Double minute in acute myeloid leukemia and myelodysplastic syndrome: Identification of new amplification regions by fluorescence in situ hybridization and spectral karyotyping

Clinical Cytogenetics Laboratory, Roswell Park Cancer Institute, Buffalo, New York 14263, USA.
Genes Chromosomes and Cancer (Impact Factor: 3.84). 05/2002; 34(1):42-7. DOI: 10.1002/gcc.10038
Source: PubMed

ABSTRACT Double minute chromosomes (dmin) are small chromatin bodies consisting of genes amplified in an extrachromosomal location. dmins are uncommon in hematologic malignancies; they are seen primarily in acute myeloid leukemia, with amplification of the MYC oncogene or, less frequently, the MLL transcription factor. Nine patients with hematologic malignancies with dmin were seen at the Roswell Park Cancer Institute between 1985 and 2000; eight had acute myeloid leukemia and one a myelodysplastic syndrome. Fluorescence in situ hybridization (FISH) demonstrated MYC amplification on dmin in four patients, but MLL amplification was not seen. Spectral karyotyping showed that the dmin derived from chromosome 11 in one patient and from chromosome 19 in two others without MYC or MLL amplification; derivation from these chromosomes was confirmed by FISH with chromosome paint probes. The dmin of chromosome 11 origin hybridized to a bacterial artificial chromosome (BAC) RP11-112M22 that maps to 11q24.3 and is predicted to contain ETS1 and other markers, including D11S11351 and D11S4091. The dmin of chromosome 19 origin in one patient hybridized to BACs RP11-46I12 and RP11-110J19; in the other patient, these clones did not hybridize with the dmin, but were found to be amplified on a marker chromosome that was derived from chromosome 19 in that patient's cells. These BACs have been mapped to 19q12-19q13.1 and 19q11-19q13.1, respectively, and are predicted to contain the markers D19S409 and D19S919 and the gene for ubiquinol-cytochrome C reductase, Rieske iron-sulfur polypeptide1 (UQCRFS1). dmin originating from chromosome 19 have not been reported previously in hematologic malignancies.

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    • "Of particular interest is ST14, also known as matripase. The gene maps to amplicon 11qIII, which can be found amplified independently and even in higher copy numbers than MLL (Patient P14; Table 1 (Nacheva et al., 1993; Crossen et al., 1999; Sait et al., 2002; Martinez-Ramirez et al., 2004, 2005)). ST14 codes for a type II transmembrane serine protease, which is known to cleave and thereby activate hepatocyte/scattering factor (HGF) (Uhland, 2006), which is also among the top 100 up-regulated genes in cases with MLL amplification in our datasets. "
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    ABSTRACT: AML/MDS patients carrying 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are characterized by a complex aberrant karyotype (CAK) frequently including deletions within 5q, 17p, and 7q, older age and fast progression of the disease with extremely poor prognosis. MLL has been shown to be overexpressed in cases with 11q amplification. However, in most of the cases, the amplified region is not restricted to the MLL locus. In this study, we investigated 19 patients with AML/MDS and MLL gain/amplification. By means of array CGH performed in 12 patients, we were able to delineate the minimal deleted regions within 5q and 17p and identified three independent regions 11q/I-III that were amplified in all cases. Gene expression profiles established in 15 cases were used to identify candidate genes within these regions. Notably, analysis of our data suggests a correlation of loss of 5q and 17p and expression of genes present in 11q23-25. Furthermore, we demonstrate that the gene expression signature can be used to discriminate AML/MDS with MLL amplification from several other types of AML.
    Genes Chromosomes and Cancer 06/2009; 48(6):510-20. DOI:10.1002/gcc.20658 · 3.84 Impact Factor
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    • "SKY analysis revealed that double minute chromosomes (DMINs) in AML and MDS patients were derived from chromosomes 8, 11 and 19. The exact origins of the amplified sequences were finally determined using FISH with BAC DNA probes (Sait et al., 2002). "
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    ABSTRACT: Spectral karyotyping (SKY) is a widely used methodology to identify genetic aberrations. Multicolor fluorescence in situ hybridization using chromosome painting probes in individual colors for all metaphase chromosomes at once is combined with a unique spectral measurement and analysis system to automatically classify normal and aberrant chromosomes. Based on countless studies and investigations in many laboratories worldwide, numerous new chromosome translocations and other aberrations have been identified in clinical and tumor cytogenetics. Thus, gene identification studies have been facilitated resulting in the dissection of tumor development and progression. For example, different translocation partners of the TEL/ETV6 transcription factor that is specially required for hematopoiesis within the bone marrow were identified. Also, the correct classification of complex karyotypes of solid tumors supports the prognostication of cancer patients. Important accomplishments for patients with genetic diseases, leukemias and lymphomas, mesenchymal tumors and solid cancers are summarized and exemplified. Furthermore, studies of disease mechanisms such as centromeric DNA breakage, DNA double strand break repair, telomere shortening and radiation-induced neoplastic transformation have been accompanied by SKY analyses. Besides the hybridization of human chromosomes, mouse karyotyping has also contributed to the comprehensive characterization of mouse models of human disease and for gene therapy studies.
    Cytogenetic and Genome Research 02/2006; 114(3-4):199-221. DOI:10.1159/000094203 · 1.91 Impact Factor
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    ABSTRACT: Chromosomal alterations in leukemia have been shown to have prognostic and predictive significance and are also important minimal residual disease (MRD) markers in the follow-up of leukemia patients. Although specific oncogenes and tumor suppressors have been discovered in some of the chromosomal alterations, the role and target genes of many alterations in leukemia remain unknown. In addition, a number of leukemia patients have a normal karyotype by standard cytogenetics, but have variability in clinical course and are often molecularly heterogeneous. Cytogenetic methods traditionally used in leukemia analysis and diagnostics; G-banding, various fluorescence in situ hybridization (FISH) techniques, and chromosomal comparative genomic hybridization (cCGH), have enormously increased knowledge about the leukemia genome, but have limitations in resolution or in genomic coverage. In the last decade, the development of microarray comparative genomic hybridization (array-CGH, aCGH) for DNA copy number analysis and the SNP microarray (SNP-array) method for simultaneous copy number and loss of heterozygosity (LOH) analysis has enabled investigation of chromosomal and gene alterations genome-wide with high resolution and high throughput. In these studies, genetic alterations were analyzed in acute myeloid leukemia (AML) and chronic lymphocytic leukemia (CLL). The aim was to screen and characterize genomic alterations that could play role in leukemia pathogenesis by using aCGH and SNP-arrays. One of the most important goals was to screen cryptic alterations in karyotypically normal leukemia patients. In addition, chromosomal changes were evaluated to narrow the target regions, to find new markers, and to obtain tumor suppressor and oncogene candidates. The work presented here shows the capability of aCGH to detect submicroscopic copy number alterations in leukemia, with information about breakpoints and genes involved in the alterations, and that genome-wide microarray analyses with aCGH and SNP-array are advantageous methods in the research and diagnosis of leukemia. The most important findings were the cryptic changes detected with aCGH in karyotypically normal AML and CLL, characterization of amplified genes in 11q marker chromosomes, detection of deletion-based mechanisms of MLL-ARHGEF12 fusion gene formation, and detection of LOH without copy number alteration in karyotypically normal AML. These alterations harbor candidate oncogenes and tumor suppressors for further studies. Kromosomimuutokset ovat tärkeitä ennusteeseen vaikuttavia tekijöitä leukemioiden diagnostiikassa ja niitä voidaan myös hyödyntää jäännöstaudin havaitsemiseksi hoidon jälkeisessä seurannassa. Useiden tunnettujen kromosomimuutosten kohdegeenejä ja mahdollisia muutosten taustalla vaikuttavia molekyylimekanismeja ei kuitenkaan tunneta. Lisäksi normaali karyotyyppi on yleinen löydös mm. akuutissa myelooisessa leukemiassa (AML) ja kroonisessa lymfaattisessa leukemiassa (KLL). Submikroskooppiset muutokset voisivat osittain selittää normaalikaryotyyppisten potilaiden ryhmän sisäistä heterogeenisuutta. Kromosomeja on analysoitu periteisesti G-raita karyotyypityksellä, erilaisilla fluoresenssi in situ hybridisaatio (FISH) menetelmillä ja kromosomien vertailevalla genomisella hybridisaatiolla (kromosomi-VGH). Vaikka nämä menetelmät ovat tuottaneet paljon tietoa kromosomimuutoksista, on niiden rajoitteena ollut alhainen erotuskyky tai ne ovat kerralla tuottaneet tietoa vain pienestä genomin alueesta. DNA-mikrosiruanalyysit ovat mahdollistaneet koko genomin laajuisen ja erotuskykyisen geenien kopiomäärien analyysin. Mikrosiru-VGH (array-CGH) menetelmällä voidaan analysoida geenien kopiolukuja ja SNP-siruilla (single nucleotide polymorphism array) voidaan geenien kopiolukujen lisäksi analysoida myös alleelista epätasapainoa (LOH). Tässä työssä tutkittiin AML ja KLL näytteitä käyttäen näitä mikrosiruanalyysejä. Tarkoituksena oli löytää uusia markkereita sekä kasvunrajoitegeeni ja onkogeeni kandidaatteja. Erityisesti haluttiin etsiä submikroskooppisia muutoksia normaalikaryotyypin leukemioissa. Osatyössä I tutkittiin kromosomin 11 q varren muutoksia AML:ssä, osatöissä II ja IV analysoitiin normaalikaryotyypin AML näytteitä ja osatyössä III tutkittiin kromosomimuutoksia KLL potilailla. Näissä tutkimuksissa havaittiin uusia kromosomi ja geenimuutoksia sekä karakterisoitiin jo tunnettujen muutosten katkoskohtia ja geenejä. Osatöissä havaittiin submikroskooppisia kopiolukumuutoksia normaalikaryotyypin AML:ssa ja KLL:ssa sekä LOH alueita normaalikaryotyypin AML:ssa. Lisäksi AML:ssa tunnistettiin kromosomin 11 materiaalista koostuvien markkeri-kromosomien monistuneet geenit sekä löydettiin MLL-ARHGEF12 fuusiogeenin muodostumiseen liittyvä submikroskooppinen deleetio. Tulosten perusteella mikrosiru-VGH ja SNP-siru menetelmät ovat hyödyllisiä leukemian diagnostiikassa ja tutkimuksessa, sillä ne voivat paljastaa tavanomaisilla menetelmillä huomaamattomia kromosomi- ja geenimuutoksia.
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