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Ragusa D, Makarov EM, Britten O, Moralli D, Green CM, Tosi S. The RS4;11 cell line as a model for leukaemia with t(4;11)(q21;q23): Revised characterisation of cytogenetic features. Cancer Rep (Hoboken) 2019; 2:e1207. [PMID: 32721124 PMCID: PMC7941496 DOI: 10.1002/cnr2.1207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/03/2019] [Accepted: 06/19/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Haematological malignancies harbouring rearrangements of the KMT2A gene represent a unique subtype of leukaemia, with biphenotypic clinical manifestations, a rapid and aggressive onset, and a generally poor prognosis. Chromosomal translocations involving KMT2A often cause the formation of oncogenic fusion genes, such as the most common translocation t(4;11)(q21;q23) producing the KMT2A-AFF1 chimera. AIM The aim of this study was to confirm and review the cytogenetic and molecular features of the KMT2A-rearranged RS4;11 cell line and put those in context with other reports of cell lines also harbouring a t(4;11) rearrangement. METHODS AND RESULTS The main chromosomal rearrangements t(4;11)(q21;q23) and i(7q), described when the cell line was first established, were confirmed by fluorescence in situ hybridisation (FISH) and 24-colour karyotyping by M-FISH. Additional cytogenetic abnormalities were investigated by further FISH experiments, including the presence of trisomy 18 as a clonal abnormality and the discovery of one chromosome 8 being an i(8q), which indicates a duplication of the oncogene MYC. A homozygous deletion of 9p21 containing the tumour-suppressor genes CDKN2A and CDKN2B was also revealed by FISH. The production of the fusion transcript KMT2A-AFF1 arising from the der(11)t(4;11) was confirmed by RT-PCR, but sequencing of the amplified fragment revealed the presence of multiple isoforms. Two transcript variants, resulting from alternative splicing, were identified differing in one glutamine residue in the translated protein. CONCLUSION As karyotype evolution is a common issue in cell lines, we highlight the need to monitor cell lines in order to re-confirm their characteristics over time. We also reviewed the literature to provide a comparison of key features of several cell lines harbouring a t(4;11). This would guide scientists in selecting the most suitable research model for this particular type of KMT2A-leukaemia.
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Affiliation(s)
- Denise Ragusa
- Division of Biosciences, College of Health and Life Sciences, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK
| | - Evgeny M Makarov
- Division of Biosciences, College of Health and Life Sciences, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK.,Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK
| | - Oliver Britten
- Division of Biosciences, College of Health and Life Sciences, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK
| | - Daniela Moralli
- Chromosome Dynamics, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Catherine M Green
- Chromosome Dynamics, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sabrina Tosi
- Division of Biosciences, College of Health and Life Sciences, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK.,Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Uxbridge, UK
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Veigaard C, Kjeldsen E. Exploring the genome-wide relation between copy number status and microRNA expression. Genomics 2014; 104:271-8. [PMID: 25124499 DOI: 10.1016/j.ygeno.2014.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 07/29/2014] [Accepted: 08/02/2014] [Indexed: 12/19/2022]
Abstract
The deregulation of miRNAs has been associated with several different cancer types. Deregulation occurs in several ways, but generally little is known about the basis for the distorted expression of miRNAs. We investigated the relation between copy number status and miRNA expression at the genome-wide level using cytogenetic and array-based methods to characterize genomic aberrations in hematopoietic cell lines. For the same cell lines, we obtained global miRNA expression profiles, and analyzed the genome-wide correlation using the Spearman's rank test. This analysis showed that the expression of only a two miRNAs (miR-324-5p encoded by MIR324 at 17p13.1 and miR-660 encoded by MIR660 at Xp11.23) was influenced by copy number status. Our data imply that no direct relation between copy number status and miRNA expression exists in the investigated cell lines.
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Affiliation(s)
- Christopher Veigaard
- Department of Hematology, Aarhus University Hospital, Aarhus University, 8000 Aarhus C, Denmark
| | - Eigil Kjeldsen
- Department of Hematology, Aarhus University Hospital, Aarhus University, 8000 Aarhus C, Denmark.
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Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM. Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia. Genome Res 2012; 22:1833-44. [PMID: 22628462 PMCID: PMC3460179 DOI: 10.1101/gr.138511.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/22/2012] [Indexed: 02/03/2023]
Abstract
Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication-timing profiles for pediatric leukemias from 17 patients and three cell lines, as well as normal B and T cells. Nonleukemic EBV-transformed lymphoblastoid cell lines displayed highly stable replication-timing profiles that were more similar to normal T cells than to leukemias. Leukemias were more similar to each other than to B and T cells but were considerably more heterogeneous than nonleukemic controls. Some differences were patient specific, while others were found in all leukemic samples, potentially representing early epigenetic events. Differences encompassed large segments of chromosomes and included genes implicated in other types of cancer. Remarkably, differences that distinguished leukemias aligned in register to the boundaries of developmentally regulated replication-timing domains that distinguish normal cell types. Most changes did not coincide with copy-number variation or translocations. However, many of the changes that were associated with translocations in some leukemias were also shared between all leukemic samples independent of the genetic lesion, suggesting that they precede and possibly predispose chromosomes to the translocation. Altogether, our results identify sites of abnormal developmental control of DNA replication in cancer that reveal the significance of replication-timing boundaries to chromosome structure and function and support the replication domain model of replication-timing regulation. They also open new avenues of investigation into the chromosomal basis of cancer and provide a potential novel source of epigenetic cancer biomarkers.
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Affiliation(s)
- Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Dana Battaglia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Bill H. Chang
- Division of Hematology and Oncology, Department of Pediatrics, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - James W. Shirley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Meenakshi Devidas
- COG and Department of Biostatistics, College of Medicine, University of Florida, Gainesville, Florida 32601, USA
| | - Brian J. Druker
- Division of Hematology and Medical Oncology, and OHSU Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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Markova EN, Kantidze OL, Razin SV. Transcription of the AML1/ETO chimera is guided by the P2 promoter of the AML1 gene in the Kasumi-1 cell line. Gene 2012; 510:142-6. [PMID: 22995345 DOI: 10.1016/j.gene.2012.09.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/31/2012] [Accepted: 09/07/2012] [Indexed: 02/06/2023]
Abstract
Chromosomal translocation t (8;21)(q22;22) is one of the most frequent cytogenetic abnormalities found in acute myeloid leukaemia (AML). It generates the AML1/ETO fusion gene, which itself supports human haematopoietic stem cell self-renewal. However, the mechanism guiding transcription of this chimeric gene remains unclear. In our work, we attempted to shed light on this essential issue. We investigated the promoter from which transcription of the AML1/ETO gene is initiated and defined the three-dimensional structure of the whole rearranged locus.
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Affiliation(s)
- Elena N Markova
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
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Identification of copy number alterations by array comparative genomic hybridization in patients with late chronic or accelerated phase chronic myeloid leukemia treated with imatinib mesylate. Int J Hematol 2011; 93:465-473. [PMID: 21387093 DOI: 10.1007/s12185-011-0796-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Revised: 02/01/2011] [Accepted: 02/13/2011] [Indexed: 10/18/2022]
Abstract
The outcome of treating chronic myeloid leukemia (CML) with imatinib mesylate (IM) is inferior when therapy is commenced in late chronic or accelerated phase as compared to early chronic phase. This may be attributed to additional genomic alterations that accumulate during disease progression. We sought to identify such lesions in patients showing suboptimal response to IM by performing array-CGH analysis on 39 sequential samples from 15 CML patients. Seventy-four cumulative copy number alterations (CNAs) consisting of 35 losses and 39 gains were identified. Alterations flanking the ABL1 and BCR genes on chromosomes 9 and 22, respectively, were the most common identified lesions with 5 patients losing variable portions of 9q34.11 proximal to ABL1. Losses involving 1p36, 5q31, 17q25, Y and gains of 3q21, 8q24, 22q11, Xp11 were among other recurrent lesions identified. Aberrations were also observed in individual patients, involving regions containing known leukemia-associated genes; CDKN2A/2B, IKZF1, RB1, TLX1, AFF4. CML patients in late stages of their disease, harbor pre-existing and evolving sub-microscopic CNAs that may influence disease progression and IM response.
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Pedranzini L, Mottadelli F, Ronzoni S, Rossella F, Ferracin M, Magnani I, Roversi G, Colapietro P, Negrini M, Pelicci PG, Larizza L. Differential cytogenomics and miRNA signature of the Acute Myeloid Leukaemia Kasumi-1 cell line CD34+38- compartment. Leuk Res 2010; 34:1287-95. [PMID: 20227111 DOI: 10.1016/j.leukres.2010.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 02/13/2010] [Accepted: 02/13/2010] [Indexed: 01/23/2023]
Abstract
The t(8;21) Acute Myeloid Leukaemia (AML) Kasumi-1 cell line with N822K KIT mutation, is a model system for leukemogenesis. As AML initiating cells reside in the CD34(+)CD38(-) fraction, we addressed the refined cytogenomic characterization and miRNA expression of Kasumi-1 cell line and its FACS-sorted subpopulations focussing on this compartment. By conventional cytogenetics, Spectral-Karyotyping and array-CGH the cytogenomic profile of Kasumi-1 cells evidenced only subtle regions differentially represented in CD34(+)CD38(-) cells. Expression profiling by a miRNA platform showed a set of miRNA differentially expressed in paired subpopulations and the signature of miR-584 and miR-182 upregulation in the CD34(+)CD38(-) fraction.
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Affiliation(s)
- Laura Pedranzini
- Genetica Medica, Dipartimento di Medicina, Chirurgia e Odontoiatria, Università di Milano, Via A di Rudinì 8, 20142 Milan, Italy
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Asou H, Matsui H, Ozaki Y, Nagamachi A, Nakamura M, Aki D, Inaba T. Identification of a common microdeletion cluster in 7q21.3 subband among patients with myeloid leukemia and myelodysplastic syndrome. Biochem Biophys Res Commun 2009; 383:245-51. [PMID: 19358830 DOI: 10.1016/j.bbrc.2009.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 04/01/2009] [Indexed: 11/24/2022]
Abstract
Monosomy 7 and interstitial deletions in the long arm of chromosome 7 (-7/7q-) is a common nonrandom chromosomal abnormality found frequently in myeloid disorders including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and juvenile myelomonocytic leukemia (JMML). Using a short probe-based microarray comparative genomic hybridization (mCGH) technology, we identified a common microdeletion cluster in 7q21.3 subband, which is adjacent to 'hot deletion region' thus far identified by conventional methods. This common microdeletion cluster contains three poorly characterized genes; Samd9, Samd9L, and a putative gene LOC253012, which we named Miki. Gene copy number assessment of three genes by real-time PCR revealed heterozygous deletion of these three genes in adult patients with AML and MDS at high frequency, in addition to JMML patients. Miki locates to mitotic spindles and centrosomes and downregulation of Miki by RNA interference induced abnormalities in mitosis and nuclear morphology, similar to myelodysplasia. In addition, a recent report indicated Samd9 as a tumor suppressor. These findings indicate the usefulness of the short probe-based CGH to detect microdeletions. The three genes located to 7q21.3 would be candidates for myeloid tumor-suppressor genes on 7q.
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Affiliation(s)
- Hiroya Asou
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology & Medicine, Hiroshima University, Hiroshima, Japan
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Specialized fluorescence in situ hybridization (FISH) techniques for leukaemia research. Methods Mol Biol 2009. [PMID: 19277577 DOI: 10.1007/978-1-59745-418-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence in situ hybridization (FISH) provides one of the few ways of analysing the genotype of individual cells, an important consideration for mixed cell populations such as those found in leukaemia. A more sophisticated variation combines fluorescence immunophenotyping and FISH for specific leukaemia-associated chromosome rearrangements. Combined immunophenotyping and FISH is a powerful tool to identify the cell lineage in which the leukaemia-specific chromosome rearrangement occurs and has been used to identify putative pre-leukaemic cells in normal cord blood. Another valuable FISH-based research technique is multi-fluor FISH (M-FISH). This multicolour approach is effectively a molecular karyotype of individual cells and has a range of applications, from chromosome breakage studies and characterising mouse models of leukaemia, to providing a perfect complementary approach to the emerging genomic microarray technologies.
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Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Res 2008; 18:751-62. [PMID: 18292219 DOI: 10.1101/gr.068304.107] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.
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Affiliation(s)
- Jun Chen
- Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA
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Strefford JC, Worley H, Barber K, Wright S, Stewart ARM, Robinson HM, Bettney G, van Delft FW, Atherton MG, Davies T, Griffiths M, Hing S, Ross FM, Talley P, Saha V, Moorman AV, Harrison CJ. Genome complexity in acute lymphoblastic leukemia is revealed by array-based comparative genomic hybridization. Oncogene 2007; 26:4306-18. [PMID: 17237825 DOI: 10.1038/sj.onc.1210190] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosomal abnormalities are important for the classification and risk stratification of patients with acute lymphoblastic leukemia (ALL). However, approximately 30% of childhood and 50% of adult patients lack abnormalities with clinical relevance. Here, we describe the use of array-based comparative genomic hybridization (aCGH) to identify copy number alterations (CNA) in 58 ALL patients. CNA were identified in 83% of cases, and most frequently involved chromosomes 21 (n=42), 9 (n=21), 6 (n=16), 12 (n=11), 15 (n=11), 8 (n=10) and 17 (n=10). Deletions of 6q (del(6q)) were heterogeneous in size, in agreement with previous data, demonstrating the sensitivity of aCGH to measure CNA. Although 9p deletions showed considerable variability in both the extent and location, all encompassed the CDKN2A locus. Six patients showed del(12p), with a common region encompassing the ETV6 gene. Complex CNA were observed involving chromosomes 6 (n=2), 15 (n=2) and 21 (n=11) with multiple regions of loss and gain along each chromosome. Chromosome 21 CNA shared a common region of gain, with associated subtelomeric deletions. Other recurrent findings included dim(13q), dim(16q) and enh(17q). This is the first report of genome-wide detection of CNA in ALL patients using aCGH, and it has demonstrated a higher level of karyotype complexity than anticipated from conventional cytogenetic analysis.
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Affiliation(s)
- J C Strefford
- Leukaemia Research Cytogenetics Group, Cancer Sciences Division, University of Southampton, UK.
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Calhoun ES, Gallmeier E, Cunningham SC, Eshleman JR, Hruban RH, Kern SE. Copy-number methods dramatically underestimate loss of heterozygosity in cancer. Genes Chromosomes Cancer 2006; 45:1070-1. [PMID: 16897743 DOI: 10.1002/gcc.20365] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Kearney L. Multiplex-FISH (M-FISH): technique, developments and applications. Cytogenet Genome Res 2006; 114:189-98. [PMID: 16954655 DOI: 10.1159/000094202] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 04/06/2006] [Indexed: 01/08/2023] Open
Abstract
Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.
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Affiliation(s)
- L Kearney
- Section of Haemato-Oncology, Institute of Cancer Research, London, UK.
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