUP98-homeobox (HOX)A9, NUP98-HOXD13, and NUP98-JARID1A, have been used to generate animal models of both lymphoid and myeloid malignancy; these models typically up-regulate HOXA cluster genes, including HOXA5, HOXA7, HOXA9, and HOXA10. In addition, several of the NUP98 fusion proteins have been shown to inhibit differentiation of hematopoietic precursors and to increase self-renewal of hematopoietic stem or progenitor cells, providing a potential mechanism for malignant transformation. (Blood. 2011;118(24): 6247-6257) IntroductionOne of the oldest, and most useful, whole genome screens for genes involved in malignant transformation is a simple karyotype of the malignant cell. 1 Analysis of recurrent, nonrandom chromosomal translocation breakpoints has identified numerous genes important for malignant transformation and provided critical insight into the biology, classification, and prognosis of hematopoietic malignancies. 2 The study of these genes (such as BCR-ABL and BCL2) has led to vastly improved therapy 3 and has opened an entire field of scientific inquiry. 4 The Nucleoporin 98 gene (NUP98) was originally identified as a structural component of the nuclear pore complex (NPC), 5 and was subsequently shown to be a fusion partner with homeobox (HOX)A9 in acute myeloid leukemia (AML) patients with a t(7;11) (p15;p15). 6,7 Twenty-eight distinct NUP98 gene fusions have been identified, caused primarily by balanced translocations and inversions, in the malignant cells of patients with a wide array of distinct hematopoietic malignancies, including AML, chronic myeloid leukemia in blast crisis (CML-bc), myelodysplastic syndrome (MDS), acute lymphoblastic leukemia (ALL), and bilineage/ biphenotypic leukemia. 8 In this overview, we present a summary of the known roles of NUP98 in normal cell physiology, the association of NUP98 fusion proteins with hematopoietic malignancies, the incidence and prognostic importance of these fusions, and the mechanisms by which NUP98 fusion oncoproteins contribute to the process of malignant transformation. Normal functions of NUP98NUP98 is a component of the NPC NUP98 is an ϳ 90...

Cooperation between the stem cell leukemia (SCL) transcription factor and its nuclear partners LMO1 or LMO2 induces aggressive T cell acute lymphoblastic leukemia when inappropriately expressed in T cells. This study examined the cellular and molecular targets of the SCL-LMO complex at the preleukemic stage. We show that SCL and its partners are coexpressed in the most primitive thymocytes. Maturation to the pre-T cell stage is associated with a down-regulation of SCL and LMO1 and LMO2, and a concomitant up-regulation of E2A and HEB expression. Moreover, enforced expression of SCL-LMO1 inhibits T cell differentiation and recapitulates a loss of HEB function, causing a deregulation of the transition checkpoint from the CD4-CD8- to CD4+CD8+ stages. Finally, we identify the gene encoding pT alpha as a downstream target of HEB that is specifically repressed by the SCL-LMO complex.

No abstract