1
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Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M, Graf T, Vingron M, Hnisz D. An activity-specificity trade-off encoded in human transcription factors. Nat Cell Biol 2024; 26:1309-1321. [PMID: 38969762 PMCID: PMC11321997 DOI: 10.1038/s41556-024-01411-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2024] [Indexed: 07/07/2024]
Abstract
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences. Mutation of periodic aromatic residues reduced transcriptional activity, whereas increasing the aromatic dispersion of multiple human TFs enhanced transcriptional activity and reprogramming efficiency, promoted liquid-liquid phase separation in vitro and more promiscuous DNA binding in cells. Together with recent work on enhancer elements, these results suggest an important evolutionary role of suboptimal features in transcriptional control. We propose that rational engineering of amino acid features that alter phase separation may be a strategy to optimize TF-dependent processes, including cellular reprogramming.
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Affiliation(s)
- Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alexandre P Magalhaes
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gregoire Stik
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Yaotian Zhang
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hannah M Wieler
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Francesca Rossi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rene Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie Christou-Kent
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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2
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Bérouti M, Lammens K, Heiss M, Hansbauer L, Bauernfried S, Stöckl J, Pinci F, Piseddu I, Greulich W, Wang M, Jung C, Fröhlich T, Carell T, Hopfner KP, Hornung V. Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation. Immunity 2024; 57:1482-1496.e8. [PMID: 38697119 DOI: 10.1016/j.immuni.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 05/04/2024]
Abstract
Toll-like receptor 7 (TLR7) is essential for recognition of RNA viruses and initiation of antiviral immunity. TLR7 contains two ligand-binding pockets that recognize different RNA degradation products: pocket 1 recognizes guanosine, while pocket 2 coordinates pyrimidine-rich RNA fragments. We found that the endonuclease RNase T2, along with 5' exonucleases PLD3 and PLD4, collaboratively generate the ligands for TLR7. Specifically, RNase T2 generated guanosine 2',3'-cyclic monophosphate-terminated RNA fragments. PLD exonuclease activity further released the terminal 2',3'-cyclic guanosine monophosphate (2',3'-cGMP) to engage pocket 1 and was also needed to generate RNA fragments for pocket 2. Loss-of-function studies in cell lines and primary cells confirmed the critical requirement for PLD activity. Biochemical and structural studies showed that PLD enzymes form homodimers with two ligand-binding sites important for activity. Previously identified disease-associated PLD mutants failed to form stable dimers. Together, our data provide a mechanistic basis for the detection of RNA fragments by TLR7.
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Affiliation(s)
- Marleen Bérouti
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Heiss
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Larissa Hansbauer
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Stefan Bauernfried
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jan Stöckl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Francesca Pinci
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Ignazio Piseddu
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany; Department of Medicine II, University Hospital Munich, Munich, Germany
| | - Wilhelm Greulich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Meiyue Wang
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Christophe Jung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Fröhlich
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.
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3
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Van Outersterp I, Hormann FM, Hoogkamer AQ, Boeree A, Van den Broek SA, Den Boer ML, Boer JM. Characterization of a novel MEF2D-BCL9 fusion-positive acute lymphoblastic leukemia cell line. Haematologica 2023; 108:2859-2864. [PMID: 37051743 PMCID: PMC10542830 DOI: 10.3324/haematol.2022.281712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Affiliation(s)
- Inge Van Outersterp
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands
| | - Femke M Hormann
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands; Erasmus MC - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands
| | - Alex Q Hoogkamer
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands
| | - Aurélie Boeree
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands
| | - Stijn A Van den Broek
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands
| | - Monique L Den Boer
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands; Erasmus MC - Sophia Children's Hospital, Department of Pediatric Oncology and Hematology, Rotterdam, Netherlands
| | - Judith M Boer
- Princess Máxima Center for pediatric oncology, Utrecht, Netherlands; Oncode Institute, Utrecht, Netherlands.
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4
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Christou-Kent M, Cuartero S, Garcia-Cabau C, Ruehle J, Naderi J, Erber J, Neguembor MV, Plana-Carmona M, Alcoverro-Bertran M, De Andres-Aguayo L, Klonizakis A, Julià-Vilella E, Lynch C, Serrano M, Hnisz D, Salvatella X, Graf T, Stik G. CEBPA phase separation links transcriptional activity and 3D chromatin hubs. Cell Rep 2023; 42:112897. [PMID: 37516962 DOI: 10.1016/j.celrep.2023.112897] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell-to-macrophage transdifferentiation. Mechanistically, we find that the intrinsically disordered region (IDR) of CEBPA undergoes in vitro phase separation (PS) dependent on aromatic residues. Both overexpressing B cells and native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors, liver cells, and trophectoderm cells reveal nuclear CEBPA foci and long-range 3D chromatin hubs at CEBPA-bound regions. In short, we show that CEBPA can undergo PS through its IDR, which may underlie in vivo foci formation and suggest a potential role of PS in regulating CEBPA function.
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Affiliation(s)
- Marie Christou-Kent
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Sergi Cuartero
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain; Germans Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Julia Ruehle
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Julia Erber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marcos Plana-Carmona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Luisa De Andres-Aguayo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Antonios Klonizakis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Cian Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Altos Labs, Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Grégoire Stik
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.
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5
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The Impact of Exosomes/Microvesicles Derived from Myeloid Dendritic Cells Cultured in the Presence of Calcitriol and Tacalcitol on Acute B-Cell Precursor Cell Lines with MLL Fusion Gene. J Clin Med 2022; 11:jcm11082224. [PMID: 35456315 PMCID: PMC9032710 DOI: 10.3390/jcm11082224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022] Open
Abstract
Vitamin D analogs (VDAs) may directly inhibit the growth of normal and malignant (derived from acute lymphoblastic leukemia (ALL)) B cells, as both types of cells express vitamin D receptor (VDR). We performed anti-proliferative, morphology tests and phenotyping to evaluate the sensitivity of monocytes and iDCs (immature myeloid-derived dendritic cells) on calcitriol and tacalcitol treatment, phenotyping, morphology, and size distribution measurement to determine the characteristics of microvesicles (MVs) and exosomes (EXs) derived from them and, finally, phenotyping and Elisa test to determine the effects of VDAs on modulation of the phenotype of B cells through extracellular vesicles (EVs) released by iDCs. Our results confirmed that both SC cells and iDCs were sensitive to the VDAs and showed altered surface expression of markers associated with monocyte differentiation, which was resulting in the phenotypic changes in EVs derived from them. We also showed that obtained EVs could change the morphology and phenotype of ALL-B-derived precursor cells in a different way, depending on their origin. The differential effect of VDAs on ALL-B cells, which was associated with increased or decreased expression of CD27, CD24, CD38, and CD23 expression, was observed. Hence, further studies to explain the modulation in the composition of EVs by VDAs are required.
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6
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Díaz-García C, Herraiz S, Such E, Andrés MDM, Villamón E, Mayordomo-Aranda E, Cervera JV, Sanz MA, Pellicer A. Dexamethasone does not prevent malignant cell reintroduction in leukemia patients undergoing ovarian transplant: risk assessment of leukemic cell transmission by a xenograft model. Hum Reprod 2020; 34:1485-1493. [PMID: 31339993 DOI: 10.1093/humrep/dez115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/01/2019] [Indexed: 01/11/2023] Open
Abstract
STUDY QUESTION Does dexamethasone (DXM) incubation avoid the reintroduction of leukemic malignant cells after ovarian tissue retransplantation in vivo? SUMMARY ANSWER DXM incubation prior to retransplantation of ovarian tissue does not prevent reintroduction of leukemic cells. WHAT IS KNOWN ALREADY Retransplantation of cryopreserved ovarian cortex from patients diagnosed with acute lymphoblastic leukemia (ALL) involves a risk of reintroducing malignant cells. DXM treatment is effective at inducing leukemic cell death in vitro. STUDY DESIGN, SIZE, DURATION This was an experimental study where ovarian cortex fragments from patients with ALL were randomly allocated to incubation with or without DXM (n = 11/group) and grafted to 22 immunodeficient mice for 6 months. In a parallel experiment, 22 immunodeficient mice were injected i.p. with varying amounts of RCH-ACV ALL cells (human leukemia cell line) and maintained for 4 months. PARTICIPANTS/MATERIALS, SETTING, METHODS Cryopreserved ovarian fragments from patients with ALL were exposed in vitro to 0.4 μM DXM or basal media (control) prior to xenograft into ovariectomized severe combined immunodeficiency (SCID) mice (experiment 1). After 6 months of monitoring, leukemia cell contamination was assessed in ovarian grafts and mouse organs by histology, PCR (presence of mouse mtDNA and absence of p53 were together considered a negative result for the presence of human cells) and detection of immunoglobulin monoclonality and specific ALL markers if present in the patient.In experiment 2, a series of 22 immunodeficient female mice was injected with specific doses of the leukemia cell line RCH-ACV (103 - 5 × 106, n = 4/group) to assess the engraftment competence of the SCID model. MAIN RESULTS AND THE ROLE OF CHANCE ALL metastatic cells were detected, by PCR, in five DXM-treated and one control human ovarian tissue graft as well as in a control mouse liver, although malignant cell infiltration was not detected by histology in any sample after 6 months. In total, minimal residual disease was present in three DXM-treated and three control mice.RCH-ACV cells were detected in liver and spleen samples after the injection of as little as 103 cells, although only animals receiving 5 × 106 cells developed clinical signs of disease and metastases. LIMITATIONS, REASONS FOR CAUTION This is an experimental study where the malignant potential of leukemic cells contained in human ovarian tissues has been assessed in immunodeficient mice. WIDER IMPLICATIONS OF THE FINDINGS These results indicate that DXM incubation prior to retransplantation of ovarian tissue does not prevent reintroduction of leukemic cells. Therefore, caution should be taken in retransplanting ovarian tissue from patients with leukemia until safer systems are developed, as leukemic cells present in ovarian grafts were able to survive, proliferate and migrate after cryopreservation and xenograft. STUDY FUNDING/COMPETING INTEREST(S) Funded by the Regional Valencian Ministry of Education (PROMETEO/2018/137) and by the Spanish Ministry of Economy and Competitiveness (PI16/FIS PI16/01664 and PTQ-16-08222 for S.H. participation). There are no competing interests.
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Affiliation(s)
- César Díaz-García
- IVI-RMA London, London, UK.,Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, UK
| | - Sonia Herraiz
- Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,IVI Foundation, Valencia, Spain
| | - Esperanza Such
- Department of Hematology, La Fe University Hospital, Valencia, Spain
| | - María Del Mar Andrés
- Pediatric Oncology Unit, Child's Health Area, La Fe University Hospital, Valencia, Spain
| | - Eva Villamón
- Department of Hematology, La Fe University Hospital, Valencia, Spain
| | | | - José V Cervera
- Department of Hematology, La Fe University Hospital, Valencia, Spain
| | - Miguel A Sanz
- Department of Hematology, La Fe University Hospital, Valencia, Spain
| | - Antonio Pellicer
- Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,IVI Foundation, Valencia, Spain.,IVI-RMA Roma, Rome, Italy
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7
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Godfrey L, Crump NT, O'Byrne S, Lau IJ, Rice S, Harman JR, Jackson T, Elliott N, Buck G, Connor C, Thorne R, Knapp DJHF, Heidenreich O, Vyas P, Menendez P, Inglott S, Ancliff P, Geng H, Roberts I, Roy A, Milne TA. H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells. Leukemia 2020; 35:90-106. [PMID: 32242051 PMCID: PMC7787973 DOI: 10.1038/s41375-020-0808-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
Abstract
MLL gene rearrangements (MLLr) are a common cause of aggressive, incurable acute lymphoblastic leukemias (ALL) in infants and children, most of which originate in utero. The most common MLLr produces an MLL-AF4 fusion protein. MLL-AF4 promotes leukemogenesis by activating key target genes, mainly through recruitment of DOT1L and increased histone H3 lysine-79 methylation (H3K79me2/3). One key MLL-AF4 target gene is PROM1, which encodes CD133 (Prominin-1). CD133 is a pentaspan transmembrane glycoprotein that represents a potential pan-cancer target as it is found on multiple cancer stem cells. Here we demonstrate that aberrant PROM1/CD133 expression is essential for leukemic cell growth, mediated by direct binding of MLL-AF4. Activation is controlled by an intragenic H3K79me2/3 enhancer element (KEE) leading to increased enhancer–promoter interactions between PROM1 and the nearby gene TAPT1. This dual locus regulation is reflected in a strong correlation of expression in leukemia. We find that in PROM1/CD133 non-expressing cells, the PROM1 locus is repressed by polycomb repressive complex 2 (PRC2) binding, associated with reduced expression of TAPT1, partially due to loss of interactions with the PROM1 locus. Together, these results provide the first detailed analysis of PROM1/CD133 regulation that explains CD133 expression in MLLr ALL.
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Affiliation(s)
- Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sorcha O'Byrne
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Siobhan Rice
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Joe R Harman
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas Jackson
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Gemma Buck
- Department of Paediatrics, University of Oxford, Oxford, UK
| | | | - Ross Thorne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - David J H F Knapp
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Olaf Heidenreich
- Princess Maxima Centrum for Pediatric Oncology, Utrecht, The Netherlands.,Wolfson Childhood Cancer Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute, Barcelona, Spain.,Institucio Catalana of Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red en cancer (CIBERONC)-ISCIII, Barcelona, Spain
| | - Sarah Inglott
- Great Ormond Street Hospital for Children, London, UK
| | | | - Huimin Geng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Department of Paediatrics, University of Oxford, Oxford, UK
| | - Anindita Roy
- Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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8
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Lin CH, Wang Z, Duque-Afonso J, Wong SHK, Demeter J, Loktev AV, Somervaille TCP, Jackson PK, Cleary ML. Oligomeric self-association contributes to E2A-PBX1-mediated oncogenesis. Sci Rep 2019; 9:4915. [PMID: 30894657 PMCID: PMC6426973 DOI: 10.1038/s41598-019-41393-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
The PBX1 homeodomain transcription factor is converted by t(1;19) chromosomal translocations in acute leukemia into the chimeric E2A-PBX1 oncoprotein. Fusion with E2A confers potent transcriptional activation and constitutive nuclear localization, bypassing the need for dimerization with protein partners that normally stabilize and regulate import of PBX1 into the nucleus, but the mechanisms underlying its oncogenic activation are incompletely defined. We demonstrate here that E2A-PBX1 self-associates through the PBX1 PBC-B domain of the chimeric protein to form higher-order oligomers in t(1;19) human leukemia cells, and that this property is required for oncogenic activity. Structural and functional studies indicate that self-association facilitates the binding of E2A-PBX1 to DNA. Mutants unable to self-associate are transformation defective, however their oncogenic activity is rescued by the synthetic oligomerization domain of FKBP, which confers conditional transformation properties on E2A-PBX1. In contrast to self-association, PBX1 protein domains that mediate interactions with HOX DNA-binding partners are dispensable. These studies suggest that oligomeric self-association may compensate for the inability of monomeric E2A-PBX1 to stably bind DNA and circumvents protein interactions that otherwise modulate PBX1 stability, nuclear localization, DNA binding, and transcriptional activity. The unique dependence on self-association for E2A-PBX1 oncogenic activity suggests potential approaches for mechanism-based targeted therapies.
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MESH Headings
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Carcinogenesis/genetics
- Cell Line, Tumor
- Chromosomes, Human, Pair 1/chemistry
- Chromosomes, Human, Pair 19/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Pre-B-Cell Leukemia Transcription Factor 1/genetics
- Pre-B-Cell Leukemia Transcription Factor 1/metabolism
- Protein Binding
- Protein Multimerization
- Protein Stability
- Tacrolimus Binding Proteins/genetics
- Tacrolimus Binding Proteins/metabolism
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Chiou-Hong Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhong Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, 510006, China
| | - Jesús Duque-Afonso
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephen Hon-Kit Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander V Loktev
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tim C P Somervaille
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4GJ, UK
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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9
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Duque-Afonso J, Lin CH, Han K, Morgens DW, Jeng EE, Weng Z, Jeong J, Wong SHK, Zhu L, Wei MC, Chae HD, Schrappe M, Cario G, Duyster J, Xiao X, Sakamoto KM, Bassik MC, Cleary ML. CBP Modulates Sensitivity to Dasatinib in Pre-BCR + Acute Lymphoblastic Leukemia. Cancer Res 2018; 78:6497-6508. [PMID: 30262461 PMCID: PMC6283070 DOI: 10.1158/0008-5472.can-18-1703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/18/2018] [Accepted: 09/24/2018] [Indexed: 01/18/2023]
Abstract
Dasatinib is a multi-tyrosine kinase inhibitor approved for treatment of Ph+ acute lymphoblastic leukemia (ALL), but its efficacy is limited by resistance. Recent preclinical studies suggest that dasatinib may be a candidate therapy in additional ALL subtypes including pre-BCR+ ALL. Here we utilized shRNA library screening and global transcriptomic analysis to identify several novel genes and pathways that may enhance dasatinib efficacy or mitigate potential resistance in human pre-BCR+ ALL. Depletion of the transcriptional coactivator CBP increased dasatinib sensitivity by downregulating transcription of the pre-BCR signaling pathway previously associated with dasatinib sensitivity. Acquired resistance was due, in part, to upregulation of alternative pathways including WNT through a mechanism, suggesting transcriptional plasticity. Small molecules that disrupt CBP interactions with the CREB KID domain or β-catenin showed promising preclinical efficacy in combination with dasatinib. These findings highlight novel modulators of sensitivity to targeted therapies in human pre-BCR+ ALL, which can be reversed by small-molecule inhibitors. They also identify promising therapeutic approaches to ameliorate dasatinib sensitivity and prevent resistance in ALL.Significance: These findings reveal mechanisms that modulate sensitivity to dasatinib and suggest therapeutic strategies to improve the outcome of patients with acute lymphoblastic leukemia.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/22/6497/F1.large.jpg Cancer Res; 78(22); 6497-508. ©2018 AACR.
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Affiliation(s)
- Jesús Duque-Afonso
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Chiou-Hong Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - David W Morgens
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Edwin E Jeng
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Ziming Weng
- Department of Pathology, Stanford University School of Medicine, Stanford, California
- Stanford Center for Genomics and Personalized Medicine, Stanford, California
| | - Johan Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Stephen Hon Kit Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Li Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Michael C Wei
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Hee-Don Chae
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Justus Duyster
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Xiangshu Xiao
- Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, Oregon
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, California.
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10
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Haverland NA, Waas M, Ntai I, Keppel T, Gundry RL, Kelleher NL. Cell Surface Proteomics of N-Linked Glycoproteins for Typing of Human Lymphocytes. Proteomics 2018; 17. [PMID: 28834292 DOI: 10.1002/pmic.201700156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/27/2017] [Indexed: 11/12/2022]
Abstract
Lymphocytes are immune cells that are critical for the maintenance of adaptive immunity. Differentiation of lymphoid progenitors yields B-, T-, and NK-cell subtypes that individually correlate with specific forms of leukemia or lymphoma. Therefore, it is imperative a precise method of cell categorization is utilized to detect differences in distinct disease states present in patients. One viable means of classification involves evaluation of the cell surface proteome of lymphoid malignancies. Specifically, this manuscript details the use of an antibody independent approach known as Cell Surface Capture Technology, to assess the N-glycoproteome of four human lymphocyte cell lines. Altogether, 404 cell surface N-glycoproteins were identified as markers for specific cell types involved in lymphocytic malignancies, including 82 N-glycoproteins that had not been previously been described for B or T cells within the Cell Surface Protein Atlas. Comparative analysis, hierarchical clustering techniques, and label-free quantitation were used to reveal proteins most informative for each cell type. Undoubtedly, the characterization of the cell surface proteome of lymphoid malignancies is a first step toward improving personalized diagnosis and treatment of leukemia and lymphoma.
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Affiliation(s)
- Nicole A Haverland
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ioanna Ntai
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Theodore Keppel
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
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11
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Liu Y, Kirkland B, Shirley J, Wang Z, Zhang P, Stembridge J, Wong W, Takebayashi SI, Gilbert DM, Lenhert S, Guan J. Development of a single-cell array for large-scale DNA fluorescence in situ hybridization. LAB ON A CHIP 2013; 13:1316-24. [PMID: 23370691 PMCID: PMC3594524 DOI: 10.1039/c2lc40364a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
DNA fluorescence in situ hybridization (FISH) is a powerful cytogenetic assay, but conventional sample-preparation methods for FISH do not support large-scale high-throughput data acquisition and analysis, which are potentially useful for several biomedical applications. To address this limitation, we have developed a novel FISH sample-preparation method based on generating a centimetre-sized cell array, in which all cells are precisely positioned and separated from their neighbours. This method is simple and capable of patterning nonadherent human cells. We have successfully performed DNA FISH on the single-cell arrays, which facilitates analysis of the FISH results with the FISH-FINDER computer program.
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Affiliation(s)
- Yingru Liu
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-2870, USA
| | - Brett Kirkland
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-2870, USA
| | - James Shirley
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Zhibin Wang
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-2870, USA
| | - Peipei Zhang
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-2870, USA
| | - Jacquelyn Stembridge
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Wilson Wong
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA
| | - Shin-ichiro Takebayashi
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Steven Lenhert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
- Integrative NanoScience Institute, Florida State University, Tallahassee, Florida 32306-4370, USA
| | - Jingjiao Guan
- Department of Chemical and Biomedical Engineering, FAMU-FSU College of Engineering, Florida State University, 2525 Pottsdamer Street, Tallahassee, Florida 32310-2870, USA
- Integrative NanoScience Institute, Florida State University, Tallahassee, Florida 32306-4370, USA
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12
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Rapino F, Robles EF, Richter-Larrea JA, Kallin EM, Martinez-Climent JA, Graf T. C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity. Cell Rep 2013; 3:1153-63. [PMID: 23545498 DOI: 10.1016/j.celrep.2013.03.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 02/15/2013] [Accepted: 03/01/2013] [Indexed: 12/22/2022] Open
Abstract
Earlier work demonstrated that the transcription factor C/EBPα can convert immature and mature murine B lineage cells into functional macrophages. Testing >20 human lymphoma and leukemia B cell lines, we found that most can be transdifferentiated at least partially into macrophage-like cells, provided that C/EBPα is expressed at sufficiently high levels. A tamoxifen-inducible subclone of the Seraphina Burkitt lymphoma line, expressing C/EBPαER, could be efficiently converted into phagocytic and quiescent cells with a transcriptome resembling normal macrophages. The converted cells retained their phenotype even when C/EBPα was inactivated, a hallmark of cell reprogramming. Interestingly, C/EBPα induction also impaired the cells' tumorigenicity. Likewise, C/EBPα efficiently converted a lymphoblastic leukemia B cell line into macrophage-like cells, again dramatically impairing their tumorigenicity. Our experiments show that human cancer cells can be induced by C/EBPα to transdifferentiate into seemingly normal cells at high frequencies and provide a proof of principle for a potential new therapeutic strategy for treating B cell malignancies.
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Affiliation(s)
- Francesca Rapino
- Center for Genomic Regulation, Universidad Pompeu Fabra and Institució Catalana de Recerca i Estudis Avançats, Dr. Aiguader 88, 08003 Barcelona, Spain
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13
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Wilkinson A, Ballabio E, Geng H, North P, Tapia M, Kerry J, Biswas D, Roeder R, Allis C, Melnick A, de Bruijn M, Milne T. RUNX1 is a key target in t(4;11) leukemias that contributes to gene activation through an AF4-MLL complex interaction. Cell Rep 2013; 3:116-27. [PMID: 23352661 PMCID: PMC3607232 DOI: 10.1016/j.celrep.2012.12.016] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 11/08/2012] [Accepted: 12/26/2012] [Indexed: 12/22/2022] Open
Abstract
The Mixed Lineage Leukemia (MLL) protein is an important epigenetic regulator required for the maintenance of gene activation during development. MLL chromosomal translocations produce novel fusion proteins that cause aggressive leukemias in humans. Individual MLL fusion proteins have distinct leukemic phenotypes even when expressed in the same cell type, but how this distinction is delineated on a molecular level is poorly understood. Here, we highlight a unique molecular mechanism whereby the RUNX1 gene is directly activated by MLL-AF4 and the RUNX1 protein interacts with the product of the reciprocal AF4-MLL translocation. These results support a mechanism of transformation whereby two oncogenic fusion proteins cooperate by activating a target gene and then modulating the function of its downstream product.
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Affiliation(s)
- Adam C. Wilkinson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Huimin Geng
- Departments of Medicine/Hematology and Oncology Division, Weill Medical College of Cornell University, New York, NY, 10065, USA
- Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10065, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Phillip North
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Marta Tapia
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Debabrata Biswas
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Robert G. Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - C. David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Ari Melnick
- Departments of Medicine/Hematology and Oncology Division, Weill Medical College of Cornell University, New York, NY, 10065, USA
- Department of Pharmacology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Marella F.T.R. de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Thomas A. Milne
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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14
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Behan JW, Yun JP, Proektor MP, Ehsanipour EA, Arutyunyan A, Moses AS, Avramis VI, Louie SG, Butturini A, Heisterkamp N, Mittelman SD. Adipocytes impair leukemia treatment in mice. Cancer Res 2009; 69:7867-74. [PMID: 19773440 DOI: 10.1158/0008-5472.can-09-0800] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Obesity is associated with increased cancer incidence and mortality. We have previously found that obesity in children is associated with a 50% increased recurrence of acute lymphoblastic leukemia (ALL) in high-risk patients. We have therefore developed novel in vivo and in vitro preclinical models to study the mechanism(s) of this association. Obesity increased relapse after monotherapy with vincristine (P = 0.03) in obese mice injected with syngeneic ALL cells. This occurred although the drug was dosed proportionally to body weight, equalizing blood and tissue drug levels. In coculture, 3T3-L1 adipocytes significantly impaired the antileukemia efficacy of vincristine, as well as three other chemotherapies (P < 0.05). Interestingly, this protection was independent of cell-cell contact, and it extended to human leukemia cell lines as well. Adipocytes prevented chemotherapy-induced apoptosis, and this was associated with increased expression of the two prosurvival signals Bcl-2 and Pim-2. These findings highlight the role of the adipocyte in fostering leukemia chemotherapy resistance, and may help explain the increased leukemia relapse rate in obese children and adults. Given the growing prevalence of obesity worldwide, these effects are likely to have increasing importance to cancer treatment.
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Affiliation(s)
- James W Behan
- Divisions of Endocrinology, Childrens Hospital Los Angeles, Los Angeles, CA, USA
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15
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Skotheim RI, Thomassen GOS, Eken M, Lind GE, Micci F, Ribeiro FR, Cerveira N, Teixeira MR, Heim S, Rognes T, Lothe RA. A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Mol Cancer 2009; 8:5. [PMID: 19152679 PMCID: PMC2633275 DOI: 10.1186/1476-4598-8-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Accepted: 01/19/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings. RESULTS We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies. CONCLUSION This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.
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Affiliation(s)
- Rolf I Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Gard OS Thomassen
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet University Hospital, Oslo, Norway
| | - Marthe Eken
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Department of Cancer Genetics, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
| | - Franclim R Ribeiro
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Nuno Cerveira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Manuel R Teixeira
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sverre Heim
- Department of Cancer Genetics, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Medical Faculty, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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16
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Jackman KM, Frye CB, Hunger SP. Flavopiridol displays preclinical activity in acute lymphoblastic leukemia. Pediatr Blood Cancer 2008; 50:772-8. [PMID: 18000861 DOI: 10.1002/pbc.21386] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND New agents are needed for treatment of children with relapsed acute lymphoblastic leukemia (ALL). Based on altered expression of cell cycle regulatory proteins, including frequent p16 (INK4A) and p15 (INK4B) deletions, flavopiridol (FP; Alvocidib) is an attractive agent for relapsed ALL. PROCEDURE We evaluated the efficacy of FP in ALL cell lines using cell proliferation assays, determined the effects of FP treatment on cell growth and viability in cell lines and patient samples, examined cell cycle kinetics, and evaluated the effect of FP on endogenous cyclin-dependent kinase (CDK) activity, Mcl-1 expression, and RNA polymerase II expression and phosphorylation. RESULTS ALL cell lines are sensitive to FP. At lower concentrations, FP induces transient G(1)-S cell cycle arrest and modest levels of apoptosis in cell lines. In contrast, a sustained G(1)-S and G(2)-M arrest and substantial apoptosis are observed following exposure to higher FP concentrations. After treatment with FP, ALL cell lines have decreased expression of retinoblastoma protein phosphorylated at serines 795 and 807/811, indicating reduced CDK activity. We also show that ALL cell lines are sensitive to clinically achievable concentrations of FP in medium supplemented with human serum and that FP reduces the expression of Mcl-1 and phosphorylated forms of the C-terminal domain of RNA polymerase II. FP also increases cell death by approximately twofold over baseline in primary ALL blasts. CONCLUSIONS These data provide a biological rationale for testing FP in relapsed ALL.
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Affiliation(s)
- Kelly M Jackman
- Department of Pediatrics, University of Florida College of Medicine and the University of Florida Shands Cancer Center, Gainesville, Florida, USA
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17
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Baudis M, Prima V, Tung YH, Hunger SP. ABCB1 over-expression and drug-efflux in acute lymphoblastic leukemia cell lines with t(17;19) and E2A-HLF expression. Pediatr Blood Cancer 2006; 47:757-64. [PMID: 16206189 DOI: 10.1002/pbc.20635] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND The t(17;19)(q21;p13), which occurs in a small subset of acute lymphoblastic leukemias (ALLs) and is associated with a dismal prognosis, creates a chimeric E2A-HLF transcription factor with transforming properties. PROCEDURE We used representational difference analysis to identify candidate E2A-HLF target genes. Transient transfection assays and an inducible expression model system were then used to evaluate the ability of E2A-HLF to modulate target gene expression. RESULTS We identified ABCB1 (MDR1, P-glycoprotein) as a gene differentially expressed in ALL cell lines with and without E2A-HLF expression and demonstrated that t(17;19)+ ALL cell lines expressed high levels of ABCB1 protein and had a drug efflux-positive phenotype. Although ABCB1 transcription is regulated by C/EBPbeta via interaction with a DNA response element that shares significant homology with the optimal E2A-HLF binding site, E2A-HLF did not directly activate transcription of reporter genes under control of ABCB1 promoter elements in transient transfection assays. However, ABCB1 expression was induced in a DNA-binding independent manner by E2A-HLF, E2A-PBX1, and truncated E2A polypeptides consisting of those portions of E2A present in leukemic fusion proteins. CONCLUSIONS E2A-HLF-mediated over-expression of ABCB1 may play a critical role in defining the clinical phenotype of ALLs with a t(17;19), suggesting pharmacologic modulation of ABCB1 activity as a rational therapeutic strategy for this chemotherapy resistant subtype of ALL.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B
- ATP Binding Cassette Transporter, Subfamily B, Member 1
- Binding Sites
- Biological Transport, Active/drug effects
- Biological Transport, Active/genetics
- Cell Line, Tumor
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 19/genetics
- DNA-Binding Proteins/biosynthesis
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Humans
- Oncogene Proteins, Fusion/biosynthesis
- Oncogene Proteins, Fusion/genetics
- Organic Anion Transporters/drug effects
- Organic Anion Transporters/genetics
- Phenotype
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/metabolism
- Prognosis
- RNA, Messenger/drug effects
- RNA, Messenger/genetics
- Rhodamines/pharmacokinetics
- Transcription Factors/biosynthesis
- Transcription Factors/genetics
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Michael Baudis
- Department of Pediatrics, University of Florida College of Medicine and the University of Florida Shands Cancer Center, Gainesville, FL 32610-0296, USA
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18
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Horsley SW, Mackay A, Iravani M, Fenwick K, Valgeirsson H, Dexter T, Ashworth A, Kearney L. Array CGH of fusion gene-positive leukemia-derived cell lines reveals cryptic regions of genomic gain and loss. Genes Chromosomes Cancer 2006; 45:554-64. [PMID: 16523483 DOI: 10.1002/gcc.20317] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human leukemia-derived cell lines containing characteristic chromosomal translocations and inversions have been instrumental in identifying fusion genes implicated in the pathogenesis of the corresponding leukemia. Although chimeric fusion genes usually provide early and essential steps in the development of leukemia, they are not in themselves sufficient, requiring additional genetic events. The nature of these secondary, cooperating genetic events is not known. The advent of genome wide microarray-based methods for assessing copy number changes made it possible to search for cytogenetically invisible regions of chromosome imbalance. We used BAC microarrays with a resolution of 1 Mb to determine whether cryptic regions of deletion or gain were associated with specific leukemia-associated fusion genes in a series of cell lines. To complement the array analysis, we also applied 24-color karyotyping by M-FISH. This revealed cryptic chromosomal translocations and regions of loss or gain in all the cell lines studied. The chromosomal origin of previously unidentified marker chromosomes was revealed. In all cases, chromosomes described as monosomic were shown to be involved in unbalanced translocations with concurrent loss and/or gain of chromosomal material. The extent of these amplified and deleted regions was more accurately defined. Finally, small regions of deletion and amplification, often including genes known to be involved in leukemia progression (for example MYC, TP53, CDKN2A, and KIT), were identified.
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Affiliation(s)
- Sharon W Horsley
- Section of Haemato-Oncology, Institute of Cancer Research, London, United Kingdom
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19
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Prima V, Gore L, Caires A, Boomer T, Yoshinari M, Imaizumi M, Varella-Garcia M, Hunger SP. Cloning and functional characterization of MEF2D/DAZAP1 and DAZAP1/MEF2D fusion proteins created by a variant t(1;19)(q23;p13.3) in acute lymphoblastic leukemia. Leukemia 2005; 19:806-13. [PMID: 15744350 DOI: 10.1038/sj.leu.2403684] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We analyzed the TS-2 acute lymphoblastic leukemia (ALL) cell line that contains a t(1;19)(q23;p13.3) but lacks E2A-PBX1 fusion typically present in leukemias with this translocation. We found that the t(1;19) in TS-2 fuses the 19p13 gene DAZAP1 (Deleted in Azoospermia-Associated Protein 1) to the 1q23 gene MEF2D (Myocyte Enhancer Factor 2D), leading to expression of reciprocal in-frame DAZAP1/MEF2D and MEF2D/DAZAP1 transcripts. MEF2D is a member of the MEF2 family of DNA binding proteins that activate transcription of genes involved in control of muscle cell differentiation, and signaling pathways that mediate response to mitogenic signals and survival of neurons and T-lymphocytes. DAZAP1 is a novel RNA binding protein expressed most abundantly in the testis. We demonstrate that MEF2D/DAZAP1 binds avidly and specifically to DNA in a manner indistinguishable from that of native MEF2D and is a substantially more potent transcriptional activator than MEF2D. We also show that DAZAP1/MEF2D is a sequence-specific RNA-binding protein. MEF2D has been identified as a candidate oncogene in murine retroviral insertional mutagenesis studies. Our data implicate MEF2D in human cancer and suggest that MEF2D/DAZAP1 and/or DAZAP1/MEF2D contribute to leukemogenesis by altering signaling pathways normally regulated by wild-type MEF2D and DAZAP1.
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Affiliation(s)
- V Prima
- Department of Pediatrics, University of Florida College of Medicine and the University of Florida Shands Cancer Center, Gainesville, FL 32610, USA
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20
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Fine BM, Kaspers GJ, Ho M, Loonen AH, Boxer LM. A Genome-Wide View of the In vitro Response to l-Asparaginase in Acute Lymphoblastic Leukemia. Cancer Res 2005. [DOI: 10.1158/0008-5472.291.65.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. In particular, baseline expression of asparagine synthetase (ASNS) was not predictive of response to l-asparaginase. After exposure to l-asparaginase, 5 cell lines and 10 clinical samples exhibited very similar changes in the expression of a large number of genes. However, the gene expression changes occurred more slowly in the clinical samples. These changes included a consistent increase in expression of tRNA synthetases and solute transporters and activating transcription factor and CCAAT/enhancer binding protein family members, a response similar to that observed with amino acid starvation. There was also a consistent decrease in many genes associated with proliferation. Taken together, the changes seem to reflect a consistent coordinated response to asparagine starvation in both cell lines and clinical samples. Importantly, in the clinical samples, increased expression of ASNS after l-asparaginase exposure was not associated with in vitro resistance to l-asparaginase, indicating that ASNS-independent mechanisms of in vitro l-asparaginase resistance are common in ALL. These results suggest that targeting particular genes involved in the response to amino acid starvation in ALL cells may provide a novel way to overcome l-asparaginase resistance.
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Affiliation(s)
- Bernard M. Fine
- 1Center for Molecular Biology in Medicine, Veterans Affairs Palo Alto Health Care System and Department of Medicine
- 2Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California and
| | - Gertjan J.L. Kaspers
- 3Pediatric Hematology/Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Minh Ho
- 1Center for Molecular Biology in Medicine, Veterans Affairs Palo Alto Health Care System and Department of Medicine
| | - Anne H. Loonen
- 3Pediatric Hematology/Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Linda M. Boxer
- 1Center for Molecular Biology in Medicine, Veterans Affairs Palo Alto Health Care System and Department of Medicine
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21
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Curry JD, Glaser MC, Smith MT. Real-time reverse transcription polymerase chain reaction detection and quantification of t(1;19) (E2A-PBX1) fusion genes associated with leukaemia. Br J Haematol 2001; 115:826-30. [PMID: 11843816 DOI: 10.1046/j.1365-2141.2001.03190.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A real-time reverse transcription polymerase chain reaction (RT-PCR) method is described that enabled the detection and quantification of E2A-PBX1 fusion gene transcripts associated with t(1;19). The method was highly reproducible and offered exceptional sensitivity at 5 fg of fusion transcript per reaction, without the need for a nested PCR primer design. To illustrate the usefulness of this new technology the E2A-PBX1 fusion gene transcript expression level for several human leukaemia cell lines that are positive and negative for cytogenetically detectable t(1;19) was determined. The RCH-ACV had a threefold higher expression of E2A-PBX1 transcripts (600 transcripts per cell) than the other t(1;19) positive 697 (150 transcripts per cell). The only other cell line with detectable E2A-PBX1 was CEM, but the level of expression was < 1 transcript per cell.
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Affiliation(s)
- J D Curry
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720-7360, USA
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22
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Boomer T, Varella-Garcia M, McGavran L, Meltesen L, Olsen AS, Hunger SP. Detection of E2A translocations in leukemias via fluorescence in situ hybridization. Leukemia 2001; 15:95-102. [PMID: 11243406 DOI: 10.1038/sj.leu.2401988] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Three rearrangements in ALL disrupt E2A and create E2A fusion proteins: the t(1;19)(q23;p13) and E2A-PBX1, t(17;19)(q22;p13) and E2A-HLF and a cryptic inv(19)(p13;q13) and E2A-FB1. While E2A is fused to PBX1 in most ALLs with a t(1;19), 5-10% of cases have translocations that appear identical, but do not affect E2A or PBX1. Because more intensive therapy improves the outcome of patients with E2A-PBX1positive (1;19) translocations, it is critical to identify this subset of patients so that appropriate therapy can be administered. In addition, there are balanced and unbalanced variants of the t(1;19) and controversy exists regarding the clinical significance of this distinction. We have developed a two-color fluorescence in situ hybridization assay that accurately detects E2A translocations in metaphase and interphase cells, distinguishes between balanced and unbalanced variants and identifies patients with a t(1;19) who lack E2A-PBX1 fusion. We found that clonal microheterogeneity is common in patients with E2A translocations and most patients have mixtures of cells with balanced and unbalanced translocations, suggesting that this distinction represents two ends of a continuum rather than distinct biological entities. These reagents should have widespread clinical utility and be useful for translational and basic research studies involving E2A translocations and this region of chromosome 19p13.
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MESH Headings
- Basic Helix-Loop-Helix Transcription Factors
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 19
- DNA-Binding Proteins/genetics
- Homeodomain Proteins/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia/genetics
- Oncogene Proteins, Fusion/genetics
- Transcription Factors/analysis
- Transcription Factors/genetics
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- T Boomer
- Department of Pediatrics, University of Colorado School of Medicine, Denver, CO, USA
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23
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Magnani I, Chiariello E, Conti AM, Finocchiaro G. A recurrent 19q11-12 breakpoint suggested by cytogenetic and fluorescence in situ hybridization analysis of three glioblastoma cell lines. CANCER GENETICS AND CYTOGENETICS 1999; 110:82-6. [PMID: 10214354 DOI: 10.1016/s0165-4608(98)00190-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Loss of genetic material at chromosome 19 is a rather frequent finding in malignant gliomas. Loss of heterozygosity at region 19q13.3 is common in oligodendrogliomas and is also present, together with other genetic alterations on the same chromosome, in glioblastoma multiforme (GBM). Here we describe the results of cytogenetic and fluorescence in situ hybridization analysis on three GBM cell lines in which a series of complex chromosomal rearrangements affecting chromosome 19 were present. These genetic alterations suggest the presence of a common breakpoint at 19q11-12 which may point to the localization of a fragile site and/or to the presence of tumor suppressor gene(s) in the pericentromeric region of chromosome 19.
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Affiliation(s)
- I Magnani
- Department of Biology and Genetics, School of Medicine, University of Milan, Italy
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24
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Mbangkollo D, Burnett R, McCabe N, Thirman M, Gill H, Yu H, Rowley JD, Diaz MO. The human MLL gene: nucleotide sequence, homology to the Drosophila trx zinc-finger domain, and alternative splicing. DNA Cell Biol 1995; 14:475-83. [PMID: 7598802 DOI: 10.1089/dna.1995.14.475] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We have previously reported the cloning of several cDNAs corresponding to the MLL gene. The predicted primary amino acid sequence of two of these clones, 14p-18B and 14-7, reveals nearly complete identity with parts of the sequences of HRX, ALL-1, and Htrx-1, including a Zinc-finger region with homology to the Drosophila trithorax gene. However, we found that there is a stretch of 39 amino acids that is absent from 14p-18B when compared to ALL-1 and HRX. Another sequence of three amino acids is present in ALL-1, but is absent from 14p-18B and HRX. Nucleotide sequence examination reveals that these differences arise from alternative splicing, suggesting that MLL, HRX, and ALL-1 each represents a different alternative splicing product from the same gene. At least two cDNA clones, 14-7 and 14p-18C, correspond to incompletely processed transcripts including intron sequences. Northern blots using a subclone of 14p-18B revealed mRNA species of 14-16 kb in size in various human tissues. RNase protection assays show that the splice variant containing exon 8 and lacking a 9-bp extension 3' of exon 12 is predominantly expressed in hematopoietic cell lines.
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Affiliation(s)
- D Mbangkollo
- Section of Hematology and Oncology, University of Chicago, IL 60637, USA
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25
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Ashley DM, Bol SJ, Waugh C, Kannourakis G. A novel approach to the measurement of different in vitro leukaemic cell growth parameters: the use of PKH GL fluorescent probes. Leuk Res 1993; 17:873-82. [PMID: 7692186 DOI: 10.1016/0145-2126(93)90153-c] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The application of the fluorescent cell membrane probes PKH2 and PKH 26 GL in the measurement of leukaemic cell growth was examined on four cell lines K562, NALM-6, ACV (a pre-B cell line) and HL-60 using flow cytometry. As the amount of probe per cell reduces at each cell division, the fluorescence can be used to measure cell proliferation. By measuring the mean fluorescence intensity of the cells at the beginning of culture and at various time points, and by combining this information with a viable cell count, it was possible to determine: (1) the number of viable cells; (2) their rate of proliferation; (3) their number of cell divisions; and (4) the maintenance of cells in a viable state over a period of time. It was demonstrated that these parameters could be reliably established using the red fluorescent probe PKH26 GL. In contrast, the green fluorescent probe PKH2 GL showed dye transfer resulting in an underestimation of the number of cell divisions and an overestimation of the maintenance of cells in a viable state. The potential advantages of the use of PKH26 GL over conventional assays for the measurement of leukaemic cell growth parameters are discussed.
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Affiliation(s)
- D M Ashley
- L.A.R.C.H. Cancer Research Unit, Department of Clinical Haematology and Oncology, Royal Children's Hospital, Melbourne, Australia
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26
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McCabe NR, Burnett RC, Gill HJ, Thirman MJ, Mbangkollo D, Kipiniak M, van Melle E, Ziemin-van der Poel S, Rowley JD, Diaz MO. Cloning of cDNAs of the MLL gene that detect DNA rearrangements and altered RNA transcripts in human leukemic cells with 11q23 translocations. Proc Natl Acad Sci U S A 1992; 89:11794-8. [PMID: 1465401 PMCID: PMC50643 DOI: 10.1073/pnas.89.24.11794] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recurring chromosomal abnormalities involving translocations at chromosome 11 band q23 are associated with human myeloid and lymphoid leukemia as well as lymphoma. We have identified the gene located at this break-point and have named it MLL (for myeloid-lymphoid, or mixed-lineage, leukemia). The t(4;11), t(6;11), t(9;11), and t(11;19) are among the most common reciprocal translocations in leukemia cells involving this chromosomal band. We now have evidence that the breakpoints in all of these translocations are clustered within a 9-kilobase (kb) BamHI genomic region of the MLL gene. By Southern blot hybridization using a 0.7-kb BamHI cDNA fragment of the MLL gene called MLL 0.7B, we have detected rearrangements of DNA from cell lines and patient material with an 11q23 translocation in this region. Northern blot analyses indicate that this gene has multiple transcripts, some of which appear to be lineage-specific. In normal pre-B cells, four transcripts of 12.5, 12.0, 11.5, and 2.0 kb are detected. These transcripts are also present in monocytoid cell lines with additional hybridization to a 5.0-kb transcript, indicating that expression of different-sized MLL transcripts may be associated with normal hematopoietic lineage development. In a cell line with a t(4;11), the expression of the 12.5-, 12.0-, and 11.5-kb transcripts is reduced, and there is evidence of three other altered transcripts of 11.5, 11.25, and 11.0 kb. Thus, these 11q23 translocations result in rearrangements of the MLL gene and may lead to altered function(s) of MLL and of other gene(s) involved in the translocation.
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Affiliation(s)
- N R McCabe
- Department of Pediatrics, University of Chicago, IL 60637
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27
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Newman JD, Harrison LC, Eckardt GS, Jack I. Enhanced insulin-receptor tyrosine kinase activity associated with chromosomal translocation (1;19) in a pre-B-cell leukemia line. Int J Cancer 1992; 50:500-4. [PMID: 1310491 DOI: 10.1002/ijc.2910500328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The gene for the insulin receptor has been assigned to chromosome 19 near the breakpoint of the translocation t(1;19) which occurs in 25% of pre-B-cell leukemias. Insulin receptors in a pre-B-cell leukemia cell line (ACV) with t(1;19) were found to have 2-fold higher affinity for insulin, 5-fold higher basal and insulin-stimulated beta sub-unit autophosphorylation, and 2-fold higher basal and 4-fold higher insulin-stimulated beta sub-unit kinase activity on the synthetic peptide poly(Glu,Tyr), compared to receptors in a B-cell line (ADD) with normal karyotype from the same patient. ACV cells had a novel 13-kb receptor mRNA species and expressed a DNA polymorphism localized to the tyrosine kinase domain of the receptor gene. These findings suggest that t(1;19) in the ACV cell may result in rearrangement of the insulin receptor gene and translation of a receptor with enhanced tyrosine kinase activity.
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MESH Headings
- Blotting, Northern
- Blotting, Southern
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 19
- DNA, Neoplasm/genetics
- Gene Expression
- Humans
- In Vitro Techniques
- Insulin/metabolism
- Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- RNA, Messenger/genetics
- RNA, Neoplasm/genetics
- Receptor, Insulin/metabolism
- Translocation, Genetic
- Tumor Cells, Cultured
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Affiliation(s)
- J D Newman
- Burnet Clinical Research Unit, Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
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28
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Ziemin-van der Poel S, McCabe NR, Gill HJ, Espinosa R, Patel Y, Harden A, Rubinelli P, Smith SD, LeBeau MM, Rowley JD. Identification of a gene, MLL, that spans the breakpoint in 11q23 translocations associated with human leukemias. Proc Natl Acad Sci U S A 1991; 88:10735-9. [PMID: 1720549 PMCID: PMC53005 DOI: 10.1073/pnas.88.23.10735] [Citation(s) in RCA: 445] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recurring chromosomal translocations involving chromosome 11, band q23, have been observed in acute lymphoid leukemias and especially in acute myeloid leukemias. We recently showed that breakpoints in four 11q23 translocations, t(4;11)(q21;q23), t(6;11)(q27;q23), t(9;11)(p22;q23), and t(11;19)(q23;p13.3), were contained within a yeast artificial chromosome clone bearing the CD3D and CD3G gene loci. We have identified within the CD3 yeast artificial chromosome a transcription unit that spans the breakpoint junctions of the 4;11, 9;11, and 11;19 translocations, and we describe two other, related transcripts that are upregulated in the RS4;11 cell line. We have named this gene MLL (myeloid/lymphoid, or mixed-lineage, leukemia.
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MESH Headings
- Adult
- Blotting, Northern
- Blotting, Southern
- Cell Line
- Child, Preschool
- Chromosome Banding
- Chromosomes, Human, Pair 11
- Cloning, Molecular
- DNA, Neoplasm/genetics
- DNA, Neoplasm/isolation & purification
- Female
- Gene Expression/drug effects
- Genes
- Humans
- Karyotyping
- Leukemia/genetics
- Male
- Middle Aged
- Poly A/genetics
- Poly A/isolation & purification
- RNA/genetics
- RNA/isolation & purification
- RNA, Messenger
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Restriction Mapping
- Tetradecanoylphorbol Acetate/pharmacology
- Translocation, Genetic
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29
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Secker-Walker LM. Prognostic and biological importance of chromosome findings in acute lymphoblastic leukemia. CANCER GENETICS AND CYTOGENETICS 1990; 49:1-13. [PMID: 2204479 DOI: 10.1016/0165-4608(90)90158-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
At least 25 structural chromosomal abnormalities are now found in acute lymphoblastic leukemia (ALL). Many of the abnormalities are associated with particular clinical or blast cell features. Chromosomal translocation breakpoints in ALL are among those that define regions of the genome of oncogenic potential, the recognition of which has led to an improved understanding of the mechanisms of leukemogenesis. The prognostic importance of chromosome findings in ALL concerns demonstration of long-term survival in patients with high hyperdiploid leukemic clones and identification of patients with certain translocations who are at high risk of treatment failure and for whom alternative therapy such as bone marrow transplantation may be desirable. This review summarizes the more recent chromosomal findings in childhood and adult ALL and discusses how increasing recognition of structural change and adoption of alternative therapy for high-risk chromosomal groups may change the prognostic role of cytogenetics in this type of leukemia.
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30
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Mellentin JD, Nourse J, Hunger SP, Smith SD, Cleary ML. Molecular analysis of the t(1;19) breakpoint cluster region in pre-B cell acute lymphoblastic leukemias. Genes Chromosomes Cancer 1990; 2:239-47. [PMID: 2078515 DOI: 10.1002/gcc.2870020313] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The t(1;19) chromosomal translocation in acute lymphoblastic pre-B cell leukemias involves the gene E2A for helix-loop-helix (HLH) proteins E12 and E47, ubiquitous transcriptional proteins implicated in the regulation of various lymphoid and nonlymphoid genes. To characterize the molecular features of the t(1;19)(q23;p13) translocation, we molecularly cloned breakpoint DNA from t(1;19)-carrying pre-B cell leukemias. In all cases, breakpoints on chromosome 19 occurred within 2 kb of each other in a single intron of the E2A gene. This clustered arrangement resulted in specific truncation of the E2A gene and transcript, with loss of sequences encoding the basic DNA-binding and HLH dimerization motifs from the derivative 19 chromosome. In contrast, breakpoints on chromosome 1 were distributed over a large region and could not be linked to exonic sequences of the PBX1 gene, although identical chromosome 1 sequences are joined to E2A sequences in 1;19 fusion transcripts. These data show that the 1;19 translocation consistently results in exchange of 3' exons encoding the HLH motifs of E2A with DNA from chromosome 1 to form a fusion gene on the derivative 19 chromosome.
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Affiliation(s)
- J D Mellentin
- Department of Pathology, Stanford University School of Medicine, California 94305
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31
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Kees UR, Lukeis R, Ford J, Willoughby ML, Garson OM. Establishment and characterization of a childhood pre-B acute lymphoblastic leukemia cell line, PER-278, with chromosome translocations t(1;19) and t(1;9). CANCER GENETICS AND CYTOGENETICS 1990; 46:201-8. [PMID: 2340491 DOI: 10.1016/0165-4608(90)90105-j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cell line PER-278 was established from a bone marrow sample of a 10-year-old boy diagnosed with pre-B acute lymphoblastic leukemia (ALL). PER-278 cells show the pre-B phenotype, express cytoplasmic Ig, and exhibit two translocations: t(1;19)(q23;p13) and t(1;9)(q23;p13). Assessment of the immunoglobulin rearrangements confirmed the clonal origin of cell line PER-278, and comparison with the patients's leukemic cells showed an identical pattern: loci involved at the breakpoint on chromosome 1 code for the oncogene SKI and for the Fc receptor II and on chromosome 19 for the insulin receptor. The t(1;19) may contribute to the malignant transformation in leukemic cells of pre-B phenotype.
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Affiliation(s)
- U R Kees
- Leukemia Research Laboratory, Princess Margaret Hospital, Perth, Western Australia
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32
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Webber LM, Garson OM, Tate B, McKenzie IF, Hogarth PM. Fc receptor gene translocation in a t(1;19) pre-B ALL cell line. Immunogenetics 1990; 31:356-60. [PMID: 2370080 DOI: 10.1007/bf02115010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have recently mapped the human FCGR2 gene to chromosome 1 bands q23-q24. In situ hybridization of FCGR2 cDNA with a cell line containing a t(1:19)(q23;p13) derived from a patient with pre-B ALL has allowed a more accurate localization of this gene to chromosome 1 band q23. Furthermore, this study indicated a splitting of the FCGR2 gene or gene cluster by the t(1;19). However, Southern analysis showed no genetic rearrangement when compared with a karyotypically normal Epstein-Barr virus (EBV)-transformed cell line from the same patient. This suggests that the translocation breakpoint does not occur within the coding region of this gene.
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Affiliation(s)
- L M Webber
- Department of Cytogenetics and Medicine, St. Vincent's Hospital, Fitzroy, Victoria, Australia
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33
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Nourse J, Mellentin JD, Galili N, Wilkinson J, Stanbridge E, Smith SD, Cleary ML. Chromosomal translocation t(1;19) results in synthesis of a homeobox fusion mRNA that codes for a potential chimeric transcription factor. Cell 1990; 60:535-45. [PMID: 1967982 DOI: 10.1016/0092-8674(90)90657-z] [Citation(s) in RCA: 504] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gene (E2A) for enhancer binding transcription factors E12 and E47 maps to the t(1;19) chromosomal translocation breakpoint in pre-B cell leukemias. Altered E2A transcripts lacking sequences coding for the helix-loop-helix DNA binding motif were detected in several t(1;19)-carrying cell lines. Fusion cDNAs that crossed the t(1;19) breakpoint were cloned and shown to code for an 85 kd protein consisting of the amino-terminal two-thirds of E2A fused to a chromosome 1-derived protein. The fusion protein has the features of a chimeric transcription factor in which the DNA binding domain of E2A is replaced by the putative DNA binding domain of a homeoprotein from chromosome 1 for which the name Prl (pre-B cell leukemia) is proposed. Identical E2A-prl mRNA junctions were detected by PCR in three t(1;19)-carrying cell lines, indicating that the fusion transcripts and predicted chimeric protein are a consistent feature of this translocation.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Burkitt Lymphoma/genetics
- Cell Line
- Chimera
- Chromosome Mapping
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 19
- Cloning, Molecular
- DNA Probes
- DNA, Neoplasm/genetics
- Genes, Homeobox
- Humans
- Molecular Sequence Data
- Oligonucleotide Probes
- RNA, Messenger/genetics
- Restriction Mapping
- Sequence Homology, Nucleic Acid
- Transcription Factors/genetics
- Translocation, Genetic
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Affiliation(s)
- J Nourse
- Department of Pathology, Stanford University School of Medicine, California 94305
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34
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Kaplan GC, Pillion DJ, Rutter WJ, Kim H, Barker PE. Insulin receptor overexpression in a human pre-B acute lymphocytic leukemia cell line with a t(1;19) chromosome translocation near the INSR locus. Biochem Biophys Res Commun 1989; 159:1275-82. [PMID: 2539148 DOI: 10.1016/0006-291x(89)92248-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human pre-B acute lymphocytic leukemia (ALL) cell line 697 contains a disease-specific chromosomal translocation, t(1;19), near the insulin receptor locus (INSR). Insulin binding, insulin receptor kinase and cell surface immunofluorescence experiments all show that 697 cells express more surface insulin receptors than 207 cells, a line of pre-B ALL cells that lack the t(1;19). Northern blot analysis confirms that 697 cells have increased levels of mRNA for the insulin receptor. Gene dosage and in situ hybridization analysis indicate that only two copies of the INSR locus are present in 697 cells, one on the translocation chromosome and one on the normal chromosome 19. The results described here demonstrate that transcriptional up-regulation of the INSR locus is correlated with the t(1;19) translocation found in human pre-B ALL cell line 697.
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MESH Headings
- Blotting, Northern
- Blotting, Southern
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/metabolism
- Cell Line
- Chromosomes, Human, Pair 1
- Chromosomes, Human, Pair 19
- Gene Expression Regulation
- Genes
- Humans
- Protein-Tyrosine Kinases/metabolism
- Receptor, Insulin/genetics
- Receptor, Insulin/metabolism
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- G C Kaplan
- Laboratory of Medical Genetics, Univ. of Alabama, Birmingham 35294
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35
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Coventry BJ, Nacey JN, Orell S, Marshall VR, Seshadri R. Bilateral testicular and adrenal malignant lymphoma of pre B-cell type. THE AUSTRALIAN AND NEW ZEALAND JOURNAL OF SURGERY 1989; 59:79-83. [PMID: 2783648 DOI: 10.1111/j.1445-2197.1989.tb01469.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A rare case of pre B-lymphoblastic lymphoma of the testes and adrenal glands is presented. No lymph node, central nervous system or bone marrow involvement was demonstrated at diagnosis. The primary presentation was of acute unilateral pain and swelling, mimicking simple orchitis. The diagnosis was made using aspiration cytology and the lymphoma characterized using immunohistochemical, electron microscopic and karyotype analysis techniques. Pre B-cell markers were clearly demonstrated by all criteria used. Monoclonal antibodies (FMC 29 and FMC 31) were used to define the early B-cell nature of the lymphoma. Confirmation using karyotype analysis in addition to immunoglobulin and T-cell beta-receptor gene rearrangement was obtained. Intrathecal chemotherapy was used prophylactically. Combination chemotherapy produced regression of the primary lymphomatous lesions, but subsequent bone marrow spread led to death.
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Affiliation(s)
- B J Coventry
- Department of Surgery, Flinders Medical Centre, Adelaide, South Australia
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Matthews C, Kutlaca B, Seshadri R. In vitro cytotoxic drug sensitivity of human normal and malignant lymphocyte-clone-forming cells. INTERNATIONAL JOURNAL OF CELL CLONING 1987; 5:149-57. [PMID: 3471818 DOI: 10.1002/stem.5530050207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cytotoxic drug sensitivity of normal human lymphocytes and malignant lymphocytes was estimated by a clonogenic method. Malignant T and B lymphocytes were relatively more sensitive than normal T lymphocytes to vincristine and Adriamycin. Since no plateau was observed in the clone survival with associated increasing drug concentration, spontaneous mutants could not be detected. It is suggested that the resistance to "natural product" drugs such as vincristine arises from induced mutations and not from the selection of already existing spontaneous mutants.
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Westbrook CA, Rubin CM, Le Beau MM, Kaminer LS, Smith SD, Rowley JD, Diaz MO. Molecular analysis of TCRB and ABL in a t(7;9)-containing cell line (SUP-T3) from a human T-cell leukemia. Proc Natl Acad Sci U S A 1987; 84:251-5. [PMID: 3025859 PMCID: PMC304181 DOI: 10.1073/pnas.84.1.251] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A translocation between chromosomes 7 and 9, t(7;9), has been described in cell lines derived from the malignant cells of children with acute T-cell lymphoblastic leukemia or lymphoma. Our cytogenetic analysis of one such cell line, SUP-T3, demonstrates that the breakpoints on chromosomes 7 and 9 lie within bands q36 and q34, respectively, corresponding to the location of the gene encoding the beta chain of the T-cell receptor, TCRB, and the gene homologous to the transforming gene of the Abelson murine leukemia virus, ABL. We investigated the role of these genes in the t(7;9). In situ chromosomal hybridization of TCRB and ABL probes to metaphase cells from SUP-T3 demonstrated that ABL is translocated from chromosome 9 to 7 and that all or part of TCRB is translocated from chromosome 7 to 9. Southern blot analysis revealed that both TCRB alleles were rearranged; however, it could not be determined whether the translocation breakpoint lies within this gene. Pulsed-field gel electrophoresis and Southern blot analysis were used to examine more than 500 kilobases of the ABL locus; we concluded that there are no rearrangements within 250 kb in either direction of the sequences homologous to v-abl. Additionally, no abnormal ABL protein was detected in an in vitro phosphorylation assay. These results indicate that, in SUP-T3, the breakpoint on chromosome 9 lies proximal to ABL and that the break results in no apparent alteration of the ABL protein. We therefore hypothesize that another gene on chromosome 9, at band q34, plays a role in this translocation. This study also demonstrates that pulsed-field gel electrophoresis is a powerful new tool for the analysis of human chromosomal translocations.
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Gurney ME, Apatoff BR, Spear GT, Baumel MJ, Antel JP, Bania MB, Reder AT. Neuroleukin: a lymphokine product of lectin-stimulated T cells. Science 1986; 234:574-81. [PMID: 3020690 DOI: 10.1126/science.3020690] [Citation(s) in RCA: 162] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Neuroleukin is a lymphokine product of lectin-stimulated T cells that induces immunoglobulin secretion by cultured human peripheral blood mononuclear cells. Neuroleukin acts early in the in vitro response that leads to formation of antibody-secreting cells, but continued production of immunoglobulin by differentiated antibody-secreting cells is neuroleukin-independent. Although the factor is not directly mitogenic, cellular proliferation is a late component of the response to neuroleukin. Neuroleukin does not have B-cell growth factor (BCGF) or B-cell differentiation factor (BCDF) activity in defined assays. Neuroleukin-evoked induction of immunoglobulin secretion is both monocyte- and T-cell-dependent.
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