383 results on '"Janet D. Rowley"'
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2. Supplementary Figure 1 Legend from Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
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Linda Wolff, P. Paul Liu, Janet D. Rowley, Michelle M. Le Beau, Michael J. Thirman, Azra Raza, Naomi Galili, Juraj Bies, Matthew T. Garin, and Jan Markus
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Supplementary Figure 1 Legend from Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
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- 2023
3. Supplementary Tables 1-2 from Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
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Linda Wolff, P. Paul Liu, Janet D. Rowley, Michelle M. Le Beau, Michael J. Thirman, Azra Raza, Naomi Galili, Juraj Bies, Matthew T. Garin, and Jan Markus
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Supplementary Tables 1-2 from Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
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- 2023
4. Data from Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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Michael J. Thirman, Jianjun Chen, Janet D. Rowley, San Ming Wang, Huanming Yang, Jun Yu, Jian Wang, Xiuqing Zhang, Charles Tseng, Yanming Zhang, Catherine Lavau, Lili Wang, Deborah S. Johnson, Nimanthi Jayathilaka, Mary Beth Neilly, Jingyue Bao, Ping Chen, Miao Sun, Shuangli Mi, Roger T. Luo, and Zejuan Li
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Important biological and pathologic properties are often conserved across species. Although several mouse leukemia models have been well established, the genes deregulated in both human and murine leukemia cells have not been studied systematically. We performed a serial analysis of gene expression in both human and murine MLL-ELL or MLL-ENL leukemia cells and identified 88 genes that seemed to be significantly deregulated in both types of leukemia cells, including 57 genes not reported previously as being deregulated in MLL-associated leukemias. These changes were validated by quantitative PCR. The most up-regulated genes include several HOX genes (e.g., HOX A5, HOXA9, and HOXA10) and MEIS1, which are the typical hallmark of MLL rearrangement leukemia. The most down-regulated genes include LTF, LCN2, MMP9, S100A8, S100A9, PADI4, TGFBI, and CYBB. Notably, the up-regulated genes are enriched in gene ontology terms, such as gene expression and transcription, whereas the down-regulated genes are enriched in signal transduction and apoptosis. We showed that the CpG islands of the down-regulated genes are hypermethylated. We also showed that seven individual microRNAs (miRNA) from the mir-17-92 cluster, which are overexpressed in human MLL rearrangement leukemias, are also consistently overexpressed in mouse MLL rearrangement leukemia cells. Nineteen possible targets of these miRNAs were identified, and two of them (i.e., APP and RASSF2) were confirmed further by luciferase reporter and mutagenesis assays. The identification and validation of consistent changes of gene expression in human and murine MLL rearrangement leukemias provide important insights into the genetic base for MLL-associated leukemogenesis. [Cancer Res 2009;69(3):OF1109–16]
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- 2023
5. Supplementary Tables 5-8 from Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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Michael J. Thirman, Jianjun Chen, Janet D. Rowley, San Ming Wang, Huanming Yang, Jun Yu, Jian Wang, Xiuqing Zhang, Charles Tseng, Yanming Zhang, Catherine Lavau, Lili Wang, Deborah S. Johnson, Nimanthi Jayathilaka, Mary Beth Neilly, Jingyue Bao, Ping Chen, Miao Sun, Shuangli Mi, Roger T. Luo, and Zejuan Li
- Abstract
Supplementary Tables 5-8 from Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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- 2023
6. Data from Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
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Linda Wolff, P. Paul Liu, Janet D. Rowley, Michelle M. Le Beau, Michael J. Thirman, Azra Raza, Naomi Galili, Juraj Bies, Matthew T. Garin, and Jan Markus
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The tumor suppressor gene INK4b (p15) is silenced by CpG island hypermethylation in most acute myelogenous leukemias (AML), and this epigenetic phenomenon can be reversed by treatment with hypomethylating agents. Thus far, it was not investigated whether INK4b is hypermethylated in all cytogenetic subtypes of AML. A comparison of levels of INK4b methylation in AML with the three most common cytogenetic alterations, inv(16), t(8;21), and t(15;17), revealed a strikingly low level of methylation in all leukemias with inv(16) compared with the other types. Surprisingly, the expression level of INK4b in inv(16)+ AML samples was low and comparable with that of the other subtypes. An investigation into an alternative mechanism of INK4b silencing determined that the loss of INK4b expression was caused by inv(16)-encoded core binding factor β-smooth muscle myosin heavy chain (CBFβ-SMMHC). The silencing was manifested in an inability to activate the normal expression of INK4b RNA as shown in vitamin D3–treated U937 cells expressing CBFβ-SMMHC. CBFβ-SMMHC was shown to displace RUNX1 from a newly determined CBF site in the promoter of INK4b. Importantly, this study (a) establishes that the gene encoding the tumor suppressor p15INK4b is a target of CBFβ-SMMHC, a finding relevant to the leukemogenesis process, and (b) indicates that, in patients with inv(16)-containing AML, reexpression from the INK4b locus in the leukemia would not be predicted to occur using hypomethylating drugs. [Cancer Res 2007;67(3):992–1000]
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- 2023
7. Supplementary Tables 1-4 from Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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Michael J. Thirman, Jianjun Chen, Janet D. Rowley, San Ming Wang, Huanming Yang, Jun Yu, Jian Wang, Xiuqing Zhang, Charles Tseng, Yanming Zhang, Catherine Lavau, Lili Wang, Deborah S. Johnson, Nimanthi Jayathilaka, Mary Beth Neilly, Jingyue Bao, Ping Chen, Miao Sun, Shuangli Mi, Roger T. Luo, and Zejuan Li
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Supplementary Tables 1-4 from Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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- 2023
8. New fusion transcripts identified in normal karyotype acute myeloid leukemia.
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Hongxiu Wen, Yongjin Li, Sami N Malek, Yeong C Kim, Jia Xu, Peixian Chen, Fengxia Xiao, Xin Huang, Xianzheng Zhou, Zhenyu Xuan, Shiva Mankala, Guihua Hou, Janet D Rowley, Michael Q Zhang, and San Ming Wang
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Medicine ,Science - Abstract
Genetic aberrations contribute to acute myeloid leukemia (AML). However, half of AML cases do not contain the well-known aberrations detectable mostly by cytogenetic analysis, and these cases are classified as normal karyotype AML. Different outcomes of normal karyotype AML suggest that this subgroup of AML could be genetically heterogeneous. But lack of genetic markers makes it difficult to further study this subgroup of AML. Using paired-end RNAseq method, we performed a transcriptome analysis in 45 AML cases including 29 normal karyotype AML, 8 abnormal karyotype AML and 8 AML without karyotype informaiton. Our study identified 134 fusion transcripts, all of which were formed between the partner genes adjacent in the same chromosome and distributed at different frequencies in the AML cases. Seven fusions are exclusively present in normal karyotype AML, and the rest fusions are shared between the normal karyotype AML and abnormal karyotype AML. CIITA, a master regulator of MHC class II gene expression and truncated in B-cell lymphoma and Hodgkin disease, is found to fuse with DEXI in 48% of normal karyotype AML cases. The fusion transcripts formed between adjacent genes highlight the possibility that certain such fusions could be involved in oncological process in AML, and provide a new source to identify genetic markers for normal karyotype AML.
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- 2012
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9. No chromosome arm unturned: in memory of Roland Berger 1934–2012
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M Le Coniat-Busson, Anne Hagemeijer, H. Van den Berghe, Alain Bernheim, M Gautier, Florence Nguyen-Khac, Serge Romana, Nicole Dastugue, Janet D. Rowley, Philippe Jonveaux, Christine J. Harrison, M Martineau, Olivier Bernard, Leukaemia Research Cytogenetics Group [Northern Institute for Cancer Research - Newcastle University], Northern Institute for Cancer Research [Newcastle] (NICR), Newcastle University [Newcastle]-Newcastle University [Newcastle], Section of Hematology/Oncology [Chicago], The University of Chicago Medicine, Center for the Biology of Disease, and KU Leuven (VIB), Génétique des tumeurs (U985), Institut Gustave Roussy (IGR)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Cancer Sciences Unit, Faculty of Medicine, University of Southampton, UK, Service de génétique et embryologie médicales [CHU Trousseau], CHU Trousseau [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire Histologie Embryologie Cytogénétique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire d'Hématologie [Purpan], Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], Nutrition-Génétique et Exposition aux Risques Environnementaux (NGERE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL), Service de Génétique [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service d'hématologie biologique [CHU Pitié-Salpêtrière], Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Service d'Hématologie Biologique [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Service de Génétique et d'Embryologie Médicales [CHU Trousseau], Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Trousseau [APHP], Université de Lorraine (UL)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP]
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Chromosome Aberrations ,0303 health sciences ,Cancer Research ,Leukemia ,business.industry ,[SDV]Life Sciences [q-bio] ,Hematology ,History, 20th Century ,History, 21st Century ,Pediatrics ,Genealogy ,03 medical and health sciences ,0302 clinical medicine ,Oncology ,Physicians ,030220 oncology & carcinogenesis ,Chromosome Arm ,Medicine ,France ,business ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology - Abstract
International audience
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- 2014
10. TET1 plays an essential oncogenic role in MLL -rearranged leukemia
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James C. Mulloy, Meelad M. Dawlaty, Chun-Xiao Song, Miao Sun, Xi Jiang, Zejuan Li, Keith E. Szulwach, Janet D. Rowley, Chunjiang He, Abdel G. Elkahloun, Mary Beth Neilly, Jinhua Wang, Hao Huang, Jiapeng Wang, Li Lin, Chuan He, Feng Chun Yang, Peng Jin, Ping Chen, Stephen Arnovitz, Yuanyuan Li, Paul P. Liu, Craig Street, Mingjiang Xu, Rudolf Jaenisch, Sandeep Gurbuxani, Mark Wunderlich, Jianjun Chen, and Gia Ming Hong
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Chromatin Immunoprecipitation ,Myeloid ,Immunoblotting ,Biology ,Mixed Function Oxygenases ,Cytosine ,Tandem Mass Spectrometry ,Proto-Oncogene Proteins ,hemic and lymphatic diseases ,medicine ,Humans ,Myeloid Ecotropic Viral Integration Site 1 Protein ,neoplasms ,Oligonucleotide Array Sequence Analysis ,Homeodomain Proteins ,Multidisciplinary ,ABL ,Gene Expression Profiling ,RUNX1T1 ,Myeloid leukemia ,Histone-Lysine N-Methyltransferase ,Biological Sciences ,Microarray Analysis ,medicine.disease ,Neoplasm Proteins ,DNA-Binding Proteins ,Gene Expression Regulation, Neoplastic ,Leukemia, Myeloid, Acute ,homeobox A9 ,Leukemia ,medicine.anatomical_structure ,5-Methylcytosine ,Cancer research ,Homeobox ,Myeloid-Lymphoid Leukemia Protein ,Chromatography, Liquid ,Signal Transduction - Abstract
The ten-eleven translocation 1 ( TET1 ) gene is the founding member of the TET family of enzymes (TET1/2/3) that convert 5-methylcytosine to 5-hydroxymethylcytosine. Although TET1 was first identified as a fusion partner of the mixed lineage leukemia ( MLL ) gene in acute myeloid leukemia carrying t(10,11), its definitive role in leukemia is unclear. In contrast to the frequent down-regulation (or loss-of-function mutations) and critical tumor-suppressor roles of the three TET genes observed in various types of cancers, here we show that TET1 is a direct target of MLL-fusion proteins and is significantly up-regulated in MLL -rearranged leukemia, leading to a global increase of 5-hydroxymethylcytosine level. Furthermore, our both in vitro and in vivo functional studies demonstrate that Tet1 plays an indispensable oncogenic role in the development of MLL -rearranged leukemia, through coordination with MLL-fusion proteins in regulating their critical cotargets, including homeobox A9 ( Hoxa9 )/myeloid ecotropic viral integration 1 ( Meis1 )/pre-B-cell leukemia homeobox 3 ( Pbx3 ) genes. Collectively, our data delineate an MLL-fusion/Tet1/Hoxa9/Meis1/Pbx3 signaling axis in MLL -rearranged leukemia and highlight TET1 as a potential therapeutic target in treating this presently therapy-resistant disease.
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- 2013
11. Critical role of miR-9 in myelopoiesis and EVI1-induced leukemogenesis
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Zhijian Qian, Yang Liu, Vitalyi Senyuk, Ping Chen, Ming Ming, Lan Zhou, Kavitha Premanand, Yunyuan Zhang, Janet D. Rowley, Giuseppina Nucifora, and Jianjun Chen
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Chromatin Immunoprecipitation ,Myeloid ,Biology ,medicine.disease_cause ,Colony-Forming Units Assay ,Mice ,Proto-Oncogenes ,medicine ,Animals ,Humans ,DNA Primers ,Myelopoiesis ,Multidisciplinary ,Forkhead Box Protein O1 ,Reverse Transcriptase Polymerase Chain Reaction ,Forkhead Box Protein O3 ,Neurogenesis ,Forkhead Transcription Factors ,Sequence Analysis, DNA ,DNA Methylation ,Biological Sciences ,Flow Cytometry ,Hematopoietic Stem Cells ,MDS1 and EVI1 Complex Locus Protein ,DNA-Binding Proteins ,MicroRNAs ,Haematopoiesis ,HEK293 Cells ,medicine.anatomical_structure ,Gene Expression Regulation ,DNA methylation ,NIH 3T3 Cells ,Cancer research ,Ectopic expression ,Stem cell ,Carcinogenesis ,Transcription Factors - Abstract
MicroRNA-9 (miR-9) is emerging as a critical regulator of organ development and neurogenesis. It is also deregulated in several types of solid tumors; however, its role in hematopoiesis and leukemogenesis is not yet known. Here we show that miR-9 is detected in hematopoietic stem cells and hematopoietic progenitor cells, and that its expression increases during hematopoietic differentiation. Ectopic expression of miR-9 strongly accelerates terminal myelopoiesis and promotes apoptosis in vitro and in vivo. Conversely, in hematopoietic progenitor cells, the inhibition of miR-9 with a miRNA sponge blocks myelopoiesis. Ecotropic viral integration site 1 (EVI1), required for normal embryogenesis, is considered an oncogene because its inappropriate up-regulation induces malignant transformation in solid and hematopoietic cancers. Here we show that EVI1 binds to the promoter of miR-9-3, leading to DNA hypermethylation of the promoter and repression of miR-9. Moreover, miR-9 expression reverses a myeloid differentiation block that is induced by EVI1. Our findings indicate that EVI1, when inappropriately expressed, delays or blocks myeloid differentiation at least in part by DNA hypermethylation and down-regulation of miR-9. It was reported that Forkhead box class O genes ( FoxO s) inhibit myeloid differentiation and prevent differentiation of leukemia-initiating cells. Here we identify both FoxO1 and FoxO3 as direct targets of miR-9 in hematopoietic cells and find that up-regulation of FoxO3 inhibits miR-9–induced myelopoiesis. These results reveal a unique role of miR-9 in myelopoiesis and in the pathogenesis of EVI1-induced myeloid neoplasms and provide insights into the epigenetic regulation of miR9 in tumorigenesis.
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- 2013
12. Identification of a 24-Gene Prognostic Signature That Improves the European LeukemiaNet Risk Classification of Acute Myeloid Leukemia: An International Collaborative Study
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Michael A. Caligiuri, Bob Löwenberg, Xinan Yang, Stefan K. Bohlander, Tobias Herold, Zejuan Li, Jianjun Chen, Ulrich Mansmann, Kati Maharry, Paul P. Liu, Mary Beth Neilly, Michael D. Radmacher, Konstanze Döhner, Yanming Zhang, Guido Marcucci, Peter J. M. Valk, Maria Cristina Sauerland, Janet D. Rowley, Clara D. Bloomfield, Ruud Delwel, Thomas Büchner, Richard A. Larson, Xi Jiang, Lars Bullinger, Michelle M. Le Beau, Vindi Jurinovic, Ping Chen, Miao Sun, Hao Huang, Wolfgang Hiddemann, Chunjiang He, Abdel G. Elkahloun, Hematology, and Rehabilitation Medicine
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Cancer Research ,Myeloid ,International Cooperation ,Kaplan-Meier Estimate ,Bioinformatics ,European LeukemiaNet ,Humans ,Medicine ,Proportional Hazards Models ,Microarray analysis techniques ,business.industry ,Proportional hazards model ,Gene Expression Profiling ,Myeloid leukemia ,ORIGINAL REPORTS ,Middle Aged ,Microarray Analysis ,Prognosis ,medicine.disease ,Gene expression profiling ,Leukemia, Myeloid, Acute ,Leukemia ,medicine.anatomical_structure ,Oncology ,Meta-analysis ,business - Abstract
Purpose To identify a robust prognostic gene expression signature as an independent predictor of survival of patients with acute myeloid leukemia (AML) and use it to improve established risk classification. Patients and Methods Four independent sets totaling 499 patients with AML carrying various cytogenetic and molecular abnormalities were used as training sets. Two independent patient sets composed of 825 patients were used as validation sets. Notably, patients from different sets were treated with different protocols, and their gene expression profiles were derived using different microarray platforms. Cox regression and Kaplan-Meier methods were used for survival analyses. Results A prognostic signature composed of 24 genes was derived from a meta-analysis of Cox regression values of each gene across the four training sets. In multivariable models, a higher sum value of the 24-gene signature was an independent predictor of shorter overall (OS) and event-free survival (EFS) in both training and validation sets (P < .01). Moreover, this signature could substantially improve the European LeukemiaNet (ELN) risk classification of AML, and patients in three new risk groups classified by the integrated risk classification showed significantly (P < .001) distinct OS and EFS. Conclusion Despite different treatment protocols applied to patients and use of different microarray platforms for expression profiling, a common prognostic gene signature was identified as an independent predictor of survival of patients with AML. The integrated risk classification incorporating this gene signature provides a better framework for risk stratification and outcome prediction than the ELN classification.
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- 2013
13. Chromosomal Translocations and Genome Rearrangements in Cancer
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Janet D. Rowley, Michelle M. Le Beau, Terence H. Rabbitts, Janet D. Rowley, Michelle M. Le Beau, and Terence H. Rabbitts
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- Cancer--Genetic aspects
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This volume collates world experts'insights into the molecular biology of cancer chromosomes, their abnormalities and the subsequent cellular consequences. Exploring themes involving oncogenes, such as by chromosomal translocations, other genome rearrangements and somatic mutations, this book is a review of the field of cancer genetics that presages a new era, as whole genome sequencing becomes more accessible.The work begins with a look at historical themes, such as the analysis of metaphase chromosomes using microscopy and staining techniques, advances in which provided our first broad glimpse into the genetic anatomy of a malignant cell. Readers will learn about the application of DNA molecular cloning techniques in the 1980s, that led to the identification of the genes involved in the Philadelphia and Burkitt's lymphoma chromosomal translocations, solidifying the role of oncogenes and tumour suppressor genes in cancer aetiology via chromosomal alterations and which launched a field in cancer genetics.Subsequent chapters bring the reader up to date by reviewing recent developments in the field, with dedicated sections on leukaemia/lymphoma, sarcomas and epithelial tumours.Contributions feature numerous colour tables and illustrations and this volume will provide a basis for understanding cancer chromosomes for many years to come.
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- 2015
14. Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically abnormal AML
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Zhiyu Zhang, Kati Maharry, Zejuan Li, Colles Price, Xi Jiang, Peter J. M. Valk, Lars Bullinger, Michael D. Radmacher, Janet D. Rowley, Konstanze Döhner, Yves A. Lussier, Miao He, Michelle M. Le Beau, Clara D. Bloomfield, Hao Huang, Xinan Yang, Richard A. Larson, Jianjun Chen, Yuanyuan Li, Stephen Arnovitz, Ruud Delwel, Chunjiang He, Abdel G. Elkahloun, Yanming Zhang, Ping Chen, Mary Beth Neilly, Paul P. Liu, Guido Marcucci, Michael A. Caligiuri, Bob Löwenberg, Rehabilitation Medicine, and Hematology
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Adult ,Male ,medicine.medical_specialty ,Adolescent ,Immunology ,Down-Regulation ,Kaplan-Meier Estimate ,Biology ,Biochemistry ,Young Adult ,Internal medicine ,Proto-Oncogene Proteins ,microRNA ,medicine ,Humans ,Child ,Aged ,Oligonucleotide Array Sequence Analysis ,Aged, 80 and over ,Homeodomain Proteins ,Hematology ,Myeloid Neoplasia ,Proportional hazards model ,Gene Expression Profiling ,Infant, Newborn ,Cancer ,Infant ,Cell Biology ,Middle Aged ,medicine.disease ,Prognosis ,Up-Regulation ,Gene expression profiling ,Leukemia ,MicroRNAs ,Leukemia, Myeloid ,Child, Preschool ,Acute Disease ,Cancer research ,Homeobox ,Ectopic expression ,Female - Abstract
Increased expression levels of miR-181 family members have been shown to be associated with favorable outcome in patients with cytogenetically normal acute myeloid leukemia. Here we show that increased expression of miR-181a and miR-181b is also significantly (P < .05; Cox regression) associated with favorable overall survival in cytogenetically abnormal AML (CA-AML) patients. We further show that up-regulation of a gene signature composed of 4 potential miR-181 targets (including HOXA7, HOXA9, HOXA11, and PBX3), associated with down-regulation of miR-181 family members, is an independent predictor of adverse overall survival on multivariable testing in analysis of 183 CA-AML patients. The independent prognostic impact of this 4-homeobox-gene signature was confirmed in a validation set of 271 CA-AML patients. Furthermore, our in vitro and in vivo studies indicated that ectopic expression of miR-181b significantly promoted apoptosis and inhibited viability/proliferation of leukemic cells and delayed leukemogenesis; such effects could be reversed by forced expression of PBX3. Thus, the up-regulation of the 4 homeobox genes resulting from the down-regulation of miR-181 family members probably contribute to the poor prognosis of patients with nonfavorable CA-AML. Restoring expression of miR-181b and/or targeting the HOXA/PBX3 pathways may provide new strategies to improve survival substantially.
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- 2012
15. Chronic Myeloid Leukemia: Current Perspectives
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Janet D. Rowley and Yanming Zhang
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ABL ,Biochemistry (medical) ,Clinical Biochemistry ,breakpoint cluster region ,Myeloid leukemia ,Imatinib ,Biology ,Philadelphia chromosome ,medicine.disease ,Myelogenous ,Leukemia ,Leukemia, Myelogenous, Chronic, BCR-ABL Positive ,hemic and lymphatic diseases ,Cytogenetic Analysis ,Cancer research ,medicine ,Humans ,Philadelphia Chromosome ,Epigenetics ,neoplasms ,In Situ Hybridization, Fluorescence ,medicine.drug - Abstract
Chronic myeloid leukemia (CML), characterized by the t(9;22) and BCR/ABL1 fusion, is a disease model for studying the mechanisms of genetic abnormalities in leukemogenesis. The detection of the t(9;22), characterization of the BCR/ABL fusion, and the discovery of imatinib have elegantly reflected the success of our research efforts in CML. However, genomic instabilities that lead to the formation of the BCR/ ABL1 fusion are not fully understood. It is important to understand how various genes that are involved in regulating the signaling pathway and epigenetic deregulation cooperate with the BCR/ABL1 fusion in the initiation and progression of CML.
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- 2011
16. Philadelphia Chromosome Symposium: commemoration of the 50th anniversary of the discovery of the Ph chromosome
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Alice Hungerford, H. Sharat Chandra, Joseph R. Testa, Peter C. Nowell, Jennifer J.D. Morrissette, Nora Heisterkamp, and Janet D. Rowley
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Genetics ,Cancer Research ,Ph chromosome ,medicine.medical_specialty ,ABL ,Cytogenetics ,breakpoint cluster region ,Imatinib ,Chromosomal translocation ,Biology ,Philadelphia chromosome ,medicine.disease ,Article ,humanities ,Genealogy ,Imatinib mesylate ,medicine ,Molecular Biology ,medicine.drug - Abstract
This report summarizes highlights of the ‘Philadelphia Chromosome Symposium: Past, Present and Future’, held September 28, 2010, to commemorate the 50th anniversary of the discovery of the Philadelphia chromosome. The symposium sessions included presentations by investigators who made seminal contributions concerning the discovery and molecular characterization of the Ph chromosome and others who developed a highly successful therapy based on the specific molecular alteration observed in chronic myelogenous leukemia. Additional presentations highlighted future opportunities for the design of molecularly targeted therapies for various types of cancer. Also included here are reminiscences connected with the discovery of the Ph chromosome by David Hungerford and Peter Nowell, the discovery that the abnormality arises from a chromosomal translocation, by Janet Rowley, and the cloning of the 9;22 translocation breakpoints by Nora Heisterkamp, John Groffen and colleagues.
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- 2011
17. Aberrant overexpression and function of the miR-17-92 cluster in MLL -rearranged acute leukemia
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Janet D. Rowley, Paul P. Liu, Luis A. Pelloso, Miao He, Donglin Cao, Roger T. Luo, Zejuan Li, Mark Wunderlich, Shuangli Mi, Jianjun Chen, Miao Sun, Chunjiang He, Abdel G. Elkahloun, Nancy J. Zeleznik-Le, Mary Beth Neilly, Ping Chen, Jun Lu, Hao Huang, James C. Mulloy, and Michael J. Thirman
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Regulation of gene expression ,Multidisciplinary ,Gene Expression Regulation, Leukemic ,Cell growth ,Cellular differentiation ,Biological Sciences ,Cell cycle ,Biology ,Molecular biology ,Epigenesis, Genetic ,Fusion gene ,Leukemia, Myeloid, Acute ,Mice ,MicroRNAs ,Haematopoiesis ,Cell Line, Tumor ,Multigene Family ,hemic and lymphatic diseases ,microRNA ,Cancer research ,Animals ,Humans ,Histone H3 acetylation ,HeLa Cells - Abstract
MicroRNA (miRNA)- 17-92 cluster (miR-17-92), containing seven individual miRNAs, is frequently amplified and overexpressed in lymphomas and various solid tumors. We have found that it is also frequently amplified and the miRNAs are aberrantly overexpressed in mixed lineage leukemia ( MLL )-rearranged acute leukemias. Furthermore, we show that MLL fusions exhibit a much stronger direct binding to the locus of this miRNA cluster than does wild-type MLL; these changes are associated with elevated levels of histone H3 acetylation and H3K4 trimethylation and an up-regulation of these miRNAs. We further observe that forced expression of this miRNA cluster increases proliferation and inhibits apoptosis of human cells. More importantly, we show that this miRNA cluster can significantly increase colony-forming capacity of normal mouse bone marrow progenitor cells alone and, particularly, in cooperation with MLL fusions. Finally, through combinatorial analysis of miRNA and mRNA arrays of mouse bone marrow progenitor cells transfected with this miRNA cluster and/or MLL fusion gene, we identified 363 potential miR-17-92 target genes that exhibited a significant inverse correlation of expression with the miRNAs. Remarkably, these potential target genes are significantly enriched ( P < 0.01; >2-fold) in cell differentiation, hematopoiesis, cell cycle, and apoptosis. Taken together, our studies suggest that overexpression of miR-17-92 cluster in MLL -rearranged leukemias is likely attributed to both DNA copy number amplification and direct up-regulation by MLL fusions, and that the miRNAs in this cluster may play an essential role in the development of MLL -associated leukemias through inhibiting cell differentiation and apoptosis, while promoting cell proliferation, by regulating relevant target genes.
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- 2010
18. Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias
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Michael J. Thirman, Nimanthi Jayathilaka, Roger T. Luo, Catherine Lavau, Jun Yu, Charles C. Tseng, Yanming Zhang, Jingyue Bao, Xiuqing Zhang, Lili Wang, Zejuan Li, Huanming Yang, Jian Wang, Ping Chen, Jianjun Chen, Janet D. Rowley, Miao Sun, San Ming Wang, Shuangli Mi, Deborah S. Johnson, and Mary Beth Neilly
- Subjects
Cancer Research ,Oncogene Proteins, Fusion ,Biology ,Polymerase Chain Reaction ,Article ,Mice ,hemic and lymphatic diseases ,medicine ,Animals ,Humans ,Serial analysis of gene expression ,Hox gene ,neoplasms ,Myeloid Progenitor Cells ,Gene Rearrangement ,Regulation of gene expression ,Genetics ,Gene Expression Regulation, Leukemic ,Gene Expression Profiling ,Histone-Lysine N-Methyltransferase ,Gene rearrangement ,DNA Methylation ,medicine.disease ,Gene expression profiling ,MicroRNAs ,Leukemia ,Oncology ,Leukemia, Myeloid ,DNA methylation ,Cancer research ,Myeloid-Lymphoid Leukemia Protein - Abstract
Important biological and pathologic properties are often conserved across species. Although several mouse leukemia models have been well established, the genes deregulated in both human and murine leukemia cells have not been studied systematically. We performed a serial analysis of gene expression in both human and murine MLL-ELL or MLL-ENL leukemia cells and identified 88 genes that seemed to be significantly deregulated in both types of leukemia cells, including 57 genes not reported previously as being deregulated in MLL-associated leukemias. These changes were validated by quantitative PCR. The most up-regulated genes include several HOX genes (e.g., HOX A5, HOXA9, and HOXA10) and MEIS1, which are the typical hallmark of MLL rearrangement leukemia. The most down-regulated genes include LTF, LCN2, MMP9, S100A8, S100A9, PADI4, TGFBI, and CYBB. Notably, the up-regulated genes are enriched in gene ontology terms, such as gene expression and transcription, whereas the down-regulated genes are enriched in signal transduction and apoptosis. We showed that the CpG islands of the down-regulated genes are hypermethylated. We also showed that seven individual microRNAs (miRNA) from the mir-17-92 cluster, which are overexpressed in human MLL rearrangement leukemias, are also consistently overexpressed in mouse MLL rearrangement leukemia cells. Nineteen possible targets of these miRNAs were identified, and two of them (i.e., APP and RASSF2) were confirmed further by luciferase reporter and mutagenesis assays. The identification and validation of consistent changes of gene expression in human and murine MLL rearrangement leukemias provide important insights into the genetic base for MLL-associated leukemogenesis. [Cancer Res 2009;69(3):OF1109–16]
- Published
- 2009
19. Distinct microRNA expression profiles in acute myeloid leukemia with common translocations
- Author
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Hao Zhang, Shuangli Mi, Dong-Er Zhang, Yungui Wang, Jianjun Chen, Michelle M. Le Beau, Stefan K. Bohlander, Roger T. Luo, Jie Jin, Todd R. Golub, Miao Sun, Ming Yan, Michael J. Thirman, Ping Chen, Janet D. Rowley, Zejuan Li, Mary Beth Neilly, Yanming Zhang, Richard A. Larson, Zhijian Qian, and Jun Lu
- Subjects
Myeloid ,Cell Survival ,Apoptosis ,Chromosomal translocation ,Protein Serine-Threonine Kinases ,Biology ,Translocation, Genetic ,Mice ,chemistry.chemical_compound ,hemic and lymphatic diseases ,microRNA ,medicine ,Animals ,Humans ,neoplasms ,Multidisciplinary ,Gene Expression Profiling ,Core Binding Factors ,RUNX1T1 ,Myeloid leukemia ,Biological Sciences ,medicine.disease ,Molecular biology ,Gene expression profiling ,Leukemia, Myeloid, Acute ,MicroRNAs ,Leukemia ,medicine.anatomical_structure ,RUNX1 ,chemistry ,Mutation - Abstract
MicroRNAs (miRNAs) are postulated to be important regulators in cancers. Here, we report a genome-wide miRNA expression analysis in 52 acute myeloid leukemia (AML) samples with common translocations, including t(8;21)/ AML1(RUNX1)-ETO(RUNX1T1) , inv( 16 )/ CBFB-MYH11 , t(15;17)/ PML-RARA , and MLL rearrangements. Distinct miRNA expression patterns were observed for t(15;17), MLL rearrangements, and core-binding factor (CBF) AMLs including both t(8;21) and inv( 16 ) samples. Expression signatures of a minimum of two (i.e., miR-126/126*), three (i.e., miR-224, miR-368, and miR-382), and seven (miR-17–5p and miR-20a, plus the aforementioned five) miRNAs could accurately discriminate CBF, t(15;17), and MLL -rearrangement AMLs, respectively, from each other. We further showed that the elevated expression of miR-126/126* in CBF AMLs was associated with promoter demethylation but not with amplification or mutation of the genomic locus. Our gain- and loss-of-function experiments showed that miR-126/126* inhibited apoptosis and increased the viability of AML cells and enhanced the colony-forming ability of mouse normal bone marrow progenitor cells alone and particularly, in cooperation with AML1-ETO , likely through targeting Polo-like kinase 2 ( PLK2 ), a tumor suppressor. Our results demonstrate that specific alterations in miRNA expression distinguish AMLs with common translocations and imply that the deregulation of specific miRNAs may play a role in the development of leukemia with these associated genetic rearrangements.
- Published
- 2008
20. Comparative gene mapping in cattle, Indian muntjac, and Chinese muntjac by fluorescence in situ hybridization
- Author
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Andrea E. Murmann, Pamela L. Strissel, Fentang Yang, Peter Lichter, Johannes Buitkamp, Antoaneta Mincheva, Markus O. Scheuermann, Reiner Strick, Janet D. Rowley, and Mathieu Gautier
- Subjects
Male ,Chromosomes, Artificial, Bacterial ,Plant Science ,Chromosomes ,Evolution, Molecular ,Muntjacs ,03 medical and health sciences ,Gene mapping ,Centromere ,Genetics ,medicine ,Animals ,Humans ,In Situ Hybridization, Fluorescence ,030304 developmental biology ,Synteny ,Genomic organization ,0303 health sciences ,biology ,medicine.diagnostic_test ,030305 genetics & heredity ,Chromosome Mapping ,Karyotype ,General Medicine ,biology.organism_classification ,Karyotyping ,Insect Science ,Muntiacus reevesi ,Cattle ,Female ,Animal Science and Zoology ,Muntjac ,Fluorescence in situ hybridization - Abstract
The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n = 6 in the female and 2n = 7 in the male. The karyotypic evolution of Indian muntjac via extensive tandem fusions and several centric fusions are well documented by molecular cytogenetic studies mainly utilizing chromosome paints. To achieve higher resolution mapping, a set of 42 different genomic clones coding for 37 genes and the nucleolar organizer region were used to examine homologies between the cattle (2n = 60), human (2n = 46), Indian muntjac (2n = 6/7) and Chinese muntjac (2n = 46) karyotypes. These genomic clones were mapped by fluorescence in situ hybridization (FISH). Localization of genes on all three pairs of M. m. vaginalis chromosomes and on the acrocentric chromosomes of M. reevesi allowed not only the analysis of the evolution of syntenic regions within the muntjac genus but also allowed a broader comparison of synteny with more distantly related species, such as cattle and human, to shed more light onto the evolving genome organization.
- Published
- 2008
21. Cytogenetic studies in patients with hairy cell leukemia
- Author
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Janet D. Rowley, Yoshimi Ueshima, Giuliana Alimena, and Harvey M. Golomb
- Subjects
Chromosome Aberrations ,Leukemia, Hairy Cell ,Cancer Research ,Pathology ,medicine.medical_specialty ,Cytogenetics ,Chromosome ,Chromosome Disorders ,Karyotype ,Hematology ,General Medicine ,Biology ,medicine.disease ,Leukemia, Lymphoid ,medicine.anatomical_structure ,Oncology ,Bone Marrow ,Karyotyping ,medicine ,Chromosome abnormality ,Humans ,In patient ,Hairy cell leukemia ,Bone marrow ,Metaphase - Abstract
We performed cytogenetic studies on 58 patients with hairy cell leukemia (HCL) from 1975 to 1981. Analysable metaphase cells stained with Q-banding were obtained in 77 samples from 44 patients. Cells with abnormal chromosomes were found in both unstimulated and stimulated cultures of bone marrow and peripheral blood. Patients were classified in 6 groups. Group I, 2 patients with a clonal chromosome abnormality; group II, 13 patients with nonclonal structural abnormalities; group III, 5 patients with nonclonal numerical abnormalities; group IV, 19 patients with only a normal karyotype; group V, 15 patients with no or with fewer than 5 normal metaphase cells; group VI, 4 patients with questionable abnormal chromosomes. Common abnormalities were deletion of the long arm of No. 6 or +3 each in 3 patients, and +Y, +12 or +18 in 2 patients. Actuarial survival for each group was calculated from diagnosis and also from chromosome examination. The two patients with a clonal chromosome abnormality died within one year. Eight of 13 patients with nonclonal structural abnormalities died within 5 years after diagnosis, while none of 5 patients with nonclonal numerical abnormalities and 2 of 19 patients with normal chromosomes died within 5 years. The difference in the 5-year actuarial survival between patients with nonclonal abnormalities (groups II and III) and those with a normal karyotype was significant (p less than 0.05). The difference was more marked between patients with nonclonal structural abnormalities and those with a normal karyotype (p less than 0.01). Patients with nonclonal numerical abnormalities had a longer survival than those patients with nonclonal structural abnormalities (p less than 0.05). Thus, structural chromosome abnormalities in HCL may be a poor prognostic sign even when they are not clonal.
- Published
- 2007
22. Cytogenetic and molecular study of the PRDX4 gene in a t(X;18)(p22;q23): a cautionary tale
- Author
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Yanming Zhang, Elizabeth M. Davis, Janet D. Rowley, Brigitte Schlegelberger, Heidrun D. Gerr, Michele L. Nassin, Mary E. Neilly, and Nimanthi Jayathilaka
- Subjects
Adult ,Cancer Research ,Oncogene Proteins, Fusion ,Chromosomal translocation ,Biology ,Translocation, Genetic ,Article ,PRDX4 Gene ,Chromosome 18 ,Gene Duplication ,Gene duplication ,Genetics ,medicine ,Humans ,Gene family ,Molecular Biology ,X chromosome ,Chromosomes, Human, X ,medicine.diagnostic_test ,Myeloid leukemia ,Peroxiredoxins ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Molecular biology ,Core Binding Factor Alpha 2 Subunit ,Cytogenetic Analysis ,Female ,Chromosomes, Human, Pair 18 ,Fluorescence in situ hybridization - Abstract
The PRDX4 gene located at Xp22 codes for a member of the peroxiredoxin gene family. Genes within this family exhibit thioredoxin-dependent peroxidase activity and have been implicated in cellular functioning, including proliferation and differentiation. Recently, PRDX4 has been identified as a partner gene in an X;21 translocation in a patient with acute myeloid leukemia (AML). To determine whether PRDX4 was involved in other translocations, leukemia cells from fifteen patients with Xp22 abnormalities were screened for the gene’s involvement using fluorescence in situ hybridization (FISH). One sample from a 41 year old female with acute lymphoblastic leukemia (ALL) showed three signals when hybridized with the PRDX4 probe. Cytogenetic analysis of the sample had identified a t(X;18)(p22,q23). Assuming that the three signals indicated a break within the PRDX4 gene, we performed FISH experiments and successfully narrowed the breakpoint on chromosome 18 to a 50 kB region. Subsequent analysis using spectral karyotyping showed that the leukemic cells had undergone multiple rearrangements and that a third X chromosome, albeit rearranged, was present. Additional FISH experiments revealed that the third PRDX4 signal was the result of a third copy of the gene. Analysis of the other rearrangements has helped to characterize the multiple abnormalities within the leukemic cells. Our findings are significant because they underline the importance of using multiple techniques when analyzing complex chromosomal rearrangements in malignant cells.
- Published
- 2007
23. Methylation-Independent Silencing of the Tumor Suppressor INK4b (p15) by CBFβ-SMMHC in Acute Myelogenous Leukemia with inv(16)
- Author
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Michelle M. Le Beau, Azra Raza, Janet D. Rowley, Matthew T. Garin, Jan Markus, Pengfei Liu, Michael J. Thirman, Juraj Bies, Naomi Galili, and Linda Wolff
- Subjects
Transcriptional Activation ,Cancer Research ,Tumor suppressor gene ,Biology ,Core Binding Factor beta Subunit ,chemistry.chemical_compound ,Myelogenous ,hemic and lymphatic diseases ,medicine ,Humans ,Gene silencing ,Gene Silencing ,RNA, Neoplasm ,Epigenetics ,Promoter Regions, Genetic ,Cyclin-Dependent Kinase Inhibitor p15 ,Myosin Heavy Chains ,Methylation ,DNA Methylation ,medicine.disease ,Leukemia, Myeloid, Acute ,Leukemia ,Oncology ,RUNX1 ,chemistry ,Chromosome Inversion ,Core Binding Factor Alpha 2 Subunit ,DNA methylation ,Immunology ,Cancer research ,Chromosomes, Human, Pair 6 - Abstract
The tumor suppressor gene INK4b (p15) is silenced by CpG island hypermethylation in most acute myelogenous leukemias (AML), and this epigenetic phenomenon can be reversed by treatment with hypomethylating agents. Thus far, it was not investigated whether INK4b is hypermethylated in all cytogenetic subtypes of AML. A comparison of levels of INK4b methylation in AML with the three most common cytogenetic alterations, inv(16), t(8;21), and t(15;17), revealed a strikingly low level of methylation in all leukemias with inv(16) compared with the other types. Surprisingly, the expression level of INK4b in inv(16)+ AML samples was low and comparable with that of the other subtypes. An investigation into an alternative mechanism of INK4b silencing determined that the loss of INK4b expression was caused by inv(16)-encoded core binding factor β-smooth muscle myosin heavy chain (CBFβ-SMMHC). The silencing was manifested in an inability to activate the normal expression of INK4b RNA as shown in vitamin D3–treated U937 cells expressing CBFβ-SMMHC. CBFβ-SMMHC was shown to displace RUNX1 from a newly determined CBF site in the promoter of INK4b. Importantly, this study (a) establishes that the gene encoding the tumor suppressor p15INK4b is a target of CBFβ-SMMHC, a finding relevant to the leukemogenesis process, and (b) indicates that, in patients with inv(16)-containing AML, reexpression from the INK4b locus in the leukemia would not be predicted to occur using hypomethylating drugs. [Cancer Res 2007;67(3):992–1000]
- Published
- 2007
24. Jake, Leon O. Jacobson, M.D.: The Life and Work of a Distinguished Medical Scientist (review)
- Author
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Janet D. Rowley
- Subjects
Gerontology ,Issues, ethics and legal aspects ,History and Philosophy of Science ,Work (electrical) ,Health Policy ,Philosophy ,Art history ,General Medicine - Published
- 2007
25. Local gene density predicts the spatial position of genetic loci in the interphase nucleus
- Author
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Marcus E. Peter, Mathieu Gautier, Andrea E. Murmann, Juntao Gao, Roland Eils, Peter Lichter, Janet D. Rowley, and Marissa Encinosa
- Subjects
Male ,Oncogene Proteins, Fusion ,Bone Marrow Cells ,Locus (genetics) ,Chromosomal translocation ,Biology ,Translocation, Genetic ,Muntjacs ,Fusion gene ,03 medical and health sciences ,0302 clinical medicine ,Gene density ,Gene cluster ,medicine ,Animals ,Humans ,Interphase ,Gene ,In Situ Hybridization, Fluorescence ,030304 developmental biology ,Cell Nucleus ,Chromosome Aberrations ,Genetics ,0303 health sciences ,Histone-Lysine N-Methyltransferase ,Cell Biology ,Cell nucleus ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Female ,Nucleus ,Myeloid-Lymphoid Leukemia Protein - Abstract
Specific chromosomal translocations are hallmarks of many human leukemias. The basis for these translocation events is poorly understood, but it has been assumed that spatial positioning of genes in the nucleus of hematopoietic cells is a contributing factor. Analysis of the nuclear 3D position of the gene MLL, frequently involved in chromosomal translocations and five of its translocation partners (AF4, AF6, AF9, ENL and ELL), and two control loci revealed a characteristic radial distribution pattern in all hematopoietic cells studied. Genes in areas of high local gene density were found positioned towards the nuclear center, whereas genes in regions of low gene density were detected closer to the nuclear periphery. The gene density within a 2 Mbp window was found to be a better predictor for the relative positioning of a genomic locus within the cell nucleus than the gene density of entire chromosomes. Analysis of the position of MLL, AF4, AF6 and AF9 in cell lines carrying chromosomal translocations involving these genes revealed that the position of the normal genes was different from that of the fusion genes, and this was again consistent with the changes in local gene density within a 2 Mbp window. Thus, alterations in gene density directly at translocation junctions could explain the change in the position of affected genes in leukemia cells.
- Published
- 2005
26. Deficiency of Bruton's tyrosine kinase in B cell precursor leukemia cells
- Author
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Hassan Jumaa, Janet D. Rowley, Florian Klein, Stefanie Liedtke, Peter Wernet, Paula Río, Mieke Sprangers, Niklas Feldhahn, Wolf-Karsten Hofmann, Helmut Hanenberg, Bonaventure Ndikung Bejeng Soh, and Markus Müschen
- Subjects
Cell Survival ,Somatic cell ,Cellular differentiation ,Molecular Sequence Data ,Cell ,Apoptosis ,immune system diseases ,Precursor B-Cell Lymphoblastic Leukemia-Lymphoma ,hemic and lymphatic diseases ,Agammaglobulinaemia Tyrosine Kinase ,Tumor Cells, Cultured ,medicine ,Humans ,Bruton's tyrosine kinase ,B cell ,Gene Rearrangement ,Multidisciplinary ,Base Sequence ,biology ,Cell Differentiation ,Gene rearrangement ,Protein-Tyrosine Kinases ,Biological Sciences ,medicine.disease ,Alternative Splicing ,Leukemia ,medicine.anatomical_structure ,Gamma Rays ,Mutation ,biology.protein ,Cancer research ,Tyrosine kinase - Abstract
Bruton's tyrosine kinase (BTK) deficiency results in a differentiation block at the pre-B cell stage. Likewise, acute lymphoblastic leukemia cells are typically arrested at early stages of B cell development. We therefore investigated BTK function in B cell precursor leukemia cells carrying a BCR-ABL1, E2A-PBX1, MLL-AF4, TEL-AML1 , or TEL-PDGFRB gene rearrangement. Although somatic mutations of the BTK gene are rare in B cell precursor leukemia cells, we identified kinase-deficient splice variants of BTK throughout all leukemia subtypes. Unlike infant leukemia cells carrying an MLL-AF4 gene rearrangement, where expression of full-length BTK was detectable in only four of eight primary cases, in leukemia cells harboring other fusion genes full-length BTK was typically coexpressed with kinase-deficient variants. As shown by overexpression experiments, kinase-deficient splice variants can act as a dominant-negative BTK in that they suppress BTK-dependent differentiation and pre-B cell receptor responsiveness of the leukemia cells. On the other hand, induced expression of full-length BTK rendered the leukemia cells particularly sensitive to apoptosis. Comparing BTK expression in surviving or preapoptotic leukemia cells after 10-Gy γ radiation, we observed selective survival of leukemia cells that exhibit expression of dominant-negative BTK forms. These findings indicate that lack of BTK expression or expression of dominant-negative splice variants in B cell precursor leukemia cells can ( i ) inhibit differentiation beyond the pre-B cell stage and ( ii ) protect from radiation-induced apoptosis.
- Published
- 2005
27. Characterization of genomic breakpoints inMLL andCBP in leukemia patients with t(11;16)
- Author
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Yasuhiko Kaneko, Pamela L. Strissel, Janet D. Rowley, Yasuhide Hayashi, Yanming Zhang, Nancy J. Zeleznik-Le, Jianjun Chen, Brigitte Schlegelberger, Tomohiko Taki, Nimanthi Jayathilaka, Loretta S. Li, Reiner Strick, Mary Beth Neilly, and Neelmini Emmanuel
- Subjects
Male ,Cancer Research ,Molecular Sequence Data ,Alu element ,Biology ,Polymerase Chain Reaction ,Translocation, Genetic ,Fusion gene ,Cell Line, Tumor ,hemic and lymphatic diseases ,Proto-Oncogenes ,Genetics ,Humans ,Child ,Repeated sequence ,Gene ,Aged ,DNA Primers ,Genome ,Base Sequence ,Models, Genetic ,Chromosomes, Human, Pair 11 ,Breakpoint ,Intron ,breakpoint cluster region ,Computational Biology ,Nuclear Proteins ,DNA ,Histone-Lysine N-Methyltransferase ,Molecular biology ,Introns ,DNA-Binding Proteins ,Leukemia, Myeloid, Acute ,Child, Preschool ,Trans-Activators ,Myeloid-Lymphoid Leukemia Protein ,Female ,Chromosomes, Human, Pair 16 ,Transcription Factors - Abstract
The recurring chromosome translocation t(11;16)(q23;p13) is detected in leukemia patients, virtually all of whom have received previous chemotherapy with topoisomerase (topo) II inhibitors. In the t(11;16), 3' CBP, on 16p13, is fused to 5' MLL, on 11q23, resulting in an MLL-CBP fusion gene that plays an important role in leukemogenesis. In this study, we cloned genomic breakpoints of the MLL and CBP genes in the t(11;16) in the SN-1 cell line and in five patients with therapy-related leukemia, all of whom had received topo II inhibitors for previous tumors. In all patients except one, both the genomic MLL-CBP and the reciprocal fusions were cloned. Genomic breakpoints in MLL occurred in the 8.3-kb breakpoint cluster region in all patients, whereas the breakpoints in CBP clustered in an 8.2-kb region of intron 3 in four patients. Genomic breakpoints in MLL occurred in intron 11 near the topo II cleavage site in the SN-1 cell line and in one patient, and they were close to LINE repetitive sequences in two other patients. In the remaining two patients, genomic breakpoints were in intron 9 in Alu repeats. Genomic breakpoints in CBP occurred in and around Alu repeats in one and two patients, respectively. In two patients, the breaks were near LINE repetitive sequences, suggesting that repetitive DNA sequences may play a role. No specific recombination motifs were identified at or near the breakpoint junctions. No topo II cleavage sites were detected in introns 2 and 3 of CBP. However, there were deletions and duplications at the breakpoints in both MLL and CBP and microhomologies or nontemplated nucleotides at most of the genomic fusion junctions, suggesting that a nonhomologous end-joining repair mechanism was involved in the t(11;16).
- Published
- 2004
28. PRDX4, a member of the peroxiredoxin family, is fused toAML1 (RUNX1) in an acute myeloid leukemia patient with a t(X;21)(p22;q22)
- Author
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Ginny Kamboj, Daniel L. Van Dyke, Anne E. Wiktor, Muhammad Shurafa, Neelmini Emmanuel, Janet D. Rowley, Jianjun Chen, and Yanming Zhang
- Subjects
Male ,Acute promyelocytic leukemia ,Reading Frames ,Cancer Research ,Oncogene Proteins, Fusion ,Chromosomes, Human, Pair 21 ,Molecular Sequence Data ,Chromosomal translocation ,Biology ,Polymerase Chain Reaction ,Translocation, Genetic ,Exon ,chemistry.chemical_compound ,Proto-Oncogene Proteins ,hemic and lymphatic diseases ,Genetics ,medicine ,Humans ,Aged ,Chromosomes, Human, X ,Base Sequence ,Alternative splicing ,Myeloid leukemia ,Exons ,Peroxiredoxins ,medicine.disease ,Molecular biology ,Neoplasm Proteins ,DNA-Binding Proteins ,Leukemia, Myeloid, Acute ,Leukemia ,Peroxidases ,RUNX1 ,chemistry ,Karyotyping ,Core Binding Factor Alpha 2 Subunit ,Cytogenetic Analysis ,Peroxiredoxin ,Transcription Factors - Abstract
The AML1 gene (also known as RUNX1) at 21q22 codes for core binding factor (CBF) α, which forms a heterodimer with CBF β that acts as a transcriptional activating factor. CBF is a critical regulator in the generation and differentiation of definitive hematopoietic stem cells and is frequently disrupted in leukemia through chromosome translocations. We cloned a novel AML1 partner gene, PRDX4, in an X;21 translocation in a 74-year-old male patient diagnosed with acute myeloid leukemia–M2. Chromosome analysis detected a t(X;21)(p22;q22) as the sole abnormality in bone marrow samples. The involvement of AML1 was confirmed by fluorescence in situ hybridization studies. Using 3′ RACE-PCR, we cloned a fusion between exon 5 of AML1 and exon 2 of PRDX4. RT-PCR confirmed the fusion and detected another fusion between exon 6 of AML1 and exon 2 of PRDX4, indicating alternative splicing of exon 6 of AML1 in the fusion transcripts. PRDX4 is one of six peroxiredoxin-family genes that are highly conserved in eukaryotes and prokaryotes and are ubiquitously expressed. Peroxiredoxin genes exhibit thioredoxin-dependent peroxidase activity and have been implicated in a number of other cellular functions such as cell proliferation and differentiation. PRDX4 plays a regulatory role in the activation of the transcription factor NF-κB and is significantly down-regulated in acute promyelocytic leukemia. This is the first example of antioxidant enzyme involvement in a chromosome translocation in leukemia. © 2004 Wiley-Liss, Inc.
- Published
- 2004
29. Analysis of translocations that involve theNUP98 gene in patients with 11p15 chromosomal rearrangements
- Author
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Janet D. Rowley, Jose A. Martinez-Climent, Sanggyu Lee, Yuri Kobzev, and Jianjun Chen
- Subjects
Adult ,Male ,Cancer Research ,medicine.medical_specialty ,Adolescent ,Molecular Sequence Data ,Chromosomal translocation ,Biology ,Translocation, Genetic ,Complementary DNA ,Internal medicine ,Genetics ,medicine ,Guanine Nucleotide Exchange Factors ,Humans ,Genetic Predisposition to Disease ,Gene ,In Situ Hybridization, Fluorescence ,Homeodomain Proteins ,NUP98 Gene ,Leukemia ,Hematology ,Base Sequence ,medicine.diagnostic_test ,Chromosomes, Human, Pair 11 ,Breakpoint ,Infant ,Molecular biology ,Nuclear Pore Complex Proteins ,DNA Topoisomerases, Type I ,HOXD13 ,Child, Preschool ,Transcription Factors ,Fluorescence in situ hybridization - Abstract
The NUP98 gene has been reported to be fused with at least 15 partner genes in leukemias with 11p15 translocations. We report the results of screening of cases with cytogenetically documented rearrangements of 11p15 and the subsequent identification of involvement of NUP98 and its partner genes. We identified 49 samples from 46 hematology patients with 11p15 (including a few with 11p14) abnormalities, and using fluorescence in situ hybridization (FISH), we found that NUP98 was disrupted in 7 cases. With the use of gene-specific FISH probes, in 6 cases, we identified the partner genes, which were PRRX1 (PMX1; in 2 cases), HOXD13, RAP1GDS1, HOXC13, and TOP1. In the 3 cases for which RNA was available, RT-PCR was performed, which confirmed the FISH results and identified the location of the breakpoints in patient cDNA. Our data confirm the previous findings that NUP98 is a recurrent target in various types of leukemia.
- Published
- 2004
30. Screening and Quantification of Multiple Chromosome Translocations in Human Leukemia
- Author
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Joseph Morrissey, Janet D. Rowley, and Run Zhang Shi
- Subjects
Leukemia ,Microarray ,Reverse Transcriptase Polymerase Chain Reaction ,Biochemistry (medical) ,Clinical Biochemistry ,Biology ,Molecular biology ,Translocation, Genetic ,law.invention ,Reverse transcription polymerase chain reaction ,Fusion gene ,law ,Multiplex polymerase chain reaction ,Tumor Cells, Cultured ,Humans ,Multiplex ,DNA microarray ,Gene ,Polymerase chain reaction ,Oligonucleotide Array Sequence Analysis - Abstract
Background: Characterization of fusion gene transcripts in leukemia that result from chromosome translocations provides valuable information regarding appropriate treatment and prognosis. However, screening for multiple fusion gene transcripts is difficult with conventional PCR and state-of-the-art real-time PCR and high-density microarrays. Methods: We developed a multiplex reverse transcription-PCR (RT-PCR) assay for screening and quantification of fusion gene transcripts in human leukemia cells. Chimeric primers were used that contained gene-specific and universal sequences. PCR amplification of fusion and control gene transcripts was achieved with use of an excess of universal primers to allow the ratio of abundance of fusion gene to endogenous or exogenous controls to be maintained throughout PCR. Multiplex RT-PCR products analyzed by an ABI 310 Genetic Analyzer were consistent with those of duplex RT-PCR (single analytical sample plus control). In addition, multiplex RT-PCR results were analyzed by an assay using an oligonucleotide microarray that contained probes for the splice-junction sequences of various fusion transcripts. Results: The multiplex RT-PCR assay enabled screening of >10 different fusion gene transcripts in a single reaction. RT-PCR followed by analysis with the ABI Prism 310 Genetic Analyzer consistently detected 1 fusion-transcript-carrying leukemia cell in 100–10 000 cells. The assay covered a 1000-fold range. Preliminary results indicate that multiplex RT-PCR products can also be analyzed by hybridization-based microarray assay. Conclusions: The multiplex RT-PCR analyzed by either ABI Prism 310 Genetic Analyzer or microarray provides a sensitive and specific assay for screening of multiple fusion transcripts in leukemia, with the latter an assay that is adaptable to a high-throughput system for clinical screening.
- Published
- 2003
31. A t(11;15) fuses MLL to two different genes, AF15q14 and a novel gene MPFYVE on chromosome 15
- Author
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Janet D. Rowley, María D. Odero, Andy S. Chien, Nancy J. Zeleznik-Le, Vandana Chinwalla, and Mary Beth Neilly
- Subjects
Male ,Cancer Research ,DNA, Complementary ,Oncogene Proteins, Fusion ,Acute myeloblastic leukemia ,Amino Acid Motifs ,Molecular Sequence Data ,Chromosomal translocation ,Biology ,Translocation, Genetic ,Chromosome 15 ,hemic and lymphatic diseases ,Genetics ,medicine ,Humans ,Amino Acid Sequence ,Child ,neoplasms ,Molecular Biology ,Gene ,In Situ Hybridization, Fluorescence ,Expressed Sequence Tags ,Oncogene Proteins ,Chromosomes, Human, Pair 15 ,Base Sequence ,Sequence Homology, Amino Acid ,Chromosomes, Human, Pair 11 ,Proteins ,medicine.disease ,Fusion protein ,Molecular biology ,Protein Structure, Tertiary ,Leukemia, Myeloid, Acute ,Leukemia ,Fusion transcript ,FYVE domain ,Sequence Alignment ,Myeloid-Lymphoid Leukemia Protein - Abstract
The mixed lineage leukemia gene (MLL, also known as HRX, ALL-1 and Htrx) located at 11q23 is involved in translocations with over 40 different chromosomal bands in a variety of leukemia subtypes. Here we report our analysis of a rare but recurring translocation, t(11;15)(q23;q14). This translocation has been described in a small subset of cases with both acute myeloblastic leukemia and ALL. Recent studies have shown that MLL is fused to AF15q14 in the t(11;15). Here we analyse a sample from another patient with this translocation and confirm the presence of an MLL-AF15q14 fusion. However, we have also identified and cloned another fusion transcript from the same patient sample. In this fusion transcript, MLL is fused to a novel gene, MLL partner containing FYVE domain (MPFYVE). Both MLL-AF15q14 and MLL-MPFYVE are in-frame fusion transcripts with the potential to code for novel fusion proteins. MPFYVE is also located on chromosome 15, approximately 170 kb telomeric to AF15q14. MPFYVE contains a highly conserved motif, the FYVE domain which, in other proteins, has been shown to bind to phosphotidyl-inositol-3 phosphate (PtdIns(3)P). The MLL-MPFYVE fusion may be functionally important in the leukemia process in at least some patients containing this translocation.
- Published
- 2003
32. Molecular portraits of B cell lineage commitment
- Author
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Jianjun Chen, Janet D. Rowley, Martin Krönke, Markus Müschen, Varun Singh Barath, Cordula Moers, Sanggyu Lee, Niklas Feldhahn, Guolin Zhou, and San Ming Wang
- Subjects
Transcription, Genetic ,Cellular differentiation ,Antigens, CD19 ,B-Lymphocyte Subsets ,Antigens, CD34 ,Biology ,CD19 ,Immunophenotyping ,Transcriptome ,Antigens, CD ,medicine ,Humans ,RNA, Messenger ,Serial analysis of gene expression ,Progenitor cell ,B cell ,Gene Library ,Regulation of gene expression ,B-Lymphocytes ,Multidisciplinary ,Cell Differentiation ,Biological Sciences ,Hematopoietic Stem Cells ,Cell biology ,medicine.anatomical_structure ,Gene Expression Regulation ,Cancer research ,biology.protein ,Neprilysin ,Stem cell - Abstract
In an attempt to characterize early B cell development including the commitment of progenitor cells to the B cell lineage, we generated and compared genomewide gene expression profiles of human hematopoietic stem cells (HSCs) and pre-B cells (PBCs) by using serial analysis of gene expression. From more than 100,000 serial analysis of gene expression tags collected from human CD34 + HSCs and CD10 + CD19 + PBCs, 42,399 unique transcripts were identified in HSCs but only 16,786 in PBCs, suggesting that more than 60% of transcripts expressed in HSCs were silenced during or after commitment to the B cell lineage. On the other hand, mRNAs of pre-B cell receptor (pre-BCR)-associated genes are virtually missing in HSCs but account for more than 10% of the transcriptome of PBCs, which also show increased expression of apoptosis-related genes. Both concentration of the transcriptional repertoire on pre-BCR-related genes together with marked up-regulation of apoptosis mediators in PBC might reflect selection for the expression of a functional pre-BCR within the bone marrow. Besides known regulator genes of early B cell development such as PAX5 , E2A , and EBF , the most abundantly expressed genes in PBCs include ATM , PDGFRA , SIAH1 , PIM2 , C/EBPB , WNT16 , and TCL1 , the role of which has not been established yet in early B cell development.
- Published
- 2002
33. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
- Author
-
Terry Nichols Clark, Jianjun Chen, Xiaohong Cao, Clarence J. Wang, Guolin Zhou, Sanggyu Lee, San Ming Wang, Douglas Kyung Nam, and Janet D. Rowley
- Subjects
DNA, Complementary ,Transcription, Genetic ,Sequence analysis ,Priming (immunology) ,Biology ,Polymerase Chain Reaction ,chemistry.chemical_compound ,Complementary DNA ,Animals ,Humans ,RNA, Messenger ,Cloning, Molecular ,Expressed Sequence Tags ,Expressed sequence tag ,Messenger RNA ,Multidisciplinary ,Dose-Response Relationship, Drug ,Models, Genetic ,Sequence Analysis, DNA ,Biological Sciences ,Molecular biology ,Reverse transcriptase ,Databases as Topic ,Oligodeoxyribonucleotides ,chemistry ,Primer (molecular biology) ,Poly A ,DNA - Abstract
We have analyzed a systematic flaw in the current system of gene identification: the oligo(dT) primer widely used for cDNA synthesis generates a high frequency of truncated cDNAs through internal poly(A) priming. Such truncated cDNAs may contribute to 12% of the expressed sequence tags in the current dbEST database. By using a synthetic transcript and real mRNA templates as models, we characterized the patterns of internal poly(A) priming by oligo(dT) primer. We further demonstrated that the internal poly(A) priming can be effectively diminished by replacing the oligo(dT) primer with a set of anchored oligo(dT) primers for reverse transcription. Our study indicates that cDNAs designed for genomewide gene identification should be synthesized by use of the anchored oligo(dT) primers, rather than the oligo(dT) primers, to diminish the generation of truncated cDNAs caused by internal poly(A) priming.
- Published
- 2002
34. A novel gene,MDS2,is fused toETV6/TELin a t(1;12)(p36.1;p13) in a patient with myelodysplastic syndrome
- Author
-
José P. Román, Carlos Panizo, Janet D. Rowley, María D. Odero, Idoya Lahortiga, Nancy J. Zeleznik-Le, Francisco J. Novo, María José Calasanz, and José L. Vizmanos
- Subjects
Genetics ,Cancer Research ,Bacterial artificial chromosome ,medicine.diagnostic_test ,Biology ,Molecular biology ,Exon ,ETV6 ,Fusion transcript ,RNA splicing ,medicine ,Gene ,Peptide sequence ,Fluorescence in situ hybridization - Abstract
ETV6/TEL is the first transcription factor identified that is specifically required for hematopoiesis within the bone marrow. This gene has been found to have multiple fusion partners of which 16 have been cloned. Fluorescence in situ hybridization (FISH) analysis in a patient with myelodysplastic syndrome (MDS) revealed a t(1;12)(p36;p13) involving ETV6, with the breakpoint in this gene between exon 2 and exon 3. We report here the cloning of a novel ETV6 partner located on 1p36.1, involved in the t(1;12). 3' RACE-PCR from RNA identified a novel sequence fused to exon 2 of ETV6. Database searches localized this sequence in a bacterial artificial chromosome (BAC) mapped to 1p36 by fingerprint analysis. This result was confirmed by FISH using this BAC as probe. 5' and 3' RACE experiments with primers from this novel sequence were carried out on RNA from a healthy donor and identified a novel full-length mRNA, which we named MDS2 (myelodysplastic syndrome 2). RT-PCR experiments were performed on a panel of human cDNAs to analyze the expression pattern of this gene and they revealed four splicing variants. RT-PCR analysis showed that ETV6-MDS2, but not the reciprocal MDS2-ETV6 fusion transcript, was expressed in the bone marrow of the patient. The product of the ETV6-MDS2 fusion transcript predicts a short ETV6 protein containing the first 54 amino acids of ETV6 plus four novel amino acids, lacking both the PTN and the DNA-binding domains. Possible mechanisms to account for the development of MDS in this patient are discussed.
- Published
- 2002
35. International workshop on the relationship of prior therapy to balanced chromosome aberrations in therapy-related myelodysplastic syndromes and acute leukemia: Overview report
- Author
-
Harold J. Olney and Janet D. Rowley
- Subjects
Oncology ,Cancer Research ,Acute leukemia ,medicine.medical_specialty ,Prior Therapy ,Therapy related ,Myelodysplastic syndromes ,Internal medicine ,Genetics ,medicine ,Chromosome ,Biology ,medicine.disease - Published
- 2002
36. Unique balanced chromosome abnormalities in treatment-related myelodysplastic syndromes and acute myeloid leukemia: Report from an International Workshop†
- Author
-
Janet D. Rowley, Harold J. Olney, Krzysztof Mrózek, Bertil Johansson, Roland Berger, and Felix Mitelman
- Subjects
Cancer Research ,medicine.medical_specialty ,Myelodysplastic syndromes ,Chromosome ,Myeloid leukemia ,Karyotype ,Biology ,medicine.disease ,Gastroenterology ,Leukemia ,Median latency ,Internal medicine ,Immunology ,Genetics ,medicine ,Medical genetics ,Median survival - Abstract
A total of 123 balanced rearrangements, including 26 occurring as a sole anomaly, not known to be recurrent in myelodysplastic syndromes (MDS) or acute myelold leukemia (AML) prior to the Workshop, were ascertained retrospectively from 104 patients with treatment-related MDS/AML (t-MDS/t-AML). Thirteen of the aberrations were reported previously in single cases and hence may be classified as recurrent as a result of the Workshop. Patients with Unique aberrations had complex karyotypes more often (P < 0.001 for all pairwise comparisons) than did other Workshop subgroups, with 72% having 3 or more aberrations. Among 85 cases with secondary chromosomal abnormalities, -5, -7, del(5q), and del(7q) were observed in 76%, which is significantly higher (P less than or equal to 0.007 for all pairwise comparisons) than the frequencies found in the Workshop subgroups of patients with previously known recurring aberrations. The chromosome bands most often involved in balanced aberrations were 1p36 and 3q26-27. Treatment exposure was significantly different (less topoisomerase 11 inhibitor exposure, more radiotherapy-only exposure) than for patients with 11q23 (P < 0.001 and P = 0.002, respectively) and 21q22 (P = 0.007 and P = 0.002, respectively) abnormalities. The median time from the first toxic exposure to secondary disease, 59 months, was significantly longer (P less than or equal to 0.016 for all significant pairwise comparisons) than the median latency of all other patients except those in the Rare subgroup, and the median survival time, 7 months, was significantly shorter than for patients in the 21q22, inv(16), and t(15; 17) subgroups (P less than or equal to 0.002 for all pairwise comparisons), but similar to patients in the 11q23 and Rare subgroups. In contrast to known recurring abnormalities, significantly more patients (61%, all P < 0.001) presented with t-MDS, with over one-third of these patients progressing to t-AML. Thus, this group of patients appears to be more similar to the typical t-MDS/t-AML patients, with complex karyotypes as well as chromosome 5 and 7 abnormalities, than to those with recurrent balanced rearrangements. (C) 2002 Wiley-Liss, Inc. (Less)
- Published
- 2001
37. Chromosome translocations: dangerous liaisons revisited
- Author
-
Janet D. Rowley
- Subjects
Genome instability ,Genetics ,Applied Mathematics ,General Mathematics ,Chromosome ,Epiphenomenon ,Chromosomal translocation ,Biology ,Philadelphia chromosome ,medicine.disease ,Chromosome translocations ,medicine ,sense organs ,skin and connective tissue diseases - Abstract
Although it has been clear for more than a century that the chromosomes in human tumour cells are often wildly abnormal, there has been controversy as to whether these changes are primary events or are merely secondary epiphenomena that reflect the genomic instability of these cells. The prevailing view for most of this period was that chromosome changes were secondary events. What happened to change this view?
- Published
- 2001
38. Identification of a 1.2 Kb cDNA fragment from a region on 9p21 commonly deleted in multiple tumor types
- Author
-
Susan Gursky, Olufunmilayo I. Olopade, and Janet D. Rowley
- Subjects
Cancer Research ,DNA, Complementary ,Molecular Sequence Data ,Chromosome 9 ,Biology ,Open Reading Frames ,Exon ,CDKN2A ,Neoplasms ,Sequence Homology, Nucleic Acid ,Complementary DNA ,Tumor Cells, Cultured ,Genetics ,Humans ,Genes, Tumor Suppressor ,Amino Acid Sequence ,3' Untranslated Regions ,Molecular Biology ,Gene ,Sequence Deletion ,Base Sequence ,Sequence Homology, Amino Acid ,Alternative splicing ,Physical Chromosome Mapping ,Exons ,Sequence Analysis, DNA ,Blotting, Northern ,Molecular biology ,Alternative Splicing ,Chromosome Band ,Purine-Nucleoside Phosphorylase ,5' Untranslated Regions ,Chromosomes, Human, Pair 9 - Abstract
Chromosome band 9p21 is a frequent target of homozygous deletion in many tumor types. Putative tumor suppressor genes, CDKN2A (p16), p14(ARF) and CDKN2B (p15), were localized to 9p21. However, there have been reports that suggest that there may be other genes targeted for inactivation in the region. We have developed a method to search for transcribed sequences within large genomic regions. We tested our approach in a 100-kilobase region on 9p21, which is 40 kilobases telomeric to CDKN2A. The method, termed expressed sequence selection (ESS), resulted in the isolation of genomic fragments known to be from 9q21 that are homologous to transcribed sequences. One fragment was used to obtain a 1.2 kilobase cDNA. The sequence of the 5' half of the cDNA was almost identical to exons 3-5 of the MTAP gene, which maps to chromosome band 9p21. The 3' portion of the cDNA had sequence homology to the ALA gene, which maps to chromosome arm 9q. Using Northern blot analysis, the 1.2 Kb cDNA identified several widely expressed transcripts ranging from 1 Kb to 8.5 Kb and displayed a complex pattern of alternative splicing in which certain exons of the 1.2 Kb cDNA are excluded from some of the splice products. Using cancer tissue Northern blots, we could show that all of the transcripts are absent from a leukemia cell line and a lung cancer cell line (K562, A549) with homozygous, genomic deletions within chromosome band 9p21. In addition, the 7 Kb transcript is also absent from two additional tumor cell lines (Molt4, a leukemia derived cell line, and in G361, a melanoma derived cell line) with homozygous deletions. Further investigation will determine whether the difference in the expression pattern between the 7 Kb transcript compared with the other sized transcripts could be due to specific targeting for alteration in certain tumor types.
- Published
- 2001
39. Cytogenetic analysis in leukemia and lymphoma: An introduction
- Author
-
Janet D. Rowley
- Subjects
Chromosome Aberrations ,medicine.medical_specialty ,Leukemia ,Lymphoma ,Cytogenetics ,Chromosome Disorders ,Chromosomal translocation ,Hematology ,Gene rearrangement ,Biology ,medicine.disease ,Virology ,Cytogenetic Analysis ,medicine ,Humans - Published
- 2000
40. DNA structural properties of AF9 are similar to MLL and could act as recombination hot spots resulting in MLL/AF9 translocations and leukemogenesis
- Author
-
Bruce A. Roe, Nancy J. Zeleznik-Le, Ronald J. Tomek, Reiner Strick, Janet D. Rowley, and Pamela L. Strissel
- Subjects
Oncogene Proteins, Fusion ,Molecular Sequence Data ,Biology ,Translocation, Genetic ,Cell Line ,Fusion gene ,Jurkat Cells ,hemic and lymphatic diseases ,Proto-Oncogenes ,Tumor Cells, Cultured ,Genetics ,Deoxyribonuclease I ,Humans ,Molecular Biology ,Gene ,Genetics (clinical) ,Recombination, Genetic ,Binding Sites ,Leukemia ,Breakpoint ,breakpoint cluster region ,Intron ,Nuclear Proteins ,DNA, Neoplasm ,Histone-Lysine N-Methyltransferase ,Sequence Analysis, DNA ,General Medicine ,Molecular biology ,Chromatin ,Introns ,DNA-Binding Proteins ,genomic DNA ,DNA Topoisomerases, Type II ,Myeloid-Lymphoid Leukemia Protein ,K562 Cells ,Transcription Factors - Abstract
The human AF9 gene at 9p22 is one of the most common fusion partner genes with the MLL gene at 11q23, resulting in the t(9;11)(p22;q23). The MLL-AF9 fusion gene is associated with de novo acute myelo-genous leukemia (AML), rarely with acute lymphocytic leukemia (ALL) and with therapy related leukemia (t-AML). The AF9 gene is >100 kb and two patient breakpoint cluster regions (BCRs) have been identified; BCR1 is within intron 4, previously called site A, whereas BCR2 or site B spans introns 7 and 8. Patient breakpoint locations were determined previously by RT-PCR and by genomic DNA cloning. In this study, we defined the exon-intron boundaries and identified several different structural elements in AF9 including a co-localizing in vivo DNA topo II cleavage site and an in vitro DNase I hypersensitive (DNase 1 HS) site in intron 7 in BCR2. Reversibility experiments demonstrated a religation of the topo II cleavage sites. The location of the in vivo topo II cleavage site was confirmed in vitro using a topo II cleavage assay. In addition, two scaffold associated regions (SARs) are located centromeric to the topo II and DNase I HS cleavage sites and border both patient breakpoint regions: SAR1 is located in intron 4, whereas SAR2 encompasses parts of exons 5-7. This study demonstrates that the patient breakpoint regions of AF9 share the same structural elements as the MLL BCR. We describe a DNA breakage and repair model for non-homologous recombination between MLL and its partner genes, particularly AF9.
- Published
- 2000
41. Dietary bioflavonoids induce cleavage in the MLL gene and may contribute to infant leukemia
- Author
-
Janet D. Rowley, Steve L. Smith, Pamela L. Strissel, Reiner Strick, and Susanne Borgers
- Subjects
Multidisciplinary ,DNA repair ,DNA damage ,Topoisomerase ,breakpoint cluster region ,Biology ,medicine.disease ,Molecular biology ,Leukemia ,chemistry.chemical_compound ,chemistry ,hemic and lymphatic diseases ,medicine ,biology.protein ,Myeloid-Lymphoid Leukemia Protein ,Chromosome breakage ,DNA - Abstract
Chromosomal translocations involving the MLL gene occur in about 80% of infant leukemia. In the search for possible agents inducing infant leukemia, we identified bioflavonoids, natural substances in food as well as in dietary supplements, that cause site-specific DNA cleavage in the MLL breakpoint cluster region (BCR) in vivo . The MLL BCR DNA cleavage was shown in primary progenitor hematopoietic cells from healthy newborns and adults as well as in cell lines; it colocalized with the MLL BCR cleavage site induced by chemotherapeutic agents, such as etoposide (VP16) and doxorubicin (Dox). Both in vivo and additional in vitro experiments demonstrated topoisomerase II (topo II) as the target of bioflavonoids similar to VP16 and Dox. Based on 20 bioflavonoids tested, we identified a common structure essential for topo II-induced DNA cleavage. Reversibility experiments demonstrated a religation of the bioflavonoid as well as the VP16-induced MLL cleavage site. Our observations support a two-stage model of cellular processing of topo II inhibitors: The first and reversible stage of topo II-induced DNA cleavage results in DNA repair, but also rarely in chromosome translocations; whereas the second, nonreversible stage leads to cell death because of an accumulation of DNA damage. These results suggest that maternal ingestion of bioflavonoids may induce MLL breaks and potentially translocations in utero leading to infant and early childhood leukemia.
- Published
- 2000
42. Screening poly(dA/dT) − cDNAs for gene identification
- Author
-
San Ming Wang, Jianjun Chen, Lin Zhang, Janet D. Rowley, and Scott C. Fears
- Subjects
Genetics ,chemistry.chemical_compound ,Expressed sequence tag ,Multidisciplinary ,chemistry ,Poly dA-dT ,Complementary DNA ,RNA ,Human genome ,Identification (biology) ,Biology ,Gene ,DNA - Abstract
Many genes expressed in the human genome have not been identified despite intensive efforts. We observed that the presence of long poly(dA/dT) sequences in the 3′ end of cDNA templates contributes significantly to this problem, because the hybrids formed randomly between poly(dA) and poly(dT) sequences of unrelated cDNA templates lead to loss of many templates in the normalization/subtraction reactions. The low abundant copies, which account for the majority of the expressed genes, are affected in particular by this phenomenon. We have developed a strategy called screening poly(dA/dT) − cDNAs for gene identification to overcome this obstacle. Applying this strategy can significantly enhance the efficiency of genome-wide gene identification and should have an impact on many functional genomic studies in the postgenome era.
- Published
- 2000
43. Molecular genetics in acute leukemia
- Author
-
Janet D. Rowley
- Subjects
Genetics ,Cancer Research ,medicine.medical_specialty ,Acute leukemia ,Cytogenetics ,Chromosomal translocation ,Hematology ,Biology ,medicine.disease ,Human genetics ,Leukemia ,Oncology ,hemic and lymphatic diseases ,Acute lymphocytic leukemia ,Molecular genetics ,medicine ,Myeloid-Lymphoid Leukemia Protein - Abstract
Improved techniques in identifying the chromosome changes and the affected genes that are involved in acute leukemias have led to improved treatments for these diseases. Identification of consistent chromosomal changes has allowed us to target the location of particular genes and has enabled us to focus our treatments more specifically to certain subtypes of leukemia. Translocations, in particular, are common cytogenetic abnormalities in human leukemia, and the prevalence of certain types of translocations varies with age. Cancers, lymphomas and leukemias are now known to be genetic diseases and it is recognized that genotype-specific therapies should be used that take into account the genetic alterations of the particular leukemia.
- Published
- 2000
44. Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification
- Author
-
San Ming Wang, Jianjun Chen, and Janet D. Rowley
- Subjects
Genetic Markers ,DNA, Complementary ,Colon ,Molecular Sequence Data ,Gene Expression ,Biology ,Genome ,Exon ,Complementary DNA ,Humans ,Serial analysis of gene expression ,Cloning, Molecular ,Gene ,DNA Primers ,Electrophoresis, Agar Gel ,Genetics ,Multidisciplinary ,Pfu DNA polymerase ,Reverse Transcriptase Polymerase Chain Reaction ,SAGE ,fungi ,food and beverages ,Epithelial Cells ,DNA Restriction Enzymes ,Exons ,Sequence Analysis, DNA ,Biological Sciences ,Eukaryotic Cells ,Primer (molecular biology) - Abstract
We have developed a technique called the generation of longer cDNA fragments from serial analysis of gene expression (SAGE) tags for gene identification (GLGI), to convert SAGE tags of 10 bases into their corresponding 3′ cDNA fragments covering hundred bases. A primer containing the 10-base SAGE tag is used as the sense primer, and a single base anchored oligo(dT) primer is used as an antisense primer in PCR, together with Pfu DNA polymerase. By using this approach, a cDNA fragment extending from the SAGE tag toward the 3′ end of the corresponding sequence can be generated. Application of the GLGI technique can solve two critical issues in applying the SAGE technique: one is that a longer fragment corresponding to a SAGE tag, which has no match in databases, can be generated for further studies; the other is that the specific fragment corresponding to a SAGE tag can be identified from multiple sequences that match the same SAGE tag. The development of the GLGI method provides several potential applications. First, it provides a strategy for even wider application of the SAGE technique for quantitative analysis of global gene expression. Second, a combined application of SAGE/GLGI can be used to complete the catalogue of the expressed genes in human and in other eukaryotic species. Third, it can be used to identify the 3′ cDNA sequence from any exon within a gene. It can also be used to confirm the reality of exons predicted by bioinformatic tools in genomic sequences. Fourth, a combined application of SAGE/GLGI can be applied to define the 3′ boundary of expressed genes in the genomic sequences in human and in other eukaryotic genomes.
- Published
- 2000
45. Cytogenetic and molecular analysis of the acute monocytic leukemia cell line THP-1 with anMLL-AF9 translocation
- Author
-
Nancy J. Zeleznik-Le, Janet D. Rowley, María D. Odero, and Vandana Chinwalla
- Subjects
Cancer Research ,Monosomy ,medicine.diagnostic_test ,Derivative chromosome ,Karyotype ,Chromosomal translocation ,Biology ,medicine.disease ,Molecular biology ,Genetics ,medicine ,Myeloid-Lymphoid Leukemia Protein ,THP1 cell line ,Acute monocytic leukemia ,Fluorescence in situ hybridization - Abstract
Cell lines derived from patients with leukemia are used in many molecular biology studies. Here we report the cytogenetic analysis of the THP-1 cell line using G-banding, fluorescence in situ hybridization (FISH), and spectral karyotyping (SKY), and the molecular characterization of the MLL-AF9 rearrangement by RT-PCR. The THP-1 cell line was established from the peripheral blood of a 1-year-old boy with acute monocytic leukemia (AML-M5). THP-1 is near-diploid and consists of two related subclones with a number of aberrations, including the t(9;11), associated with AML M5. The use of FISH allowed us to identify and characterize otherwise hidden cytogenetic rearrangements, which include duplication of the 3' portion of MLL in the derivative 9 chromosome and a deletion of the 5' portion of the AF9 gene involved in the translocation. In addition to confirming the FISH results, SKY allowed for a more precise characterization of the karyotype of THP-1 and allowed us to identify other abnormalities in this cell line, including der(1)t(1;12), der(20)t(1;20), deletions 6p, 12p, and 17p, trisomy 8, and monosomy 10. Sequencing of the RT-PCR product showed a direct in-frame fusion product on the derivative chromosome 11 between exon 6 (exon 9) of MLL and exon 5 of AF9, which is most commonly involved in MLL-AF9 translocations. This study demonstrates that combining different techniques to achieve a more precise characterization of the THP-1 cell line provides important information that will be valuable for understanding the critical events required for leukemogenesis.
- Published
- 2000
46. Identification and molecular characterization of CALM/AF10fusion products in T cell acute lymphoblastic leukemia and acute myeloid leukemia
- Author
-
Jose A. Martinez-Climent, Stefan K. Bohlander, M M Le Beau, Janet D. Rowley, Katrin M. Carlson, and Christine Vignon
- Subjects
Adult ,Male ,Cancer Research ,Myeloid ,Oncogene Proteins, Fusion ,Chromosomal translocation ,Biology ,Immunophenotyping ,hemic and lymphatic diseases ,Acute lymphocytic leukemia ,medicine ,Humans ,Cloning, Molecular ,Child ,neoplasms ,In Situ Hybridization, Fluorescence ,DNA Primers ,ABL ,Base Sequence ,medicine.diagnostic_test ,Reverse Transcriptase Polymerase Chain Reaction ,Myeloid leukemia ,Hematology ,Middle Aged ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,medicine.disease ,Virology ,Leukemia ,medicine.anatomical_structure ,Oncology ,Leukemia, Myeloid ,Acute Disease ,Cancer research ,Fluorescence in situ hybridization - Abstract
The t(10;11)(p12-p13;q14-q21) observed in a subset of patients with either acute lymphoblastic leukemia or acute myeloid leukemia has been shown to result in the fusion of AF10 on chromosome 10 with CALM (also named CLTH) on chromosome 11. AF10 was originally identified as a fusion partner of MLL in the t(10;11)(p12-p13;q23) observed in myeloid leukemia. CALM is a newly isolated gene, cloned as the fusion partner of AF10 in the monocytoid cell line, U937. In order to understand the relationship between MLL, AF10, CALM and the leukemic process, fluorescence in situ hybridization and reverse transcriptase polymerase chain reaction were used to study a series of nine leukemia patients with a t(10;11). Six had myeloid leukemia (AML-M0, AML-M1, AML-M4 and AML-M5) and three had T cell lymphoblastic leukemia. We identified four different CALM/AF10 fusion products in five patients and AF10/CALM reciprocal message in one. We conclude that fusion of CALM and AF10 is a recurring abnormality in both lymphoid and myeloid leukemias of various types including AML-M5, and that the breakpoints in the two types of leukemia do not differ. Our data indicate that the CALM/AF10 fusion product on the der(10) chromosome is critical to leukemogenesis. Leukemia (2000) 14, 100-104.
- Published
- 2000
47. Lineage specificity of CBFA2 fusion transcripts
- Author
-
G. Nucifora, E. J. Dann, Janet D. Rowley, H Arád-Dann, and Scott C. Fears
- Subjects
Cancer Research ,DNA, Complementary ,Myeloid ,Oncogene Proteins, Fusion ,Transcription, Genetic ,Chromosomes, Human, Pair 21 ,Cellular differentiation ,Blotting, Western ,Apoptosis ,Biology ,Translocation, Genetic ,RUNX1 Translocation Partner 1 Protein ,Myeloid Cell Differentiation ,Proto-Oncogene Proteins ,Granulocyte Colony-Stimulating Factor ,medicine ,Humans ,Cell Lineage ,Peroxidase ,Sequence Deletion ,Regulation of gene expression ,Chromosomes, Human, Pair 12 ,Gene Expression Regulation, Leukemic ,Cell Differentiation ,Hematology ,Flow Cytometry ,medicine.disease ,Fusion protein ,Molecular biology ,Neoplasm Proteins ,Protein Structure, Tertiary ,DNA-Binding Proteins ,Blot ,ETV6 ,Leukemia ,medicine.anatomical_structure ,Oncology ,Leukemia, Myeloid ,Acute Disease ,Core Binding Factor Alpha 2 Subunit ,Receptors, Granulocyte Colony-Stimulating Factor ,Cell Division ,Transcription Factors - Abstract
The CBFA2 gene on chromosome band 21q22 is one of the most commonly translocated genes in leukemia. As with other translocations, those involving CBFA2 are associated with specific disease phenotypes. Only one of the different translocations involving CBFA2, the t(12;21), has been associated with a non-myeloid lineage. Several different CBFA2 fusion transcripts were expressed in the myeloid 32Dcl3 cell line, and show that unlike the myeloid specific fusion transcripts, the lymphoid specific ETV6/CBFA2 transcript is not compatible with myeloid cell differentiation. It is shown that myeloid cells expressing the ETV6/CBFA2 transcript undergo apoptosis in response to a G-CSF differentiation signal. The molecular differences in the cells we studied are characterized using Western blot analysis to show that t(12;21) expressing cells fail to express the G-CSF receptor.
- Published
- 2000
48. Variant Three-Way Translocation of Inversion 16 in AML-M4Eo Confirmed by Fluorescence In Situ Hybridization Analysis
- Author
-
Jose A. Martinez-Climent, Carlos Solano, Pascual Bolufer, Mar Tormo, Shalini C. Reshmi, Isabel Marugán, Eva Barragán, M.Jose Terol, Felipe Prosper, Isabel Benet, Esperanza Vizcarra, Cristina Arbona, Javier García-Conde, Janet D. Rowley, and Ana M. Comes
- Subjects
Adult ,Male ,Cancer Research ,Chromosomal translocation ,Biology ,Leukemia, Myelomonocytic, Acute ,Translocation, Genetic ,Chromosome 16 ,Genetics ,medicine ,Humans ,Molecular Biology ,In Situ Hybridization, Fluorescence ,Chromosomal inversion ,medicine.diagnostic_test ,Reverse Transcriptase Polymerase Chain Reaction ,Hybridization probe ,medicine.disease ,Molecular biology ,Eosinophils ,Leukemia ,Fusion transcript ,Chromosome Inversion ,Acute myelomonocytic leukemia ,Female ,Chromosomes, Human, Pair 16 ,Fluorescence in situ hybridization - Abstract
The inv(16) and t(16;16) characterize a subgroup of acute myelomonocytic leukemia (AML) with distinct morphological features and a favorable prognosis. Both cytogenetic abnormalities result in a fusion of CBF beta at 16q22 and MYH11 gene at 16p13, whose detection by PCR and fluorescence in situ hybridization (FISH) is useful for diagnosis and monitoring of the disease. Variant translocations of inv(16)/t(16;16) are very rare and whether they are also associated with a favorable prognosis is unknown. We report a patient presenting with typical AML-M4Eo and a three-way translocation of inv(16) involving 16p13, 16q22, and 3q22. FISH studies on bone marrow (BM) chromosomes using CBFB and MYH11 DNA probes revealed a fusion of CBFB and MYH11 on 16q of the der(16), as well as a signal from MYH11 on 16p but not from CBFB; normal signals for both probes were present on the normal 16. Neither of these labeled probes was on the der(3), but the translocation between the der(3) and der(16) was confirmed by using a chromosome 16 painting probe. Molecular analysis of BM cells using RT-PCR identified a CBFB-MYH11 fusion transcript type D. After achieving complete remission, the patient relapsed. We conclude that FISH and PCR are feasible tools to distinguish cases with variant abnormalities of inv(16) from cases with other chromosome 16 abnormalities. Variant abnormalities of inv(16) may be not associated with favorable prognosis.
- Published
- 1999
49. MLL is involved in a t(2;11)(p21;q23) in a patient with acute myeloblastic leukemia
- Author
-
Elena W. Fleischman, N.N. Tupitsyn, Shalini C. Reshmi, O.E. Kulagina, Janet D. Rowley, L. N. Konstantinova, G.P. Guleva, W.I. Konovalova, and Marina A. Frenkel
- Subjects
Genetics ,Cancer Research ,Acute myeloblastic leukemia ,medicine.diagnostic_test ,Lymphoblastic Leukemia ,Breakpoint ,Chromosomal translocation ,Biology ,medicine.disease ,hemic and lymphatic diseases ,medicine ,Cancer research ,neoplasms ,Fluorescence in situ hybridization - Abstract
We describe a patient with acute myeloblastic leukemia (AML-M0) whose cells had a t(2;11)(p21;q23). Fluorescence in situ hybridization analysis with a probe for MLL showed that it was split, hybridizing to both the derivative 2 and 11 chromosomes. Nineteen other patients with 2p;11q translocations have been described; breakpoints in 14 of these are the same as in the case we describe. The phenotype of these patients is quite variable, with 14 patients having myelodysplastic syndrome which evolved to AML in six. Four patients had AML and two had acute lymphoblastic leukemia. MLL status has been studied in two other patients; one had MLL rearranged and one did not.
- Published
- 1999
50. The Cart Before the Horse
- Author
-
Janet D. Rowley and Thomas Blumenthal
- Subjects
Genetics ,Cart ,Multidisciplinary ,fungi ,food and beverages ,RNA ,Horse ,Chromosomal translocation ,Biology ,Bioinformatics - Abstract
Chimeric RNAs, transcribed from malignancy-associated chromosomal translocations, can also arise from RNA trans-splicing in normal cells.
- Published
- 2008
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