Simple Reciprocal Translocations Research Articles

Identification of a familial complex chromosomal rearrangement by optical genome mapping

BackgroundComplex chromosomal rearrangements (CCRs) are rare chromosomal structural variations, containing a variety of rearrangements such as translocation, inversion and/or insertion. With the development of cytogenetic and molecular genetic techniques, some chromosomal rearrangements that were initially considered to be simple reciprocal translocations in the past might eventually involve more complex chromosomal rearrangements.Case presentationIn this case, a pregnant woman, who had a spontaneous abortion last year, had abnormal prenatal test results again in the second pregnancy. Applying a combination of genetic methods including karyotype analysis, chromosomal microarray analysis, fluorescence in situ hybridization and optical genome mapping confirmed that the pregnant woman was a carrier of a CCR involving three chromosomes and four breakpoints, and the CCR was paternal-origin. Her first and second pregnancy abnormalities were caused by chromosomal microdeletions and microduplications due to the malsegregations of the derivative chromosomes.ConclusionsWe presented a rare familial CCR involving three chromosomes and four breakpoints. This study provided precise and detailed information for the subsequent reproductive decision-making and genetic counselling of the patient.

Molecular Cytogenetic Characterization of Novel 1RS.1BL Translocation and Complex Chromosome Translocation Lines with Stripe Rust Resistance.

Rye is the most important source for the genetic improvement of wheat. In this study, two stable wheat-rye primary 1RS.1BL translocation lines, RT855-13 and RT855-14, were selected and identified by acid polyacrylamide gel electrophoresis (A-PAGE), co-dominant PCR, and multi-color fluorescence in situ hybridization (MC-FISH) from the progeny of the crossing of the wheat cultivar Mianyang11 and a Chinese rye Weining. When more than two independent, simple reciprocal translocations are involved in a carrier, they are defined as complex chromosome translocations (CCT). The MC-FISH results also indicated that CCT occurred in RT855-13; namely that, besides 1RS.1BL translocation chromosomes, there are other two pairs of balanced reciprocal translocations. It was demonstrated that the interchange between a distal segment of 4B and long arm of 3D occurred in the RT855-13. The novel translocation chromosomes in wheat were recorded as 3DS.4BSDS and 3DL-4BSPS.4BL. Reports about CCT as a genetic resource in plant breeding programs are scarce. Both lines expressed high resistance to Puccinia striiformis f. sp. tritici, which are prevalent in China and are virulent on Yr9, and the CCT line RT855-13 retained better resistance as adult plants compared with RT855-14 in the field. Both lines, especially the CCT line RT855-13, exhibited better agronomic traits than their wheat parent, Mianyang11, indicating that both translocation lines could potentially be used for wheat improvement. The results also indicated that the position effects of CCT can lead to beneficial variations in agronomic and resistant traits, making them a valuable genetic resource to wheat breeding programs.

Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation

Research questionShould whole-genome investigations be considered systematically before a complex chromosomal abnormality preimplantation genetic testing for structural chromosomal rearrangements (PGT-SR) management is carried out using conventional cytogenetic techniques? DesignA male carrying a putative rare interchromosomal reciprocal insertion (IRI) 46,XY,ins(14;?)(q11;?).ish der(14)ins(14;22)(q11.2;q11.2q11.2)(xcp14+,xcp22+,N25+,3’TRA/D+),der(22)ins(22;14)(q11.2;q11.2q11.2)(xcp22+,xcp14+,N25-,5’TRA/D+), and his partner were referred to our centre for preimplantation genetic testing analysis after three spontaneous miscarriages. Whole-genome sequencing was used to distinguish between the proposed IRI and an alternative explanation of reciprocal translocation. Fluorescence in-situ hybridization was used to detect all chromosome segments involved in this chromosomal rearrangement, to identify transferable normal and balanced embryos. ResultsWhole-genome sequencing allowed the determination of the number of chromosomal breakpoints involved in chromosomal rearrangement between chromosomes 14 and 22. Finally, only two breakpoints were identified instead of four in IRI rearrangements, which suggests a reciprocal translocation rearrangement. A probe strategy was established to highlight all chromosomal imbalances, whether IRI or reciprocal translocation, and preimplantation genetic testing cycles were achieved. ConclusionConventional cytogenetic techniques are not capable of identifying all complex chromosomal rearrangements, especially those involving centromeric regions and short arms of acrocentric chromosomes. The advent of new sequencing technologies has allowed for a better appreciation of genome complexity. In this study, whole-genome analysis provided additional information to explain the occurrence of genomic events and confirmed that the initial diagnosis of IRI identified by conventional cytogenetic techniques was, in fact, a simple reciprocal translocation. A reliable PGT-SR strategy was proposed for this couple to achieve their parental project.

Comprehensive Analysis of MYC Translocations in Multiple Myeloma By Whole Genome Sequencing and Whole Transcriptome Sequencing

Background 8q24 translocations leading to overexpression of MYC are an established prognostic marker in multiple myeloma (MM). Currently FISH (fluorescence in situ hybridization) on CD138+ enriched cell population is the standard diagnostic approach to evaluate the presence of 8q24 translocations. Due to the heterogeneity of breakpoints and technical issues the design of FISH probes is challenging and so far no single FISH assay is capable of detecting each translocation. Aims (1) Evaluation of the frequency of 8q24 translocations in MM by whole genome sequencing (WGS). (2) Determination of the breakpoints on 8q24 and partners. (3) Correlation of WGS data with FISH and MYC expression determined by whole transcriptome sequencing (WTS). Patient cohort and methods CD138+ cell fractions were selected by MACS from bone marrow aspirate samples of 264 patients diagnosed with MM. FISH, WGS and WTS were performed in all cases. For WGS, 151bp paired-end sequences where generated on NovaSeq 6000 machines (Illumina, San Diego, CA). All reported p-values are two-sided and were considered significant at p<0.05. For gene expression (GE) analysis by WTS, estimated gene counts were normalized and the resulting log2 counts per million were used as a proxy of gene expression in each sample. For artefact exclusion, structural variants were checked against 4386 cases covering the spectrum of hematological malignancies. Results In 91/264 (34%) of cases, at least one rearrangement involving the MYC locus (MYCr) was detected by WGS. In 18 of these samples (20%), >1 MYCr was present (114 MYCr in total). Out of these 91 patients, in 32 (35%) the MYCr had been identified by FISH, in 46 cases (51%) it was not detected due to the heterogeneity of breakpoints, while in 13 (14%) patients FISH could not be evaluated (e.g. due to insufficient patient material). Of the 114 MYCr encountered in WGS, 42 involved one of the immunoglobulin loci (IGH n=25, IGK n=9, IGL n=8). The remaining 72 MYCr involved other rare partners. In 29 of these rearrangements, as well as in four complex rearrangements involving IGH or IGK, recurrent rare partners were identified, comprising 1p12/FAM46C (n=6), 6p24.3/BMP6 (n=10), 6q21/FOXO3 (n=4), 7p21.3 (n=3), 11q13/CCND1 (n=5), 20q11.22 (n=5). 43 MYCr involved non-recurrent (single) rare partners, for 4 of these a MYCr was also detected by FISH. The MYCr detected were rather complex: only 34 (30%) showed a simple reciprocal translocation (IGH n=7, IGL n=2, IGK n=4, rare partners n=21), 60 (53%) showed more complex rearrangements (IGH n=12, IGL n=4, IGK n=2, rare partners n=42) and in 20 cases (18%) at least one additional chromosome was involved (IGH n=6, IGL n=3, IGK n=2, rare partners n=9). In 80% of MYCr, breakpoints were located between genomic positions 128.203.605 and 129.375.490 encompassing the pre-described MYC surrounding locus PVT1. IGH-MYC rearrangements showed a tendency to cluster towards the centromere. MYCr involving rare partners showed the broadest breakpoint spectrum and clustered in both directions of the hotspot (Fig 1A). Regarding expression of MYC, all cases showed an overexpression (median GE: 6.9 vs 4.5 in normal controls). Median GE was similar in cases with Ig partners (IGH: 7.1, IGL: 6.7, IGK: 6.6) and non Ig partners (6.8) and also in cases with MYCr detected by FISH (7.0) and cases in which it was not detected by FISH (6.5). Analysis of additional chromosomal aberrations revealed that hyperdiploidy was significantly more frequent in MYCr (n=68/91, 75% vs n=76/173, 44%; p=0.001), while t(11;14) was found significantly less frequent (n=11/91, 12% vs n=49/173, 28%; p=0.003) (Fig 1B). No associations were found between MYCr and other frequent chromosomal abnormalities. Furthermore, molecular mutations frequently occurring in MM (ATM, BRAF, KRAS, NRAS, TP53, IRF4) were analyzed, revealing that patients with MYCr were significantly less frequently associated with mutations in the IRF4 gene (MYCr patients n=1/91; non-MYCr patients n=13/173; p =0.028) (Fig 1C). Conclusions (1) WGS detects ~3x more MYCr compared to FISH. (2) The complexity on the genomic level of MYCr is high, therefore the detection with targeted assays is limited while WGS allows a more comprehensive analysis. (3) MYC expression in cases with MYCr with non Ig partners is comparably high as for Ig-MYC translocations. (4) MYCr are associated with hyperdiploidy, whereas t(11;14) and IRF4 mutations were detected at a lower frequency. Disclosures Seliger: MLL Munich Leukemia Laboratory: Employment. Geirhos:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Walter:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Baer:MLL Munich Leukemia Laboratory: Employment. Stengel:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.

Abstract 2506: Exploring the complex etiology of oncogenic fusions in childhood cancer

Abstract Background, Rationale and Experimental Approach Oncogenic fusions are generated via chromosomal rearrangements resulting in an exchange of coding or regulatory DNA sequences. These mutations play an important role in disease onset and subsequent cancer progression, however the exact timing and mechanisms by which they arise are unknown. Through the SickKids clinical sequencing program, KiCS, we explored how and when canonical fusions arise by studying the whole-genomes of childhood cancers with diagnostic or driver fusions. Our investigation began with the pediatric bone cancer, Ewing sarcoma, and later expanded to include other solid, blood, and brain cancers such as papillary thyroid carcinoma, myeloid leukemia, and ependymoma among others. Results The starting point of our investigation was ES, where we sequenced the whole-genomes of 124 cases. Ewing sarcoma (ES) represents the prototypical fusion-driven sarcoma as it is characterized and driven by the EWSR1-ETS fusion. In ~42% of cases, we found that the ES fusion gene arises by chromoplexy, a sudden burst of complex, loop-like rearrangements, rather than by simple reciprocal translocations as previously thought. We show that these rearrangements rapidly and dramatically altered the chromosomal landscape of ES tumors, producing the driver EWSR1-ETS fusion and disrupting numerous other genes in a short time. Remarkably, these complex rearrangements are enriched for genes, including those with a clear role in oncogenesis, and are associated with the earliest replicating portions of the genome. We then sequenced the genomes of 30 other childhood cancers with oncogenic fusions to study their timing and formation mechanisms. In doing so, we have identified several novel fusions in many cancer types, which have been validated by RNA sequencing and cytogenetics. In some cases, the presence of these chromoplectic fusions indicates these patients may benefit from targeted therapy due to the generation of druggable fusions. . Conclusions Our findings provide fundamental insights into the pathogenesis of gene fusions in human cancer. They reveal complex DNA rearrangements to be a mutational process underpinning gene fusions in cancer that influences tumorigenesis. Citation Format: Nathaniel D. Anderson, Richard de Borja, Matthew D. Young, Fabio Fuligni, Andrej Rosic, Nicola D. Roberts, Nischalan Pillay, Jeffrey A. Toretsky, Yoshida Akihiko, Tatsuhiro Shibata, Markus Metzler, Gino Somers, Stephen W. Scherer, Adrienne M. Flanagan, Peter J. Campbell, Joshua D. Schiffman, Mary Shago, Ludmil B. Alexandrov, Jay S. Wunder, Irene L. Andrulis, David Malkin, Sam Behjati, Adam Shlien. Exploring the complex etiology of oncogenic fusions in childhood cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2506.

Looping together genes in cancer

Cancer A subset of human cancers are characterized by aberrant fusion of two specific genes. In some cases, the activity of the resultant fusion protein drives tumor growth. Most fusion genes in cancer appear to arise from simple reciprocal chromosomal translocations. Anderson et al. found that the characteristic fusion gene in a bone and soft tissue tumor called Ewing sarcoma is produced by a far more complicated mechanism (see the Perspective by Imielinski and Ladanyi). In nearly half of the tumors examined, the fusion gene was created by the formation of dramatic genomic loops that disrupt multiple genes. These complex rearrangements occur in early replicating and transcriptionally active regions of the genome and are associated with poor prognosis. Science , this issue p. [eaam8419][1]; see also p. [848][2] [1]: /lookup/doi/10.1126/science.aam8419 [2]: /lookup/volpage/361/848?iss=6405

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors.

Sarcomas are cancers of the bone and soft tissue often defined by gene fusions. Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors. We explored how and when EWSR1-ETS fusions arise by studying the whole genomes of Ewing sarcomas. In 52 of 124 (42%) of tumors, the fusion gene arises by a sudden burst of complex, loop-like rearrangements, a process called chromoplexy, rather than by simple reciprocal translocations. These loops always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions. Similar loops forming canonical fusions were found in three other sarcoma types. Chromoplexy-generated fusions appear to be associated with an aggressive form of Ewing sarcoma. These loops arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Two novel fusion genes, AIF1L-ETV6 and ABL1-AIF1L, result together with ETV6-ABL1 from a single chromosomal rearrangement in acute lymphoblastic leukemia with prenatal origin.

Fusion genes resulting from chromosomal rearrangements represent a hallmark of childhood acute lymphoblastic leukemia (ALL). Unlike more common fusion genes generated via simple reciprocal chromosomal translocations, formation of the ETV6-ABL1 fusion gene requires 3 DNA breaks and usually results from an interchromosomal insertion. We report a child with ALL in which a single interchromosomal insertion led to the formation of ETV6-ABL1 and 2 novel fusion genes: AIF1L-ETV6 and ABL1-AIF1L. We demonstrate the prenatal origin of this complex chromosomal rearrangement, which apparently initiated the leukemogenic process, by successful backtracking of the ETV6-ABL1 fusion into the patient's archived neonatal blood. We cloned coding sequences of AIF1L-ETV6 and ABL1-AIF1L in-frame fusion transcripts from the patient's leukemic blasts and we show that the chimeric protein containing the DNA binding domain of ETV6 is expressed from the AIF1L-ETV6 transcript and localized in both the cytoplasm and nucleus of transfected HEK293T cells. Transcriptomic and genomic profiling of the diagnostic bone marrow sample revealed Ph-like gene expression signature and loss of the IKZF1 and CDKN2A/B genes, the typical genetic lesions accompanying ETV6-ABL1-positive ALL. The prenatal origin of the rearrangement confirms that ETV6-ABL1 is not sufficient to cause overt leukemia, even when combined with the 2 novel fusions. We did not find the AIF1L-ETV6 and ABL1-AIF1L fusions in other ETV6-ABL1-positive ALL. Nevertheless, functional studies would be needed to establish the biological role of AIF1L-ETV6 and ABL1-AIF1L and to determine whether they contribute to leukemogenesis and/or to the final leukemia phenotype.

De novo double reciprocal translocations in addition to partial monosomy at another chromosome: A very rare case

Reciprocal translocations are one of the most common structural rearrangements with a frequency of 1:500 and occur when there is an exchange of distal segments to breakpoints between non-homologous chromosomes. Two or three independent, simple reciprocal or Robertsonian translocations co-exist in the same carrier were classified as complex chromosome rearrangements (CCRs). Structural chromosome rearrangements are considered balanced when there is no apparent gain or loss of chromosome material. In majority of cases, apparently balanced structural chromosome rearrangements (ABCR) are not associated with abnormal phenotypes, although these have been described in 6% of de novo ABCR and 23% of apparently balanced CCR. Here we report a patient with de novo two apparently balanced reciprocal translocations and two partial monosomies, one of these involving an independent chromosome characterized by microarray. Structural rearrangement investigations can improve the knowledge about human genome architecture and correlation of genomic imbalances to abnormal phenotype.

Molecular studies reveal a MLL-MLLT3 gene fusion displaced in a case of childhood acute lymphoblastic leukemia with complex karyotype

Rearrangement of the mixed lineage-leukemia gene (MLL-r) is common in hematological diseases and is generally associated with poor prognosis. The mixed-lineage leukemia gene translocated to, 3 (MLLT3) gene (9p22) is a frequent MLL-r partner (∼18% of leukemias with MLL rearrangement) and is characterized by the translocation t(9;11) (p22;q23), forming an MLL-MLLT3 gene fusion. MLL-r are usually simple reciprocal translocations between two different chromosomes, although karyotypes with complex MLL-r have been observed. We present a rare case of a child with acute lymphoblastic leukemia with a complex karyotype in which the classical t(9;11) (p22;q23) was cryptically relocated into a third chromosome in a balanced three-way translocation. At the genome level, however, the MLL-MLLT3 three-way translocation still displayed both reciprocal fusion transcripts. This argues in favor for a model where a simple two-way t(9;11) (p22;q23) was likely the first step that then evolved in to a more complex karyotype. Multicolor banding techniques can be used to greatly refine complex karyotypes and its chromosomal breakpoints. Also in the presence of putative new rearrangements, Long distance inverse-PCR is an important tool to identify which gene fusion is involved.

A rare complex chromosomal rearrangement in an oligospermic male: a case report and review of the Chinese literature

A rare complex chromosomal rearrangement in an oligospermic male: a case report and review of the Chinese literature

Array comparative genomic hybridization characterization of prenatally detected de novo apparently balanced reciprocal translocations with or without genomic imbalance in other chromosomes

We present our experience of array comparative genomic hybridization (aCGH) characterization of two cases of prenatally detected de novo simple and complex apparently balanced reciprocal translocations. Amniocentesis of the first case revealed a complex chromosome rearrangement and a karyotype of 46,XY,t(5;8;6)(q11.2;p23.1;q22.32)dn. aCGH of amniocytes revealed no genomic imbalance. Ultrasound findings were unremarkable. The pregnancy was carried to term, and pediatric follow-ups were normal at 3 months of age. Amniocentesis of the second case revealed a simple reciprocal translocation and a karyotype of 46,XY,t(3;11)(q14;q23)dn. aCGH of amniocytes revealed a 1.32-Mb microduplication in chromosome 2p12 [arr cgh 2p12 (75,245,747-76,563,965)×3] encompassing the genes of TACR1, FAM176A, MRPL19, and C2orf3. Ultrasound findings were unremarkable. The pregnancy was carried to term, and the pediatric follow-ups were normal at 8 months of age. In cases of prenatally detected de novo apparently balanced reciprocal translocations, cryptic intrachromosomal rearrangements may exist in addition to the cytogenetically visible structural chromosome aberrations. aCGH is useful not only in identifying the genomic imbalances at the breakpoints, but also in detecting unexpectedly complex rearrangements in other chromosomes.

High Frequency of Simple and Complex Chromosome Aberrations Detected in the Tokai-mura Survivor four and Five Years after the 1999 Criticality Accident

In September 1999 a criticality accident occurred in a uranium processing plant in Tokai-mura, Japan. During the accident, three workers (A, B and C) were exposed to high acute doses of neutrons and γ-rays: workers A and B fatally and worker C to an estimated whole body absorbed dose of 0.81 Gy neutrons and 1.3 Gy γ-rays. We obtained fixed peripheral blood lymphocytes (PBL) preparations from worker C approximately four and five years after the accident and assayed by 24 colour karyotyping (M-FISH) to determine the frequency and complexity of chromosome aberrations present. We observed a high frequency of simple reciprocal translocations, which we used to provide a rough estimation of dose and, in addition, for the assessment of the emergence of any clinically-relevant clonal exchanges. We did not observe any evidence of clonality but did find some evidence suggesting chromosome 1 as being preferentially involved in exchanges in stable cells. We also detected a relatively high frequency of damaged cells containing complex chromosome aberrations, of both the stable and unstable types. Qualitatively these complex aberrations were consistent with those observed to be induced after exposure to low doses of high-LET radiation or moderate doses of low-LET radiation, supporting the suggestion that heavily damaged cells can be quite long-lived in vivo.

Balanced Reciprocal Translocations Detected at Amniocentesis

To present perinatal findings, modes of ascertainment and parental decision in balanced reciprocal translocations detected at amniocentesis. Between January 1987 and August 2010, 82 cases with a simple reciprocal translocation, two cases with two separate simple reciprocal translocations and three cases with a complex chromosome rearrangement (CCR) were diagnosed by amniocentesis at Mackay Memorial Hospital, Taipei, Taiwan. The 87 cases originated from 76 families; 65 families with one case and 11 families with two cases. In the 76 families, the main modes of ascertainment included advanced maternal age (n=38), a previous child with an unbalanced reciprocal translocation (n=11), recurrent miscarriage (n = 9), abnormal maternal serum screening results (n = 9), elective causes (n = 5), a previous child with congenital anomalies (n =2) and abnormal ultrasound findings (n = 2). In these families, there were 17 (22.4%) de novo cases including 14 simple translocations and three CCRs. Of 14 de novo cases with a simple translocation, one (7.1%) manifested a congenital malformation, which was related to an X-autosome translocation, and four (28.6%) were terminated. Of three de novo CCRs, two manifested congenital anomalies and one was terminated. In 87 cases, additional aneuploidy was noted in two cases including one inherited simple translocation with Turner syndrome, and one de novo CCR with concomitant deletions and duplication. Balanced reciprocal translocations detected at amniocentesis may be associated with fetal anomalies in cases of concomitant aneuploidy, de novo X-autosome translocation or de novo CCR. Genetic counseling of a de novo simple reciprocal translocation at amniocentesis remains difficult because approximately one-fourth of the parents opt for termination of the pregnancy, and detailed ultrasonography and array comparative genomic hybridization are helpful for parental counseling under such circumstances.

Influence of dose rate on the induction of simple and complex chromosome exchanges by gamma rays.

Single-color painting of whole chromosomes, or protocols in which only a few chromosomes are distinctively painted, will always fail to detect a proportion of complex exchanges because they frequently produce pseudosimple painting patterns that are indistinguishable from those produced by bona fide simple exchanges. When 24-color multi-fluor FISH (mFISH) was employed for the purpose of distinguishing (truly) simple from pseudosimple exchanges, it was confirmed that the acute low-LET radiation dose-response relationship for simple exchanges lacked significant upward curvature. This result has been interpreted to indicate that the formation of simple exchanges requires only one chromosome locus be damaged (e.g. broken) by radiation to initiate an exchange-not two, as classical cytogenetic theory maintains. Because a one-lesion mechanism implies single-track action, it follows that the production of simple exchanges should not be influenced by changes in dose rate. To examine this prediction, we irradiated noncycling primary human fibroblasts with graded doses of (137)Cs gamma rays at an acute dose rate of 1.10 Gy/min and compared, using mFISH, the yield of simple exchanges to that observed after exposure to the same radiation delivered at a chronic dose rate of 0.08 cGy/min. The shape of the dose response was found to be quasi-linear for both dose rates, but, counter to providing support for a one-lesion mechanism, the yield of simple aberrations was greatly reduced by protracted exposure. Although chronic doses were delivered at rates low enough to produce damage exclusively by single-track action, this did not altogether eliminate the formation of complex aberrations, an analysis of which leads to the conclusion that a single track of low-LET radiation is capable of inducing complex exchanges requiring up to four proximate breaks for their formation. For acute exposures, the ratio of simple reciprocal translocations to simple dicentrics was near unity.

Cytogenetics, fluorescence in situ hybridization, and reverse transcriptase polymerase chain reaction are necessary to clarify the various mechanisms leading to an MLL-AF10 fusion in acute myelocytic leukemia with 10;11 rearrangement

In acute myelocytic leukemia (AML), predominantly in AML M5a, a recurrent chromosome aberration involves 11q23/ MLL and the short arm of chromosome 10. Molecular studies have shown that the AF10 gene at 10p12 is consistently a partner gene in cases with 10;11 rearrangement. A simple reciprocal translocation cannot lead to the known MLL-AF10 fusion transcript because the 3′ part of the MLL gene is orientated to the telomere and the 3′ part of the AF10 gene to the centromere. In a series of 1897 AML samples, 14 cases (0.74%) showed 10;11 rearrangements leading to a MLL-AF10 fusion transcript. These cases were analyzed in detail with G banding analyses, fluorescence in situ hybridization, and molecular investigation in a single center. Five different mechanisms of (10;11) rearrangements leading to a MLL-AF10 fusion transcript can be observed (i.e., reciprocal translocations, insertions of either 10p into 11q or 11q into 10p, as well as complex and cryptic rearrangements). Compared to translocations involving MLL and other partner genes, complex rearrangements are unique for MLL-AF10 fusions. This may result from the opposite orientation of MLL and AF10.

Transmissible and nontransmissible complex chromosome aberrations characterized by three-color and mFISH define a biomarker of exposure to high-LET alpha particles.

Insertions have been proposed as potential stable biomarkers of chronic high-LET radiation exposure. To examine this in vitro, we irradiated human peripheral blood lymphocytes in G(0) with either 50 cGy (238)Pu alpha particles (LET 121.4 keV/microm) or 3 Gy 250 kV X rays and stimulated their long-term culture up to approximately 22 population doublings postirradiation. Mitotic cells were harvested at regular intervals throughout this culture period and were assayed for chromosome aberrations using the techniques of three-color and 24-color mFISH. We observed the stable persistence of transmissible-type complex rearrangements, all involving at least one insertion. This supports the hypothesis that insertions are relevant indicators of exposure to high-LET radiation. However, one practical caveat of insertions being effective biomarkers is that their frequency is low due to the complexity and cell lethality of the majority of alpha-particle-induced complexes. Therefore, we propose a "profile of damage" that relies on the presence of insertions, a low frequency of stable simple reciprocal translocations (2B), and, significantly, the complexity of the damage initially induced. We suggest that the complexity of first- and second-division alpha-particle-induced nontransmissible complex aberrations reflects the structure of the alpha-particle track and as a consequence adds radiation-quality specificity to the biomarker, increasing the signal:noise ratio of the characteristic 2B:insertion ratio.

Deletions of the derivative chromosome 9 occur at the time of the Philadelphia translocation and provide a powerful and independent prognostic indicator in chronic myeloid leukemia

AbstractChronic myeloid leukemia (CML) is characterized by formation of theBCR-ABL fusion gene, usually as a consequence of the Philadelphia (Ph) translocation between chromosomes 9 and 22. Large deletions on the derivative chromosome 9 have recently been reported, but it was unclear whether deletions arose during disease progression or at the time of the Ph translocation. Fluorescence in situ hybridization (FISH) analysis was used to assess the deletion status of 253 patients with CML. The strength of deletion status as a prognostic indicator was then compared to the Sokal and Hasford scoring systems. The frequency of deletions was similar at diagnosis and after disease progression but was significantly increased in patients with variant Ph translocations. In patients with a deletion, all Ph+metaphases carried the deletion. The median survival of patients with and without deletions was 38 months and 88 months, respectively (P = .0001). By contrast the survival difference between Sokal or Hasford high-risk and non–high-risk patients was of only borderline significance (P = .057 andP = .034). The results indicate that deletions occur at the time of the Ph translocation. An apparently simple reciprocal translocation may therefore result in considerable genetic heterogeneity ab initio, a concept that is likely to apply to other malignancies associated with translocations. Deletion status is also a powerful and independent prognostic factor for patients with CML. The prognostic significance of deletion status should now be studied prospectively and, if confirmed, should be incorporated into management decisions and the analysis of clinical trials.

Chromosome translocations in multiple myeloma.

Multiple myeloma (MM), a malignant tumor of somatically mutated, isotype-switched plasma cells (PC), usually arises from a common benign PC tumor called Monoclonal Gammopathy of Undetermined Significance (MGUS). MM progresses within the bone marrow, and then to an extramedullary stage from which MM cell lines are generated. The incidence of IgH translocations increases with the stage of disease: 50% in MGUS, 60-65% in intramedullarly MM, 70-80% in extramedullary MM, and >90% in MM cell lines. Primary, simple reciprocal IgH translocations, which are present in both MGUS and MM, involve many partners and provide an early immortalizing event. Four chromosomal partners appear to account for the majority of primary IgH translocations: 11q13 (cyclin D1), 6p21 (cyclin D3), 4p16 (FGFR3 and MMSET), and 16q23 (c-maf). They are mediated primarily by errors in IgH switch recombination and less often by errors in somatic hypermutation, with the former dissociating the intronic and 3' enhancer(s), so that potential oncogenes can be dysregulated on each derivative chromosome (e.g., FGFR3 on der14 and MMSET on der4). Secondary translocations, which sometimes do not involve Ig loci, are more complex, and are not mediated by errors in B cell specific DNA modification mechanisms. They involve other chromosomal partners, notably 8q24 (c-myc), and are associated with tumor progression. Consistent with MM being the malignant counterpart of a long-lived PC, oncogenes dysregulated by primary IgH translocations in MM do not appear to confer an anti-apoptotic effect, but instead increase proliferation and/or inhibit differentiation. The fact that so many different primary transforming events give rise to tumors with the same phenotype suggests that there is only a single fate available for the transformed cell.

Amplification of 4q21-q22 and theMXR gene in independently derived mitoxantrone-resistant cell lines

Molecular cytogenetic studies were conducted on three multidrug-resistant cancer sublines which are highly resistant to the chemotherapeutic agent mitoxantrone, an anthracenedione. The three independently selected sublines were derived by exposure to mitoxantrone or Adriamycin and do not overexpress MDR1 or MRP. Two sublines, MCF-7 AdVp3000 and MCF-7 MX, showed an amplification peak at 4q21-q22, as demonstrated by comparative genomic hybridization (CGH), while the third, S1-M1-80, did not. FISH using a whole chromosome 4 paint demonstrated multiple rearrangements involving chromosome 4 in MCF-7 AdVp3000 and MCF-7 MX, while S1-M1-80 contained only a simple reciprocal translocation. The parental cell lines had no chromosome 4 rearrangements and no copy number gain or amplification of chromosome 4. Spectral karyotyping (SKY) analysis revealed a balanced translocation, t(4;17)(q21-q22;p13) in S1-M1-80 and multiple clonal translocations involving chromosome 4 in MCF-7 AdVp3000 and MCF-7 MX. A novel cDNA, designated MXR, which encodes an ABC half-transporter and is highly overexpressed in the three sublines, was localized to chromosome 4 by somatic cell hybrid analysis. Southern blot analysis demonstrated amplification of the MXR gene in MCF-7 AdVp3000 and MCF-7 MX, but not in S1-M1-80. FISH studies with a BAC probe for MXR localized the gene to 4q21-22 in the normal chromosome 4 and revealed in both MCF-7 AdVp3000 and MCF-7 MX amplification of MXR at one translocation juncture, shown by SKY to be t(4;5)(4qter-->4cen-->4q21-22::5q13-->5qter++ +) in MCF-7 AdVp3000 and t(6;4;6;3)(6pter-->6q15::4q21-q22::hsr::6q?::3q?27-->+ ++3qter) in MCF MX; neither of the breakpoints in the partner chromosomes showed amplification by CGH. The data are consistent with the hypothesis of a transporter, presumably that encoded by the MXR gene, mediating mitoxantrone resistance. The MXR gene encodes a half-transporter and the absence of cytogenetic evidence of coamplification of other regions suggests that a partner may not be overexpressed, and instead the MXR half-transporter homodimerizes to mediate drug transport. Genes Chromosomes Cancer 27:110-116, 2000. Published 2000 Wiley-Liss, Inc.