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Wang F, Chen Y, Jiang N, Gong S, Cao T, Yuan J, Liu J, Xie L, Wu Y, Jia Y. Acquired persistently complete remission by decitabine-based treatment for acute myeloid leukemia with the MLL-SEPT9 fusion gene. Leuk Lymphoma 2019; 60:3304-3307. [PMID: 31256701 DOI: 10.1080/10428194.2019.1625044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Fujue Wang
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Yingying Chen
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Nenggang Jiang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Shuaige Gong
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Tingyong Cao
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Jin Yuan
- Department of Hematology, The People's Hospital of Longquanyi District, Chengdu, China
| | - Jiazhuo Liu
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Liping Xie
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Yu Wu
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
| | - Yongqian Jia
- Department of Hematology and Research Laboratory of Hematology, West China Hospital of Sichuan University, Chengdu, China
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2
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Nasedkina TV, Ikonnikova AY, Tsaur GA, Karateeva AV, Ammour YI, Avdonina MA, Karachunskii AI, Zasedatelev AS. Biological microchip for establishing the structure of fusion transcripts involving MLL in children with acute leukemia. Mol Biol 2016. [DOI: 10.1134/s0026893316060145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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A pipeline with multiplex reverse transcription polymerase chain reaction and microarray for screening of chromosomal translocations in leukemia. BIOMED RESEARCH INTERNATIONAL 2013; 2013:135086. [PMID: 24288660 PMCID: PMC3816023 DOI: 10.1155/2013/135086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/01/2013] [Accepted: 08/19/2013] [Indexed: 01/22/2023]
Abstract
Chromosome rearrangements and fusion genes present major portion of leukemogenesis and contribute to leukemic subtypes. It is practical and helpful to detect the fusion genes in clinic diagnosis of leukemia. Present application of reverse transcription polymerase chain reaction (RT-PCR) method to detect the fusion gene transcripts is effective, but time- and labor-consuming. To set up a simple and rapid system, we established a method that combined multiplex RT-PCR and microarray. We selected 15 clinically most frequently observed chromosomal rearrangements generating more than 50 fusion gene variants. Chimeric reverse primers and chimeric PCR primers containing both gene-specific and universal sequences were applied in the procedure of multiplex RT-PCR, and then the PCR products hybridized with a designed microarray. With this approach, among 200 clinic samples, 63 samples were detected to have gene rearrangements. All the detected fusion genes positive and negative were validated with RT-PCR and Sanger sequencing. Our data suggested that the RT-PCR-microarray pipeline could screen 15 partner gene pairs simultaneously at the same accuracy of the fusion gene detection with regular RT-PCR. The pipeline showed effectiveness in multiple fusion genes screening in clinic samples.
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4
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Greisman HA, Hoffman NG, Yi HS. Rapid high-resolution mapping of balanced chromosomal rearrangements on tiling CGH arrays. J Mol Diagn 2011; 13:621-33. [PMID: 21907824 DOI: 10.1016/j.jmoldx.2011.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 07/01/2011] [Accepted: 07/12/2011] [Indexed: 01/27/2023] Open
Abstract
The diagnosis and classification of many cancers depends in part on the identification of large-scale genomic aberrations such as chromosomal deletions, duplications, and balanced translocations. Array-based comparative genomic hybridization (array CGH) can detect chromosomal imbalances on a genome-wide scale but cannot reliably identify balanced chromosomal rearrangements. We describe a simple modification of array CGH that enables simultaneous identification of recurrent balanced rearrangements and genomic imbalances on the same microarray. Using custom tiling oligonucleotide arrays and gene-specific linear amplification primers, translocation CGH (tCGH) maps balanced rearrangements to ∼100-base resolution and facilitates the rapid cloning and sequencing of novel rearrangement breakpoints. As proof of principle, we used tCGH to characterize nine of the most common gene fusions in mature B-cell neoplasms and myeloid leukemias. Because tCGH can be performed in any CGH-capable laboratory and can screen for multiple recurrent translocations and genome-wide imbalances, it should be of broad utility in the diagnosis and classification of various types of lymphomas, leukemias, and solid tumors.
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Affiliation(s)
- Harvey A Greisman
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
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5
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De Braekeleer E, Meyer C, Douet-Guilbert N, Basinko A, Le Bris MJ, Morel F, Berthou C, Marschalek R, Férec C, De Braekeleer M. Identification of MLL partner genes in 27 patients with acute leukemia from a single cytogenetic laboratory. Mol Oncol 2011; 5:555-63. [PMID: 21900057 DOI: 10.1016/j.molonc.2011.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 10/17/2022] Open
Abstract
Chromosomal rearrangements involving the MLL gene have been associated with many different types of hematological malignancies. Fluorescent in situ hybridization with a panel of probes coupled with long distance inverse-PCR was used to identify chromosomal rearrangements involving the MLL gene. Between 1995 and 2010, 27 patients with an acute leukemia were found to have a fusion gene involving MLL. All seven ALL patients with B cell acute lymphoblastic leukemia were characterized by the MLL/AFF1 fusion gene resulting from a translocation (5 patients) or an insertion (2 patients). In the 19 AML patients with acute myeloblastic leukemia, 31.6% of all characterized MLL fusion genes were MLL/MLLT3, 21.1% MLL/ELL, 10.5% MLL/MLLT6 and 10.5% MLL/EPS15. Two patients had rare or undescribed fusion genes, MLL/KIAA0284 and MLL/FLNA. Seven patients (26%) had a complex chromosomal rearrangement (three-way translocations, insertions, deletions) involving the MLL gene. Splicing fusion genes were found in three patients, leading to a MLL/EPS15 fusion in two and a MLL/ELL fusion in a third patient. This study showed that fusion involving the MLL gene can be generated through various chromosomal rearrangements such as translocations, insertions and deletions, some being complex or cryptic. A systematic approach should be used in all cases of acute leukemia starting with FISH analyses using a commercially available MLL split signal probe. Then, the analysis has to be completed, if necessary, by further molecular cytogenetic and genomic PCR methods.
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6
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Lee SG, Park TS, Oh SH, Park JC, Yang YJ, Marschalek R, Meyer C, Cho EH, Shin SY. De novo acute myeloid leukemia associated with t(11;17)(q23;q25) and MLL-SEPT9 rearrangement in an elderly patient: a case study and review of the literature. Acta Haematol 2011; 126:195-8. [PMID: 21846973 DOI: 10.1159/000329389] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 05/17/2011] [Indexed: 11/19/2022]
Affiliation(s)
- Sang-Guk Lee
- Department of Laboratory Medicine, Armed Forces Capital Hospital, Seongnam, Korea
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7
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Giusiano S, Formisano-Tréziny C, Benziane A, Maroc N, Picard C, Hermitte F, Taranger-Charpin C, Gabert J. Development of a biochip-based assay integrated in a global strategy for identification of fusion transcripts in acute myeloid leukemia: a work flow for acute myeloid leukemia diagnosis. Int J Lab Hematol 2010; 32:398-409. [PMID: 19930410 DOI: 10.1111/j.1751-553x.2009.01201.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Three major types of rearrangements are involved in acute myeloid leukemias (AML): t(8;21)(q22;q22), inv(16)(p13q22), and 11q23/MLL abnormalities. Their precise identification becomes essential for diagnosis, prognosis, and therapeutic choices. Resulting fusion transcripts (FT) are also powerful markers for monitoring the efficacy of treatment, the minimal residual disease (MRD) and could become therapeutic targets. Today, the challenge is to propose an individual follow-up for each patient even for those with a rare fusion event. In this study, we propose a biochip-based assay integrated in a global strategy for identification of rare FT in AML, after fluorescence in situ hybridization detection, as described by the World Health Organization classification. Using cell lines, we developed and validated a biochip-based assay called the AMLFusionChip that identifies every FT of AML1-ETO, CBFbeta-MYH11 as well as MLL-AF9, MLL-ENL, MLL-AF6, and MLL-AF10. The original design of our AMLFusionChip.v01 enables the identification of these FT wherever the breakpoint on the partner gene may be. In case of biochip negative result, our 3'RACE amplification strategy enables to clone and then sequence the new translocation partner. This AMLFusionChip strategy fits into the concept of personalized medicine for the largest number of patients.
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Affiliation(s)
- S Giusiano
- Service d' Anatomie et Cytologie Pathologiques, CHU Nord, Boulevard Pierre Dramard, Marseille Cedex 20, France.
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8
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Nasedkina TV, Guseva NA, Gra OA, Mityaeva ON, Chudinov AV, Zasedatelev AS. Diagnostic microarrays in hematologic oncology: applications of high- and low-density arrays. Mol Diagn Ther 2009; 13:91-102. [PMID: 19537844 DOI: 10.1007/bf03256318] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Microarrays have become important tools for high-throughput analysis of gene expression, chromosome aberrations, and gene mutations in cancer cells. In addition to high-density experimental microarrays, low-density, gel-based biochip technology represents a versatile platform for translation of research into clinical practice. Gel-based microarrays (biochips) consist of nanoliter gel drops on a hydrophobic surface with different immobilized biopolymers (primarily nucleic acids and proteins). Because of the high immobilization capacity of the gel, such biochips have a high probe concentration and high levels of fluorescence signals after hybridization, which allow the use of simple, portable detection systems. The notable accuracy of the analysis is reached as a result of the high level of discrimination between positive and negative gel-bound probes. Different applications of biochips in the field of hematologic oncology include analysis of chromosomal translocations in leukemias, diagnostics of T-cell lymphomas, and pharmacogenetics.
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Affiliation(s)
- Tatyana V Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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9
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Lu Q, Nunez E, Lin C, Christensen K, Downs T, Carson DA, Wang-Rodriguez J, Liu YT. A sensitive array-based assay for identifying multiple TMPRSS2:ERG fusion gene variants. Nucleic Acids Res 2008; 36:e130. [PMID: 18794177 PMCID: PMC2582611 DOI: 10.1093/nar/gkn585] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Studies of gene fusions in solid tumors are not as extensive as in hematological malignancies due to several technical and analytical problems associated with tumor heterogeneity. Nevertheless, there is a growing interest in the role of fusion genes in common epithelial tumors after the discovery of recurrent TMPRSS2:ETS fusions in prostate cancer. Among all of the reported fusion partners in the ETS gene family, TMPRSS2:ERG is the most prevalent one. Here, we present a simple and sensitive microarray-based assay that is able to simultaneously determine multiple fusion variants with a single RT-PCR in impure RNA specimens. The assay detected TMPRSS2:ERG fusion transcripts with a detection sensitivity of <10 cells in the presence of more than 3000 times excess normal RNA, and in primary prostate tumors having no >1% of cancer cells. The ability to detect multiple transcript variants in a single assay is critically dependent on both the primer and probe designs. The assay should facilitate clinical and basic studies for fusion gene screening in clinical specimens, as it can be readily adapted to include multiple gene loci.
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Affiliation(s)
- Qing Lu
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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10
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Kurosu T, Tsuji K, Ohki M, Miki T, Yamamoto M, Kakihana K, Koyama T, Taniguchi S, Miura O. A variant-type MLL/SEPT9 fusion transcript in adult de novo acute monocytic leukemia (M5b) with t(11;17)(q23;q25). Int J Hematol 2008; 88:192-196. [PMID: 18642054 DOI: 10.1007/s12185-008-0133-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Revised: 05/22/2008] [Accepted: 05/23/2008] [Indexed: 12/19/2022]
Abstract
As a result of recurrent chromosomal translocations in acute leukemias, the mixed-lineage-leukemia (MLL) gene fuses with a variety of partner genes, which include several members of the septin gene family. SEPT9 is a very rare but recurrent fusion partner of MLL, and has recently been implicated in the oncogenesis of various malignancies. Herein, we report a case of de novo acute monocytic leukemia (M5b) with t(11;17)(q23;q25). MLL involvement was revealed by fluorescent in situ hybridization (FISH) analysis, and an MLL/SEP9 fusion transcript was detected by RT-PCR. Sequencing analysis further showed that, in contrast to originally reported cases, MLL exon 8 was fused not with SEPT9 exon 3 but with exon 2, which codes for the unique N-terminal region of the SEPT9_v1 isoform, the region implicated in the regulation of gene expression and cell proliferation. We did not detect any mutation of FLT3, which was expressed at a relatively low level in the leukemic cells. Relapsing after a very short complete remission, the leukemia progressed rapidly and became fatal in spite of intensive therapies including hematopoietic stem cell transplantation. It is thus suggested that, in common with the original MLL/SEPT9 cases, monocytic differentiation and a poor prognosis may also be associated with acute myeloid leukemia with the variant MLL/SEPT9 fusion transcript.
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Affiliation(s)
- Tetsuya Kurosu
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan.
| | - Kana Tsuji
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan.,Laboratory Molecular Genetics of Hematology, Graduate School of Health Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Manabu Ohki
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Tohru Miki
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Masahide Yamamoto
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Kazuhiko Kakihana
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Takatoshi Koyama
- Laboratory Molecular Genetics of Hematology, Graduate School of Health Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
| | - Shuichi Taniguchi
- Department of Hematology, Toranomon Hospital, 2-2-2 Toranomon, Minatoku, Tokyo, 105-8470, Japan
| | - Osamu Miura
- Department of Hematology, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyoku, Tokyo, 113-8519, Japan
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11
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Chun SM, Kim YL, Choi HB, Oh YT, Kim YJ, Lee S, Kim TG, Yang EG, Park YK, Kim DW, Han BD. Identification of leukemia-specific fusion gene transcripts with a novel oligonucleotide array. Mol Diagn Ther 2007; 11:21-8. [PMID: 17286448 DOI: 10.1007/bf03256220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
BACKGROUND Identification of specific chromosomal translocations is essential for the diagnosis and prognosis of leukemia. In this study, we employ DNA microarray technology to detect chromosomal aberrations in patients with chronic myeloid leukemia (CML) and acute myeloid leukemia (AML), as well as in leukemic cell lines. METHODS Reverse transcription using a random 9-mer primer was performed with total RNA from patients and leukemic cells lines. Multiplex PCR reactions using four groups of primer sets were then performed for amplification of cDNA from reverse-transcribed total RNA samples. Normal and fusion sequences were distinguished by hybridization of the amplified cDNA to a selective oligonucleotide array (SOA) containing 20-30mer synthetic probes. A total of 23 sets of oligomers were fabricated on glass slides for the detection of normal and fusion genes, as follows: BCR/ABL, AML/EAP, AML/ETO, AML/MDS, PML/RARA, NUMA1/RARA, PLZF/RARA, and CBFB/MYH. RESULTS Gene translocation in leukemia was effectively identified with the SOA containing various leukemia-specific fusion and normal control sequences. Leukemic fusion sequences from patients and cell lines hybridized specifically to their complementary probes. The probe sets differing by approximately 50% at their 5' or 3' ends could distinguish between normal and fusion sequences. The entire process of detection was completed within 8 hours using the SOA method. CONCLUSIONS Probe sets on SOA can effectively discriminate between leukemia-specific fusion and normal sequences with a chip hybridization procedure. The oligonucleotide array presents several advantages in identifying leukemic gene translocations, such as multiplex screening, relatively low cost, and speed.
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MESH Headings
- Cell Line, Tumor
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 21
- DNA, Complementary
- DNA, Neoplasm/genetics
- DNA, Single-Stranded/genetics
- Gene Fusion
- Humans
- K562 Cells
- Leukemia/genetics
- Oligonucleotide Array Sequence Analysis
- RNA, Neoplasm/genetics
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Sung-Min Chun
- Life Sciences Division, Korea Institute of Science and Technology, Seoul, Korea
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12
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Miremadi A, Oestergaard MZ, Pharoah PDP, Caldas C. Cancer genetics of epigenetic genes. Hum Mol Genet 2007; 16 Spec No 1:R28-49. [PMID: 17613546 DOI: 10.1093/hmg/ddm021] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cancer epigenome is characterised by specific DNA methylation and chromatin modification patterns. The proteins that mediate these changes are encoded by the epigenetics genes here defined as: DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins, histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (HMT) and histone demethylases. We review the evidence that these genes can be targeted by mutations and expression changes in human cancers.
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Affiliation(s)
- Ahmad Miremadi
- Cancer Genomics Program, Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
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13
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Harrison CJ, Griffiths M, Moorman F, Schnittger S, Cayuela JM, Shurtleff S, Gottardi E, Mitterbauer G, Colomer D, Delabesse E, Castéras V, Maroc N. A multicenter evaluation of comprehensive analysis of MLL translocations and fusion gene partners in acute leukemia using the MLL FusionChip device. ACTA ACUST UNITED AC 2007; 173:17-22. [PMID: 17284365 DOI: 10.1016/j.cancergencyto.2006.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 09/07/2006] [Indexed: 10/23/2022]
Abstract
Rearrangements of the MLL gene are significant in acute leukemia. Among the most frequent translocations are t(4;11)(q21;q23) and t(9;11)(p22;q23), which give rise to the MLL-AFF1 and MLL-MLLT3 fusion genes (alias MLL-AF4 and MLL-AF9) in acute lymphoblastic and acute myeloid leukemia, respectively. Current evidence suggests that determining the MLL status of acute leukemia, including precise identification of the partner gene, is important in defining appropriate treatment. This underscores the need for accurate detection methods. A novel molecular diagnostic device, the MLL FusionChip, has been successfully used to identify MLL fusion gene translocations in acute leukemia, including the precise breakpoint location. This study evaluated the performance of the MLL FusionChip within a routine clinical environment, comprising nine centers worldwide, in the analysis of 21 control and 136 patient samples. It was shown that the assay allowed accurate detection of the MLL fusion gene, regardless of the breakpoint location, and confirmed that this multiplex approach was robust in a global multicenter trial. The MLL FusionChip was shown to be superior to other detection methods. The type of molecular information provided by MLL FusionChip gave an indication of the appropriate primers to design for disease monitoring of MLL patients following treatment.
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MESH Headings
- Acute Disease
- Adult
- Child
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 9
- Histone-Lysine N-Methyltransferase
- Humans
- In Situ Hybridization, Fluorescence
- Infant
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Myeloid-Lymphoid Leukemia Protein/genetics
- Oligonucleotide Array Sequence Analysis/instrumentation
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins, Fusion/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Translocation, Genetic
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Affiliation(s)
- Christine J Harrison
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, MP 822 Duthie Building, Southampton General Hospital, Southampton SO16 6YD, UK.
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14
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Basecke J, Whelan JT, Griesinger F, Bertrand FE. The MLL partial tandem duplication in acute myeloid leukaemia. Br J Haematol 2006; 135:438-49. [PMID: 16965385 DOI: 10.1111/j.1365-2141.2006.06301.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mixed lineage leukaemia gene-partial tandem duplications (MLL-PTD) characterise acute myeloid leukaemia (AML) with trisomy 11 and AML with a normal karyotype. MLL-PTD confer a worse prognosis with shortened overall and event free survival in childhood and adult AML. In spite of these clinical observations, the leukaemogenic mechanism has, so far, not been determined. This review summarises clinical studies on MLL-PTD positive AML and recent experimental findings on the putative leukaemogenic role of MLL-PTD.
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Affiliation(s)
- Jorg Basecke
- Division of Haematology and Oncology, University of Goettingen, Goettingen, Germany.
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15
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Strehl S, König M, Meyer C, Schneider B, Harbott J, Jäger U, von Bergh ARM, Loncarevic IF, Jarosova M, Schmidt HH, Moore SDP, Marschalek R, Haas OA. Molecular dissection of t(11;17) in acute myeloid leukemia reveals a variety of gene fusions with heterogeneous fusion transcripts and multiple splice variants. Genes Chromosomes Cancer 2006; 45:1041-9. [PMID: 16897742 DOI: 10.1002/gcc.20372] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The majority of translocations that involve the long arms of chromosomes 11 and 17 in acute myeloid leukemia appear identical on the cytogenetic level. Nevertheless, they are diverse on the molecular level. At present, two genes are known in 11q23 and four in 17q12-25 that generate five distinct fusion genes: MLL-MLLT6/AF17, MLL-LASP1, MLL-ACACA or MLL-SEPT9/MSF, and ZBTB16/PLZF-RARA. We analyzed 14 cases with a t(11;17) by fluorescence in situ hybridization and molecular genetic techniques and determined the molecular characteristics of their fusion genes. We identified six different gene fusions that comprised seven cases with a MLL-MLLT6/AF17, three with a MLL-SEPT9/MSF, and one each with MLL-LASP1, MLL-ACACA, and ZBTB16/PLZF-RARA fusions. In the remaining case, a MLL-SEPT6/Xq24 fusion suggested a complex rearrangement. The MLL-MLLT6/AF17 transcripts were extremely heterogeneous and the detection of seven different in-frame transcript and splice variants enabled us to predict the protein domains relevant for leukemogenesis. The putative MLL-MLLT6 consensus chimeric protein consists of the AT-hook DNA-binding, the methyltransferase, and the CXXC zinc-finger domains of MLL and the highly conserved octapeptide and the leucine-zipper dimerization motifs of MLLT6. The MLL-SEPT9 transcripts showed a similar high degree of variability. These analyses prove that the diverse types of t(11;17)-associated fusion genes can be reliably identified and delineated with a proper combination of cytogenetic and molecular genetic techniques. The heterogeneity of transcripts encountered in cases with MLL-MLLT6/AF17 and MLL-SEPT9/MSF fusions clearly demonstrates that thorough attention has to be paid to the appropriate selection of primers to cover all these hitherto unrecognized fusion variants.
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MESH Headings
- Adolescent
- Adult
- Aged
- Alternative Splicing
- Child
- Child, Preschool
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 17
- DNA-Binding Proteins/genetics
- Female
- Histone-Lysine N-Methyltransferase
- Homeodomain Proteins/genetics
- Humans
- In Situ Hybridization
- Infant
- Leukemia, Monocytic, Acute/genetics
- Leukemia, Myelomonocytic, Acute/genetics
- Male
- Middle Aged
- Myeloid-Lymphoid Leukemia Protein/genetics
- Neoplasm Proteins/genetics
- Oncogene Proteins, Fusion/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Translocation, Genetic
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Affiliation(s)
- Sabine Strehl
- CCRI, Children's Cancer Research Institute, Kinderspitalgasse 6, Vienna, Austria.
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16
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Honoré P, Granjeaud S, Tagett R, Deraco S, Beaudoing E, Rougemont J, Debono S, Hingamp P. MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. BMC Genomics 2006; 7:240. [PMID: 16987406 PMCID: PMC1592093 DOI: 10.1186/1471-2164-7-240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Accepted: 09/20/2006] [Indexed: 01/08/2023] Open
Abstract
Background High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. Results MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. Conclusion MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike.
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Affiliation(s)
- Paul Honoré
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Samuel Granjeaud
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
| | - Rebecca Tagett
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Stéphane Deraco
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
- Now at CNRS – DSI, Tour Gaïa, rue Pierre-Gilles de Gennes, BP 21902, 31319 LABEGE CEDEX, France
| | - Emmanuel Beaudoing
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Jacques Rougemont
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stéphane Debono
- IPSOGEN SAS, Luminy Biotech Entreprises, 163 avenue de Luminy, Case 923, 13009 Marseille, France
| | - Pascal Hingamp
- TAGC, INSERM ERM206, Parc Scientifique de Luminy, Case 928, 13288 Marseille Cedex 09, France
- Now at IGS, CNRS UPR 2589, 163 Avenue de Luminy Case 934, 13288 Marseille Cedex 09, France
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Hayne CC, Winer E, Williams T, Chaves F, Khorsand J, Mark HFL. Acute lymphoblastic leukemia with 4;11 translocation analyzed by a multi-modal strategy of conventional cytogenetics, FISH, morphology, flow cytometry and molecular genetics, and review of the literature. Exp Mol Pathol 2006; 81:62-71. [PMID: 16765346 DOI: 10.1016/j.yexmp.2006.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Revised: 04/09/2006] [Accepted: 04/17/2006] [Indexed: 11/23/2022]
Abstract
We report a case of acute lymphoblastic leukemia (ALL) with a 4;11 translocation. Metaphase cells and interphase nuclei derived from a routine unstimulated culture of bone marrow were analyzed using a combined strategy of G-banding and fluorescent in situ hybridization (FISH) in addition to hematopathological analysis, flow cytometry, and molecular genetics. This multimodal approach enables a successful correlation of pathology and cytogenetics to support a comprehensive diagnosis of the patient. Meaningful prognostication and appropriate therapeutic considerations are possible only when accurate diagnostic information is given. We further search and review the literature for the most up-to-date information currently available for this subtype of ALL in the constantly evolving field of molecular cytogenetics.
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Affiliation(s)
- Cynthia C Hayne
- Boston University School of Medicine, 700 Albany Street, Suite 408, Boston, MA 02118, USA
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18
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Abstract
In all organisms, cell proliferation is orchestrated by coordinated patterns of gene expression. Transcription results from the activity of the RNA polymerase machinery and depends on the ability of transcription activators and repressors to access chromatin at specific promoters. During the last decades, increasing evidence supports aberrant transcription regulation as contributing to the development of human cancers. In fact, transcription regulatory proteins are often identified in oncogenic chromosomal rearrangements and are overexpressed in a variety of malignancies. Most transcription regulators are large proteins, containing multiple structural and functional domains some with enzymatic activity. These activities modify the structure of the chromatin, occluding certain DNA regions and exposing others for interaction with the transcription machinery. Thus, chromatin modifiers represent an additional level of transcription regulation. In this review we focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading to cancer.
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Affiliation(s)
- Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
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Bench AJ, Erber WN, Scott MA. Molecular genetic analysis of haematological malignancies: I. Acute leukaemias and myeloproliferative disorders. ACTA ACUST UNITED AC 2005; 27:148-71. [PMID: 15938721 DOI: 10.1111/j.1365-2257.2005.00701.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular genetic techniques are now routinely applied to haematological malignancies within a clinical laboratory setting. The detection of genetic rearrangements not only assists with diagnosis and treatment decisions, but also adds important prognostic information. In addition, genetic rearrangements associated with leukaemia can be used as molecular markers allowing the detection of low levels of residual disease. This review will concentrate on the application of molecular genetic techniques to the acute leukaemias and myeloprolferative disorders.
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Affiliation(s)
- A J Bench
- Haemato-Oncology Diagnostic Service, Department of Haematology, Addenbrooke's Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK.
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