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Assi SA, Imperato MR, Coleman DJL, Pickin A, Potluri S, Ptasinska A, Chin PS, Blair H, Cauchy P, James SR, Zacarias-Cabeza J, Gilding LN, Beggs A, Clokie S, Loke JC, Jenkin P, Uddin A, Delwel R, Richards SJ, Raghavan M, Griffiths MJ, Heidenreich O, Cockerill PN, Bonifer C. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Nat Genet 2019; 51:151-162. [PMID: 30420649 PMCID: PMC6330064 DOI: 10.1038/s41588-018-0270-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/02/2018] [Indexed: 12/30/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by a variety of alterations in transcription factors, epigenetic regulators and signaling molecules. To determine how different mutant regulators establish AML subtype-specific transcriptional networks, we performed a comprehensive global analysis of cis-regulatory element activity and interaction, transcription factor occupancy and gene expression patterns in purified leukemic blast cells. Here, we focused on specific subgroups of subjects carrying mutations in genes encoding transcription factors (RUNX1, CEBPα), signaling molecules (FTL3-ITD, RAS) and the nuclear protein NPM1). Integrated analysis of these data demonstrates that each mutant regulator establishes a specific transcriptional and signaling network unrelated to that seen in normal cells, sustaining the expression of unique sets of genes required for AML growth and maintenance.
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Affiliation(s)
- Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Daniel J L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Paulynn Suyin Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Helen Blair
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds, UK
| | | | - L Niall Gilding
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Andrew Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sam Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Justin C Loke
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Phil Jenkin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ash Uddin
- CMT Laboratory NHS Blood & Transplant, Edgbaston, Birmingham, UK
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stephen J Richards
- Haematological Malignancy Diagnostic Service, St. James's University Hospital, Leeds, UK
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham, UK
| | - Michael J Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, UK
- Princess Maxima Centrum for Pediatric Oncology, Utrecht, The Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
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2
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Chernova T, Murphy FA, Galavotti S, Sun XM, Powley IR, Grosso S, Schinwald A, Zacarias-Cabeza J, Dudek KM, Dinsdale D, Le Quesne J, Bennett J, Nakas A, Greaves P, Poland CA, Donaldson K, Bushell M, Willis AE, MacFarlane M. Long-Fiber Carbon Nanotubes Replicate Asbestos-Induced Mesothelioma with Disruption of the Tumor Suppressor Gene Cdkn2a (Ink4a/Arf). Curr Biol 2018; 27:3302-3314.e6. [PMID: 29112861 PMCID: PMC5681354 DOI: 10.1016/j.cub.2017.09.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/18/2017] [Accepted: 09/05/2017] [Indexed: 02/07/2023]
Abstract
Mesothelioma is a fatal tumor of the pleura and is strongly associated with asbestos exposure. The molecular mechanisms underlying the long latency period of mesothelioma and driving carcinogenesis are unknown. Moreover, late diagnosis means that mesothelioma research is commonly focused on end-stage disease. Although disruption of the CDKN2A (INK4A/ARF) locus has been reported in end-stage disease, information is lacking on the status of this key tumor suppressor gene in pleural lesions preceding mesothelioma. Manufactured carbon nanotubes (CNTs) are similar to asbestos in terms of their fibrous shape and biopersistent properties and thus may pose an asbestos-like inhalation hazard. Here we show that instillation of either long CNTs or long asbestos fibers into the pleural cavity of mice induces mesothelioma that exhibits common key pro-oncogenic molecular events throughout the latency period of disease progression. Sustained activation of pro-oncogenic signaling pathways, increased proliferation, and oxidative DNA damage form a common molecular signature of long-CNT- and long-asbestos-fiber-induced pathology. We show that hypermethylation of p16/Ink4a and p19/Arf in CNT- and asbestos-induced inflammatory lesions precedes mesothelioma; this results in silencing of Cdkn2a (Ink4a/Arf) and loss of p16 and p19 protein, consistent with epigenetic alterations playing a gatekeeper role in cancer. In end-stage mesothelioma, silencing of p16/Ink4a is sustained and deletion of p19/Arf is detected, recapitulating human disease. This study addresses the long-standing question of which early molecular changes drive carcinogenesis during the long latency period of mesothelioma development and shows that CNT and asbestos pose a similar health hazard.
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Affiliation(s)
- Tatyana Chernova
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Fiona A Murphy
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Sara Galavotti
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Xiao-Ming Sun
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Ian R Powley
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Stefano Grosso
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Anja Schinwald
- Medical Research Council/University of Edinburgh, Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Joaquin Zacarias-Cabeza
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - Kate M Dudek
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - David Dinsdale
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
| | - John Le Quesne
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK; University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Jonathan Bennett
- University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Apostolos Nakas
- University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Peter Greaves
- Department of Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Craig A Poland
- Medical Research Council/University of Edinburgh, Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Ken Donaldson
- Medical Research Council/University of Edinburgh, Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK.
| | - Anne E Willis
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK.
| | - Marion MacFarlane
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK.
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3
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Cauchy P, Maqbool MA, Zacarias-Cabeza J, Vanhille L, Koch F, Fenouil R, Gut M, Gut I, Santana MA, Griffon A, Imbert J, Moraes-Cabé C, Bories JC, Ferrier P, Spicuglia S, Andrau JC. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2015; 44:3567-85. [PMID: 26673693 PMCID: PMC4856961 DOI: 10.1093/nar/gkv1475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 12/20/2022] Open
Abstract
Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4−/CD8− double negative (DN) to CD4+/CD8+ double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its enhancer activity was attained at the DP stage, as reflected by levels of the core transcriptional hallmarks H3K4me1/3, RNA Polymerase II and eRNA. This dual, stage-specific ability reflected a switch from non-T hematopoietic toward T-cell specific gene expression programs during the DN-to-DP transition, as indicated by transcriptome analyses of Ets1−/− thymic cells. Coincidentally, Ets1 associates more specifically with Runx1 in DN and with TCF1 in DP cells. We also provide evidence that Ets1 predominantly binds distal nucleosome-occupied regions in DN and nucleosome-depleted regions in DP. Finally and importantly, we demonstrate that Ets1 induces chromatin remodeling by displacing H3K4me1-marked nucleosomes. Our results thus provide an original model whereby the ability of a transcription factor to bind nucleosomal DNA changes during differentiation with consequences on its cognate enhancer activity.
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Affiliation(s)
- Pierre Cauchy
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Muhammad A Maqbool
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
| | - Joaquin Zacarias-Cabeza
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Laurent Vanhille
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Frederic Koch
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Romain Fenouil
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Marta Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Ivo Gut
- Centre Nacional D'Anàlisi Genòmica, Parc Científic de Barcelona, Baldiri i Reixac 4, Barcelona ES-08028, Spain
| | - Maria A Santana
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Aurélien Griffon
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean Imbert
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Carolina Moraes-Cabé
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Jean-Christophe Bories
- INSERM UMR 1126 Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris F-75475, France
| | - Pierre Ferrier
- CIML CNRS UMR7280, Case 906, Campus de Luminy, Marseille F-13009, France CIML INSERM U1104, Case 906, Campus de Luminy, Marseille F-13009, France Aix-Marseille University, 58 Boulevard Charles Livon, Marseille F-13284, France
| | - Salvatore Spicuglia
- Inserm U1090, Technological Advances for Genomics and Clinics (TAGC), Marseille F-13009, France Aix-Marseille University UMR-S 1090, TAGC, Marseille F-13009, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, 1919 Route de Mende, Montpellier F-34293, France
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4
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Cauchy P, James SR, Zacarias-Cabeza J, Ptasinska A, Imperato MR, Assi SA, Piper J, Canestraro M, Hoogenkamp M, Raghavan M, Loke J, Akiki S, Clokie SJ, Richards SJ, Westhead DR, Griffiths MJ, Ott S, Bonifer C, Cockerill PN. Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature. Cell Rep 2015. [PMID: 26212328 PMCID: PMC4726916 DOI: 10.1016/j.celrep.2015.06.069] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) is characterized by recurrent mutations that affect the epigenetic regulatory machinery and signaling molecules, leading to a block in hematopoietic differentiation. Constitutive signaling from mutated growth factor receptors is a major driver of leukemic growth, but how aberrant signaling affects the epigenome in AML is less understood. Furthermore, AML cells undergo extensive clonal evolution, and the mutations in signaling genes are often secondary events. To elucidate how chronic growth factor signaling alters the transcriptional network in AML, we performed a system-wide multi-omics study of primary cells from patients suffering from AML with internal tandem duplications in the FLT3 transmembrane domain (FLT3-ITD). This strategy revealed cooperation between the MAP kinase (MAPK) inducible transcription factor AP-1 and RUNX1 as a major driver of a common, FLT3-ITD-specific gene expression and chromatin signature, demonstrating a major impact of MAPK signaling pathways in shaping the epigenome of FLT3-ITD AML. FLT3-ITD signaling is associated with a common gene expression signature FLT3-ITD-specific gene expression is associated with a common chromatin signature FLT3-ITD AML displays chronic activation of the inducible transcription factor AP-1 AP-1 cooperates with RUNX1 to shape the epigenome of FLT3-ITD AML
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Affiliation(s)
- Pierre Cauchy
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Joaquin Zacarias-Cabeza
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Anetta Ptasinska
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Rosaria Imperato
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds LS9 7TF, UK
| | - Jason Piper
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Martina Canestraro
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Manoj Raghavan
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; Centre for Clinical Haematology, Queen Elizabeth Hospital, Birmingham B15 2TH, UK
| | - Justin Loke
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Susanna Akiki
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Samuel J Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Stephen J Richards
- Haematological Malignancy Diagnostic Service, St. James's University Hospital, Leeds LS9 7TF, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael J Griffiths
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Constanze Bonifer
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
| | - Peter N Cockerill
- School of Immunity and Infection, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
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5
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Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S. Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics 2013; 14:914. [PMID: 24365181 PMCID: PMC3882496 DOI: 10.1186/1471-2164-14-914] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 12/18/2013] [Indexed: 01/04/2023] Open
Abstract
Background Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. Results We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. Conclusions We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jean-Christophe Andrau
- Technological Advances for Genomics and Clinics (TAGC), Case 928, 163 Avenue de Luminy, 13288, Marseille cedex 09, France.
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Dadi S, Le Noir S, Payet-Bornet D, Lhermitte L, Zacarias-Cabeza J, Bergeron J, Villarèse P, Vachez E, Dik WA, Millien C, Radford I, Verhoeyen E, Cosset FL, Petit A, Ifrah N, Dombret H, Hermine O, Spicuglia S, Langerak AW, Macintyre EA, Nadel B, Ferrier P, Asnafi V. TLX homeodomain oncogenes mediate T cell maturation arrest in T-ALL via interaction with ETS1 and suppression of TCRα gene expression. Cancer Cell 2012; 21:563-76. [PMID: 22516263 DOI: 10.1016/j.ccr.2012.02.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 01/03/2012] [Accepted: 02/13/2012] [Indexed: 10/28/2022]
Abstract
Acute lymphoblastic leukemias (ALLs) are characterized by multistep oncogenic processes leading to cell-differentiation arrest and proliferation. Specific abrogation of maturation blockage constitutes a promising therapeutic option in cancer, which requires precise understanding of the underlying molecular mechanisms. We show that the cortical thymic maturation arrest in T-lineage ALLs that overexpress TLX1 or TLX3 is due to binding of TLX1/TLX3 to ETS1, leading to repression of T cell receptor (TCR) α enhanceosome activity and blocked TCR-Jα rearrangement. TLX1/TLX3 abrogation or enforced TCRαβ expression leads to TCRα rearrangement and apoptosis. Importantly, the autoextinction of clones carrying TCRα-driven TLX1 expression supports TLX "addiction" in TLX-positive leukemias and provides further rationale for targeted therapy based on disruption of TLX1/TLX3.
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Affiliation(s)
- Saïda Dadi
- Department of Hematologye, Université de Médecine Paris Descartes Sorbonne Cité, Centre National de la Recherche Scientifique (CNRS), France
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7
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Spicuglia S, Vincent-Fabert C, Benoukraf T, Tibéri G, Saurin AJ, Zacarias-Cabeza J, Grimwade D, Mills K, Calmels B, Bertucci F, Sieweke M, Ferrier P, Duprez E. Characterisation of genome-wide PLZF/RARA target genes. PLoS One 2011; 6:e24176. [PMID: 21949697 PMCID: PMC3176768 DOI: 10.1371/journal.pone.0024176] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 08/02/2011] [Indexed: 01/30/2023] Open
Abstract
The PLZF/RARA fusion protein generated by the t(11;17)(q23;q21) translocation in acute promyelocytic leukaemia (APL) is believed to act as an oncogenic transcriptional regulator recruiting epigenetic factors to genes important for its transforming potential. However, molecular mechanisms associated with PLZF/RARA-dependent leukaemogenesis still remain unclear. We searched for specific PLZF/RARA target genes by ChIP-on-chip in the haematopoietic cell line U937 conditionally expressing PLZF/RARA. By comparing bound regions found in U937 cells expressing endogenous PLZF with PLZF/RARA-induced U937 cells, we isolated specific PLZF/RARA target gene promoters. We next analysed gene expression profiles of our identified target genes in PLZF/RARA APL patients and analysed DNA sequences and epigenetic modification at PLZF/RARA binding sites. We identify 413 specific PLZF/RARA target genes including a number encoding transcription factors involved in the regulation of haematopoiesis. Among these genes, 22 were significantly down regulated in primary PLZF/RARA APL cells. In addition, repressed PLZF/RARA target genes were associated with increased levels of H3K27me3 and decreased levels of H3K9K14ac. Finally, sequence analysis of PLZF/RARA bound sequences reveals the presence of both consensus and degenerated RAREs as well as enrichment for tissue-specific transcription factor motifs, highlighting the complexity of targeting fusion protein to chromatin. Our study suggests that PLZF/RARA directly targets genes important for haematopoietic development and supports the notion that PLZF/RARA acts mainly as an epigenetic regulator of its direct target genes.
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MESH Headings
- Acetylation
- Binding Sites/genetics
- Chromatin Immunoprecipitation/methods
- Cluster Analysis
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genome-Wide Association Study
- Histones/metabolism
- Humans
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/metabolism
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Methylation
- Oligonucleotide Array Sequence Analysis/methods
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic/genetics
- Promyelocytic Leukemia Zinc Finger Protein
- Protein Binding
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription Factors/genetics
- Transcription Factors/metabolism
- U937 Cells
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Affiliation(s)
- Salvatore Spicuglia
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
| | - Christelle Vincent-Fabert
- Institut National de la Santé et de la Recherche Médicale (INSERM) U891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
| | - Touati Benoukraf
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Guillaume Tibéri
- Institut National de la Santé et de la Recherche Médicale (INSERM) U891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
| | - Andrew J. Saurin
- Institut de Biologie du Développement de Marseille Luminy, Université de la Méditerranée, Campus de Luminy, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6216, Marseille, France
| | - Joaquin Zacarias-Cabeza
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
| | - David Grimwade
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, United Kingdom
| | - Ken Mills
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Boris Calmels
- Institut National de la Santé et de la Recherche Médicale (INSERM) U891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
| | - François Bertucci
- Institut National de la Santé et de la Recherche Médicale (INSERM) U891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Oncologie Moléculaire, Institut Paoli-Calmettes, Marseille, France
| | - Michael Sieweke
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
| | - Estelle Duprez
- Centre d'Immunologie de Marseille-Luminy (CIML), Université de la Méditerranée, Campus de Luminy, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U631, Marseille, France
- Centre National de la Recherche Scientifique (CNRS), UMR 6102, Marseille, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- * E-mail:
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Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S. H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J 2011; 30:4198-210. [PMID: 21847099 DOI: 10.1038/emboj.2011.295] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 07/12/2011] [Indexed: 11/09/2022] Open
Abstract
Combinations of post-translational histone modifications shape the chromatin landscape during cell development in eukaryotes. However, little is known about the modifications exactly delineating functionally engaged regulatory elements. For example, although histone H3 lysine 4 mono-methylation (H3K4me1) indicates the presence of transcriptional gene enhancers, it does not provide clearcut information about their actual position and stage-specific activity. Histone marks were, therefore, studied here at genomic loci differentially expressed in early stages of T-lymphocyte development. The concomitant presence of the three H3K4 methylation states (H3K4me1/2/3) was found to clearly reflect the activity of bona fide T-cell gene enhancers. Globally, gain or loss of H3K4me2/3 at distal genomic regions correlated with, respectively, the induction or the repression of associated genes during T-cell development. In the Tcrb gene enhancer, the H3K4me3-to-H3K4me1 ratio decreases with the enhancer's strength. Lastly, enhancer association of RNA-polymerase II (Pol II) correlated with the presence of H3K4me3 and Pol II accumulation resulted in local increase of H3K4me3. Our results suggest the existence of functional links between Pol II occupancy, H3K4me3 enrichment and enhancer activity.
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Affiliation(s)
- Aleksandra Pekowska
- Centre d'Immunologie de Marseille-Luminy, Parc Scientifique de Luminy, Case 906, Marseille, France
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9
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Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, Spicuglia S, de la Chapelle AL, Heidemann M, Hintermair C, Eick D, Gut I, Ferrier P, Andrau JC. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol 2011; 18:956-63. [PMID: 21765417 DOI: 10.1038/nsmb.2085] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 05/12/2011] [Indexed: 11/09/2022]
Abstract
Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.
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Affiliation(s)
- Frederic Koch
- Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Campus de Luminy, Marseille, France
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10
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Abstract
V(D)J recombination assembles antigen-specific immunoglobulin and T-cell receptor variable region genes from germline V, D, and J segments during lymphocyte development. Regulation of this site-specific DNA rearrangement process occurs with respect to the cell type and stage of differentiation, order of locus recombination, and allele usage. Many of these controls are mediated via the modulation of gene accessibility to the V(D)J recombinase. Here, we summarise recent advances regarding the impact of nuclear organisation and epigenetic-based mechanisms on the regulation of V(D)J recombination.
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Affiliation(s)
- Salvatore Spicuglia
- Centre d'Immunologie de Marseille-Luminy, Université Aix MarseilleMarseilleFrance
- CNRSUMR6102, MarseilleFrance
- InsermU631, MarseilleFrance
| | - Joaquin Zacarias-Cabeza
- Centre d'Immunologie de Marseille-Luminy, Université Aix MarseilleMarseilleFrance
- CNRSUMR6102, MarseilleFrance
- InsermU631, MarseilleFrance
| | - Aleksandra Pekowska
- Centre d'Immunologie de Marseille-Luminy, Université Aix MarseilleMarseilleFrance
- CNRSUMR6102, MarseilleFrance
- InsermU631, MarseilleFrance
| | - Pierre Ferrier
- Centre d'Immunologie de Marseille-Luminy, Université Aix MarseilleMarseilleFrance
- CNRSUMR6102, MarseilleFrance
- InsermU631, MarseilleFrance
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