Microclustering ofTEL-AML1 translocation breakpoints in childhood acute lymphoblastic leukemia

Wiemels, Joseph L.; Alexander, Freda E.; Cazzaniga, Giovanni; Biondi, Andrea; Mayer, S; Greaves, Mel

doi:10.1002/1098-2264(2000)9999:9999<::aid-gcc1028>3.0.co;2-d

Cited by 59 publications

(47 citation statements)

References 39 publications

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“…Such concomitant genetic events are frequent at, or in the vicinity of, the breakpoints of fusion genes and have been reported in Ewing's sarcoma, myxoid liposarcoma and leukemias. [35][36][37][38][39] This indicates that the chromosomal translocations do not require sequence-specific recombinases or extensive homology between the recombined sequences. 40 Moreover, in all cases, topoisomerase I consensus sequences [A/T-C/G-A/T-T] were found close to the junctions, suggesting that topoisomerase I may participate in the genesis of the EWS/ATF1 chimera (Fig.…”

Section: Discussionmentioning

confidence: 98%

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Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses

Panagopoulos

Mertens

Dębiec‐Rychter

et al. 2002

Intl Journal of Cancer

138

119

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Clear cell sarcoma (CCS) is a rare malignant soft tissue tumor particularly associated with tendons and aponeuroses. The cytogenetic hallmark is the translocation t(12;22)(q13; q12) resulting in a chimeric EWS/ATF1 gene in which the 3 -terminal part of EWS at 22q is replaced by the 3 -terminal part of ATF1 at 12q. To date, only 13 cases of CCS have been analyzed for fusion genes at the transcription level, and there is no information about the breakpoints at the genomic level. In the present study, we describe the molecular genetic characteristics of CCS from 10 patients. Karyotypes were obtained from 10 cases, 7 of which showed the characteristic t(12;22). As an initial step in the characterization of the EWS/ATF1 and ATF1/EWS chimeras, we constructed an exon/ intron map of the ATF1 gene. The entire ATF1 gene spanned >40 kb and was composed of 7 exons. Intron 3, in which most of the genomic breakpoints occurred, was to a large extent (83%) composed of repetitive elements. RT-PCR amplified EWS/ATF1 cDNA fragments in all patients and ATF1/EWS cDNA fragments in 6 of 10 patients. Four types of EWS/ATF1 chimeric transcript, designated types 1-4, were identified. The most frequent chimeric transcript (type 1) was an inframe fusion of exon 8 of EWS with exon 4 of ATF1. This was the only chimeric transcript in 5 patients but found together with other variants in 3 tumors. The type 2 transcript of EWS/ATF1, an in-frame fusion of exon 7 of EWS with exon 5 of ATF1, was detected in 4 patients, as the only transcript in 1 case and together with other variants in 3 cases. An in-frame fusion of exon 10 of EWS with exon 5 of ATF1 (type 3) was found in 1 patient as the only transcript, and an out-of-frame fusion of EWS exon 7 with ATF1 exon 7 (type 4) was detected in 1 patient together with type 1 and type 2 transcripts. Sequencing of the amplified ATF1/EWS cDNA fragments showed in 5 patients that ATF1 exon 3 was fused with EWS exon 10, resulting in an out-of-frame chimeric transcript. In 1 case, nt 428 of ATF1 (exon 4) was fused with EWS exon 8; at the junction, there was an insertion of 4 nucleotides, also resulting in an out-of-frame transcript. Genomic extra long PCR and sequence analysis mapped the genomic breakpoints to introns 7, 8 and 9 of EWS and intron 3 and exon 4 of ATF1. While a simple end-to-end fusion was observed in 2 cases, additional nucleotides were found at the junctions in 2 other cases. In addition, topoisomerase I consensus sequences were found close to the junctions, suggesting that this enzyme may participate in the genesis of the EWS/ATF1 fusion.

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Section: Discussionmentioning

confidence: 98%

“…Clustering of such motifs may make a region unstable and highly plastic, increasing the likelihood of rearrangements. 35 Although homologous recombination between various repetitive elements was not observed, the involvement of these sequences in the genesis of chromosomal translocations cannot be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses

Panagopoulos

Mertens

Dębiec‐Rychter

et al. 2002

Intl Journal of Cancer

138

119

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“…25,26 but much more complex for other translocations, mainly because PCR analysis needs multiple primers, if genomic breakpoint regions are larger than 2-4 kb. [27][28][29] An alternative approach, which is suitable for detection of chromosome translocations resulting in formation of fusion genes, is detection of fusion genes or fusion gene transcripts via (nested) PCR or RT-PCR analysis. 30 The advantage of this approach is that it reaches sensitivities of one cell in 10 3 to one cell in 10 6 cells, enabling detection of minimal residual disease (MRD).…”

Section: Detection Of Chromosome Aberrationsmentioning

confidence: 99%

Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia

Burg

Poulsen²,

Hunger

et al. 2004

Leukemia

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Chromosome aberrations are frequently observed in precursor-B-acute lymphoblastic leukemias (ALL) and T-cell acute lymphoblastic leukemias (T-ALL). These translocations can form leukemia-specific chimeric fusion proteins or they can deregulate expression of an (onco)gene, resulting in aberrant expression or overexpression. Detection of chromosome aberrations is an important tool for risk classification. We developed rapid and sensitive split-signal fluorescent in situ hybridization (FISH) assays for six of the most frequent chromosome aberrations in precursor-B-ALL and T-ALL. The split-signal FISH approach uses two differentially labeled probes, located in one gene at opposite sites of the breakpoint region. Probe sets were developed for the genes TCF3 (E2A) at 19p13, MLL at 11q23, ETV6 at 12p13, BCR at 22q11, SIL-TAL1 at 1q32 and TLX3 (HOX11L2) at 5q35. In normal karyotypes, two colocalized green/red signals are visible, but a translocation results in a split of one of the colocalized signals. Split-signal FISH has three main advantages over the classical fusionsignal FISH approach, which uses two labeled probes located in two genes. First, the detection of a chromosome aberration is independent of the involved partner gene. Second, split-signal FISH allows the identification of the partner gene or chromosome region if metaphase spreads are present, and finally it reduces false-positivity. Leukemia ( Chromosome aberrations play an important role in hematological malignancies. 1 In ALL, most of these aberrations concern balanced translocations involving genes that play key roles in the development and function of lymphoid cells, such as transcription factors, cell cycle regulators, and signal transduction molecules. Balanced translocations can result in fusion of two genes that encode leukemia-specific chimeric (fusion) proteins. The fusion proteins have functional features that differ from the corresponding wild-type proteins and mostly play a role in leukemogenesis. In addition to the new features of the fusion protein, loss of wild-type activity due to the translocation (in some translocations enhanced by deletion of the second allele) might contribute to oncogenesis. Alternatively, chromosome translocations can result in deregulated expression of (onco)genes as a direct consequence of a translocation to a regulatory element, for example, an immunoglobulin (Ig) or T-cell receptor (TCR) enhancer. 2,3 The most frequent translocations in precursor-B-ALL are t(1;19)(q23;p13) t(4;11)(q21;q23), t(12;21)(p13;q22), and t(9;22)(q34;q11), all four of which result in generation of fusion genes. The t(1;19)(q23;p13) fuses the transcription factorencoding gene TCF3 (E2A) with the transcription factor PBX1. In t(4;11)(q21;q23), the MLL gene at 11q23, which encodes a putative DNA-binding protein, is translocated to the MLLT2 (AF4) gene. The MLL gene is involved in many other translocations in ALL and acute myeloid leukemia (AML). Until now, more than 30 partner genes have been identified. 4 The t(12;21)(p13;q22) involves th...

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“…[6][7][8][9][10][11][12] Progress in characterizing the majority of leukemia translocations has been slower due to dispersed nature of the chromosomal fusions and difficulties in sequencing translocations because of large intronic regions; however, large-scale sequencing efforts have recently been undertaken. [13][14][15][16][17] The only pediatric translocation to date with hypothesized etiologies are the MLL fusions in infant leukemia, in which topoisomerase II inhibition by environmental and dietary agents may play a role. [18][19][20] The most common rearrangement in childhood leukemias is t(12;21)TEL-AML1, and we and others have noted structural features of the introns that may contribute to genomic breakage and refusion, including unstable repeat sequences and signs of non-homologous end joining repair.…”

Section: Introductionmentioning

confidence: 99%

“…[18][19][20] The most common rearrangement in childhood leukemias is t(12;21)TEL-AML1, and we and others have noted structural features of the introns that may contribute to genomic breakage and refusion, including unstable repeat sequences and signs of non-homologous end joining repair. 14,[21][22][23][24] T(8;21) (AML1-ETO) is a common recurrent translocation (ෂ12% overall) in both childhood and adult AML. This translocation is primarily a de novo, or idiopathic event, by the lack of identified causal exposure in most of the cases.…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of genomic AML1-ETO fusions in childhood leukemia

et al. 2001

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T(8;21) AML1(CBFA2)-ETO(MTG8)is the most common chromosomal translocation in acute myeloid leukemia (AML) in both children and adults. We sought to understand the structure and gain insight into the fusion process between AML1 and ETO by sequencing genomic fusions in 17 primary childhood AMLs and two cell lines with t(8;21). Reciprocal translocations were sequenced for seven of the 19 samples. We assumed a null hypothesis that the translocation breakpoints would be evenly distributed along the intronic breakpoint cluster regions. Testing for multimodality via smoothed bootstrap statistical methods suggested, however, the presence of two separate cluster regions within both the AML1 and ETO breakpoint cluster regions. ETO breakpoints were predominantly located in intron 1B in a defined cluster 5Ј of exon 1A (scan statistic P value = 0.00001). All patients with available RNA expressed an AML1-ETO mRNA fusion between exon 5 of AML1 and exon 2 of ETO. Since the structural restraints for the fusion protein of AML1-ETO exclude exon 1A, we reason that ETO intron 1B harbors a structural feature with propensity for breakage and/or recombination. Chromosomal breakpoints displayed evidence of fusion by a non-homologous end joining process, with microhomologies and nontemplate nucleotides at some fusion junctions. Breakpoints in general displayed similar complexity of duplications, deletions, and insertions to other common pediatric leukemia translocations (TEL-AML1, MLL-AF4, PML-RARA, CBFB-MYH11) that we and others have analyzed. Leukemia (2001Leukemia ( ) 15, 1906Leukemia ( -1913

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Microclustering ofTEL-AML1 translocation breakpoints in childhood acute lymphoblastic leukemia

Cited by 59 publications

References 39 publications

Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses

Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses

Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia

Molecular characterization of genomic AML1-ETO fusions in childhood leukemia

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