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Dupain C, Harttrampf AC, Urbinati G, Geoerger B, Massaad-Massade L. Relevance of Fusion Genes in Pediatric Cancers: Toward Precision Medicine. MOLECULAR THERAPY-NUCLEIC ACIDS 2017; 6:315-326. [PMID: 28325298 PMCID: PMC5363511 DOI: 10.1016/j.omtn.2017.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/24/2017] [Accepted: 01/24/2017] [Indexed: 12/19/2022]
Abstract
Pediatric cancers differ from adult tumors, especially by their very low mutational rate. Therefore, their etiology could be explained in part by other oncogenic mechanisms such as chromosomal rearrangements, supporting the possible implication of fusion genes in the development of pediatric cancers. Fusion genes result from chromosomal rearrangements leading to the juxtaposition of two genes. Consequently, an abnormal activation of one or both genes is observed. The detection of fusion genes has generated great interest in basic cancer research and in the clinical setting, since these genes can lead to better comprehension of the biological mechanisms of tumorigenesis and they can also be used as therapeutic targets and diagnostic or prognostic biomarkers. In this review, we discuss the molecular mechanisms of fusion genes and their particularities in pediatric cancers, as well as their relevance in murine models and in the clinical setting. We also point out the difficulties encountered in the discovery of fusion genes. Finally, we discuss future perspectives and priorities for finding new innovative therapies in childhood cancer.
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Affiliation(s)
- Célia Dupain
- Vectorology and Anticancer Therapies, UMR 8203 CNRS, University Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Anne Catherine Harttrampf
- Vectorology and Anticancer Therapies, UMR 8203 CNRS, University Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Giorgia Urbinati
- Vectorology and Anticancer Therapies, UMR 8203 CNRS, University Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Birgit Geoerger
- Vectorology and Anticancer Therapies, UMR 8203 CNRS, University Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France
| | - Liliane Massaad-Massade
- Vectorology and Anticancer Therapies, UMR 8203 CNRS, University Paris-Sud, Gustave Roussy, Université Paris-Saclay, 94805 Villejuif, France.
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52
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Struski S, Lagarde S, Bories P, Puiseux C, Prade N, Cuccuini W, Pages MP, Bidet A, Gervais C, Lafage-Pochitaloff M, Roche-Lestienne C, Barin C, Penther D, Nadal N, Radford-Weiss I, Collonge-Rame MA, Gaillard B, Mugneret F, Lefebvre C, Bart-Delabesse E, Petit A, Leverger G, Broccardo C, Luquet I, Pasquet M, Delabesse E. NUP98 is rearranged in 3.8% of pediatric AML forming a clinical and molecular homogenous group with a poor prognosis. Leukemia 2016; 31:565-572. [PMID: 27694926 DOI: 10.1038/leu.2016.267] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 01/21/2023]
Abstract
Pediatric acute myeloid leukemia (AML) is a rare disease whose prognosis is highly variable according to factors such as chromosomal abnormalities. Recurrent genomic rearrangements are detected in half of pediatric AML by karyotype. NUcleoPorin 98 (NUP98) gene is rearranged with 31 different fusion partner genes. These rearrangements are frequently undetected by conventional cytogenetics, as the NUP98 gene is located at the end of the chromosome 11 short arm (11p15). By screening a series of 574 pediatric AML, we detected a NUP98 rearrangement in 22 cases (3.8%), a frequency similar to CBFB-MYH11 fusion gene (4.0%). The most frequent NUP98 fusion gene partner is NSD1. These cases are homogeneous regarding their biological and clinical characteristics, and associated with bad prognosis only improved by bone marrow transplantation. We detailed the biological characteristics of these AML by exome sequencing which demonstrated few recurrent mutations (FLT3 ITD, WT1, CEBPA, NBPF14, BCR and ODF1). The analysis of the clonal structure in these cases suggests that the mutation order in the NUP98-rearranged pediatric AML begins with the NUP98 rearrangement leading to epigenetic dysregulations then followed by mutations of critical hematopoietic transcription factors and finally, activation of the FLT3 signaling pathway.
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Affiliation(s)
- S Struski
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
| | - S Lagarde
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - P Bories
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - C Puiseux
- Department of Pediatric Oncology, University Hospital of Toulouse, Toulouse, France
| | - N Prade
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - W Cuccuini
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Saint-Louis, Paris, France
| | - M-P Pages
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, Hospices Civils de Lyon, Lyon, France
| | - A Bidet
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Haut-Leveque, Bordeaux, France
| | - C Gervais
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Hautepierre, Strasbourg, France
| | - M Lafage-Pochitaloff
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Medical Genetic, University Hospital of La Timone, Marseille, France
| | - C Roche-Lestienne
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Medical Genetic, University Hospital Jeanne de Flandre, University of Lille 2, Lille, France
| | - C Barin
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Bretonneau, Tours, France
| | - D Penther
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Oncology Genetic, Cancer Institute Henri Becquerel, Rouen, France
| | - N Nadal
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Saint-Étienne, Saint-Etienne, France
| | - I Radford-Weiss
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Necker, Paris, France
| | - M-A Collonge-Rame
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Saint-Jacques, Besancon, France
| | - B Gaillard
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital Robert Debré, Reims, France
| | - F Mugneret
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Cytogenetic, University Hospital of Dijon, Dijon, France
| | - C Lefebvre
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, Oncology and Immunology, University Hospital of Grenoble, Grenoble, France
| | - E Bart-Delabesse
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - A Petit
- Department of Pediatric Oncology, University Hospital of Trousseau, Paris, France
| | - G Leverger
- Department of Pediatric Oncology, University Hospital of Trousseau, Paris, France
| | - C Broccardo
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - I Luquet
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
| | - M Pasquet
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Department of Pediatric Oncology, University Hospital of Toulouse, Toulouse, France
| | - E Delabesse
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
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53
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Amin N, Nietlispach D, Qamar S, Coyle J, Chiarparin E, Williams G. NMR backbone resonance assignment and solution secondary structure determination of human NSD1 and NSD2. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:315-320. [PMID: 27356987 DOI: 10.1007/s12104-016-9691-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Proteins of the NSD family are histone-methyl transferases with critical functions in the regulation of chromatin structure and function. NSD1 and NSD2 are homologous proteins that function as epigenetic regulators of transcription through their abilities to catalyse histone methylation. Misregulation of NSD1 and NSD2 expression or mutations in their genes are linked to a number of human diseases such as Sotos syndrome, and cancers including acute myeloid leukemia, multiple myeloma, and lung cancer. The catalytic domain of both proteins contains a conserved SET domain which is involved in histone methylation. Here we report the backbone resonance assignments and secondary structure information of the catalytic domains of human NSD1 and NSD2.
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Affiliation(s)
- Nader Amin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
- Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Oxford, OX3 7LF, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge, CB2 1GA, UK
| | - Seema Qamar
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Joe Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
| | - Elisabetta Chiarparin
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK
- AstraZeneca, 310 Cambridge Science Park, Cambridge, CB4 0WG, UK
| | - Glyn Williams
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge, CB4 0QA, UK.
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54
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Biomarkers of genome instability and cancer epigenetics. Tumour Biol 2016; 37:13029-13038. [DOI: 10.1007/s13277-016-5278-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/15/2016] [Indexed: 02/06/2023] Open
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55
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Fahrenkrog B, Martinelli V, Nilles N, Fruhmann G, Chatel G, Juge S, Sauder U, Di Giacomo D, Mecucci C, Schwaller J. Expression of Leukemia-Associated Nup98 Fusion Proteins Generates an Aberrant Nuclear Envelope Phenotype. PLoS One 2016; 11:e0152321. [PMID: 27031510 PMCID: PMC4816316 DOI: 10.1371/journal.pone.0152321] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/11/2016] [Indexed: 01/15/2023] Open
Abstract
Chromosomal translocations involving the nucleoporin NUP98 have been described in several hematopoietic malignancies, in particular acute myeloid leukemia (AML). In the resulting chimeric proteins, Nup98's N-terminal region is fused to the C-terminal region of about 30 different partners, including homeodomain (HD) transcription factors. While transcriptional targets of distinct Nup98 chimeras related to immortalization are relatively well described, little is known about other potential cellular effects of these fusion proteins. By comparing the sub-nuclear localization of a large number of Nup98 fusions with HD and non-HD partners throughout the cell cycle we found that while all Nup98 chimeras were nuclear during interphase, only Nup98-HD fusion proteins exhibited a characteristic speckled appearance. During mitosis, only Nup98-HD fusions were concentrated on chromosomes. Despite the difference in localization, all tested Nup98 chimera provoked morphological alterations in the nuclear envelope (NE), in particular affecting the nuclear lamina and the lamina-associated polypeptide 2α (LAP2α). Importantly, such aberrations were not only observed in transiently transfected HeLa cells but also in mouse bone marrow cells immortalized by Nup98 fusions and in cells derived from leukemia patients harboring Nup98 fusions. Our findings unravel Nup98 fusion-associated NE alterations that may contribute to leukemogenesis.
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MESH Headings
- Animals
- Bone Marrow Cells/metabolism
- Bone Marrow Cells/pathology
- Cell Cycle
- DNA-Binding Proteins/analysis
- DNA-Binding Proteins/metabolism
- HeLa Cells
- Homeodomain Proteins/analysis
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Membrane Proteins/analysis
- Membrane Proteins/metabolism
- Mice
- Mitosis
- Nuclear Envelope/genetics
- Nuclear Envelope/metabolism
- Nuclear Envelope/pathology
- Nuclear Pore Complex Proteins/analysis
- Nuclear Pore Complex Proteins/genetics
- Nuclear Pore Complex Proteins/metabolism
- Oncogene Proteins, Fusion/analysis
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Phenotype
- Translocation, Genetic
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Affiliation(s)
- Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
- * E-mail: (BF); (JS)
| | - Valérie Martinelli
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
| | - Nadine Nilles
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
| | - Gernot Fruhmann
- Department of Biomedicine, University Children’s Hospital Basel, Basel, Switzerland
| | - Guillaume Chatel
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
| | - Sabine Juge
- Department of Biomedicine, University Children’s Hospital Basel, Basel, Switzerland
| | - Ursula Sauder
- Biozentrum, Microscopy Center, University of Basel, Basel, Switzerland
| | - Danika Di Giacomo
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Cristina Mecucci
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Perugia, Italy
| | - Jürg Schwaller
- Department of Biomedicine, University Children’s Hospital Basel, Basel, Switzerland
- * E-mail: (BF); (JS)
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56
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Berardi A, Quilici G, Spiliotopoulos D, Corral-Rodriguez MA, Martin-Garcia F, Degano M, Tonon G, Ghitti M, Musco G. Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome. Nucleic Acids Res 2016; 44:3448-63. [PMID: 26896805 PMCID: PMC4838375 DOI: 10.1093/nar/gkw103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/09/2016] [Indexed: 12/19/2022] Open
Abstract
Sotos syndrome is an overgrowth syndrome caused by mutations within the functional domains ofNSD1 gene coding for NSD1, a multidomain protein regulating chromatin structure and gene expression. In particular, PHDVC5HCHNSD1 tandem domain, composed by a classical (PHDV) and an atypical (C5HCH) plant homeo-domain (PHD) finger, is target of several pathological missense-mutations. PHDVC5HCHNSD1 is also crucial for NSD1-dependent transcriptional regulation and interacts with the C2HR domain of transcriptional repressor Nizp1 (C2HRNizp1)in vitro To get molecular insights into the mechanisms dictating the patho-physiological relevance of the PHD finger tandem domain, we solved its solution structure and provided a structural rationale for the effects of seven Sotos syndrome point-mutations. To investigate PHDVC5HCHNSD1 role as structural platform for multiple interactions, we characterized its binding to histone H3 peptides and to C2HRNizp1 by ITC and NMR. We observed only very weak electrostatic interactions with histone H3 N-terminal tails, conversely we proved specific binding to C2HRNizp1 We solved C2HRNizp1 solution structure and generated a 3D model of the complex, corroborated by site-directed mutagenesis. We suggest a mechanistic scenario where NSD1 interactions with cofactors such as Nizp1 are impaired by PHDVC5HCHNSD1 pathological mutations, thus impacting on the repression of growth-promoting genes, leading to overgrowth conditions.
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Affiliation(s)
- Andrea Berardi
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università degli Studi di Milano, Italy
| | - Giacomo Quilici
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Dimitrios Spiliotopoulos
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università Vita e Salute San Raffaele, Milano 21032, Italy
| | - Maria Angeles Corral-Rodriguez
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy Università Vita e Salute San Raffaele, Milano 21032, Italy
| | - Fernando Martin-Garcia
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Massimo Degano
- Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Giovanni Tonon
- Functional genomics of cancer, Division of Experimental Oncology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Michela Ghitti
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
| | - Giovanna Musco
- Biomolecular NMR Unit, Division of Genetics and Cell Biology, IRCCS S. Raffaele Scientific Institute, Milan 20132, Italy
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57
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Complex Commingling: Nucleoporins and the Spindle Assembly Checkpoint. Cells 2015; 4:706-25. [PMID: 26540075 PMCID: PMC4695854 DOI: 10.3390/cells4040706] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/12/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022] Open
Abstract
The segregation of the chromosomes during mitosis is an important process, in which the replicated DNA content is properly allocated into two daughter cells. To ensure their genomic integrity, cells present an essential surveillance mechanism known as the spindle assembly checkpoint (SAC), which monitors the bipolar attachment of the mitotic spindle to chromosomes to prevent errors that would result in chromosome mis-segregation and aneuploidy. Multiple components of the nuclear pore complex (NPC), a gigantic protein complex that forms a channel through the nuclear envelope to allow nucleocytoplasmic exchange of macromolecules, were shown to be critical for faithful cell division and implicated in the regulation of different steps of the mitotic process, including kinetochore and spindle assembly as well as the SAC. In this review, we will describe current knowledge about the interconnection between the NPC and the SAC in an evolutional perspective, which primarily relies on the two mitotic checkpoint regulators, Mad1 and Mad2. We will further discuss the role of NPC constituents, the nucleoporins, in kinetochore and spindle assembly and the formation of the mitotic checkpoint complex during mitosis and interphase.
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58
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Katoh M. Mutation spectra of histone methyltransferases with canonical SET domains and EZH2-targeted therapy. Epigenomics 2015; 8:285-305. [PMID: 26411517 DOI: 10.2217/epi.15.89] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Germline mutations in canonical SET-methyltransferases have been identified in autism and intellectual disability syndromes and gain-of-function somatic alterations in EZH2, MLL3, NSD1, WHSC1 (NSD2) and WHSC1L1 (NSD3) in cancer. EZH2 interacts with AR, ERα, β-catenin, FOXP3, NF-κB, PRC2, REST and SNAI2, resulting in context-dependent transcriptional activation and repression. Pharmacological EZH2 inhibitors are currently in clinical trials for the treatment of B-cell lymphomas and solid tumors. EZH2 inhibitors might also be applicable in the treatment of SWI/SNF-mutant cancers, reflecting the reciprocal expression of and functional overlap between EZH2 and SMARCA4. Because of the risks for autoimmune diseases, cognitive impairment, cardiomyopathy and myelodysplastic syndrome, EZH2 inhibitors should be utilized for cancer treatment in patients receiving long-term surveillance but not for cancer chemoprevention.
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Affiliation(s)
- Masaru Katoh
- Department of Omics Network, National Cancer Center, 5-1-1 Tsukiji, Chuo-ward, Tokyo 104-0045, Japan
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59
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60
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Nebbioso A, Benedetti R, Conte M, Iside C, Altucci L. Genetic mutations in epigenetic modifiers as therapeutic targets in acute myeloid leukemia. Expert Opin Ther Targets 2015; 19:1187-202. [PMID: 26028314 DOI: 10.1517/14728222.2015.1051728] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Despite enormous insights into the molecular mechanisms of acute myeloid leukemia (AML) pathophysiology, this disease is still fatal in the majority of patients, highlighting the urgent need for novel biomarkers useful in AML prognosis and therapy. AREAS COVERED The advent of modern sequencing technologies has allowed the identification of genetic mutations in genes encoding for specific enzymes involved in the epigenetic regulation of gene expression. The authors review recent data demonstrating the involvement of mutations in genes encoding for epigenetic players and their complex combination with somatic genetic mutations in the pathogenesis of AML. They also discuss the prognostic and therapeutic implications of these findings. EXPERT OPINION Current clinical and preclinical studies are underscoring the importance of targeting epigenetic modifiers as new biomarkers for a better prognostic risk stratification and therapeutic evaluation of intermediate-risk patients. Combining data from traditional and modern methodologies will allow a definition of the complex networks of epigenetic changes and molecular interactions between candidate epitargets and key regulators of hematopoiesis. It will thus be possible to achieve an overview of potential aberrant mechanisms driving leukemogenesis in different classes of AML patients. Such an improved approach could pave the way towards 'personalized' therapies.
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Affiliation(s)
- Angela Nebbioso
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples , Via L. De Crecchio 7, 80138 Naples , Italy
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61
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Vougiouklakis T, Hamamoto R, Nakamura Y, Saloura V. The NSD family of protein methyltransferases in human cancer. Epigenomics 2015; 7:863-74. [PMID: 25942451 DOI: 10.2217/epi.15.32] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The NSD family of protein lysine methyltransferases consists of NSD1, NSD2/WHSC1/MMSET and NSD3/WHSC1L1. NSD2 haploinsufficiency causes Wolf-Hirschhorn syndrome, while NSD1 mutations lead to the Sotos syndrome. Recently, a number of studies showed that the NSD methyltransferases were overexpressed, amplified or somatically mutated in multiple types of cancer, suggesting their critical role in cancer. These enzymes methylate specific lysine residues on histone tails and their dysfunction results in epigenomic aberrations which play a fundamental role in oncogenesis. Furthermore, NSD1 was also reported to methylate a nonhistone protein substrate, RELA/p65 subunit of NF-κB, implying its regulatory function through nonhistone methylation pathways. In this review, we summarize the current research regarding the role of the NSD family proteins in cancer and underline their potential as targets for novel cancer therapeutics.
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Affiliation(s)
- Theodore Vougiouklakis
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave, MC2115 Chicago, IL 60637, USA
| | - Ryuji Hamamoto
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave, MC2115 Chicago, IL 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave, MC2115 Chicago, IL 60637, USA
| | - Vassiliki Saloura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave, MC2115 Chicago, IL 60637, USA
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62
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Molecular characterization and testing in acute myeloid leukemia. J Hematop 2015. [DOI: 10.1007/s12308-015-0242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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63
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Drake KM, Watson VG, Kisielewski A, Glynn R, Napper AD. A sensitive luminescent assay for the histone methyltransferase NSD1 and other SAM-dependent enzymes. Assay Drug Dev Technol 2015; 12:258-71. [PMID: 24927133 DOI: 10.1089/adt.2014.583] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
A major focus of our pediatric cancer research is the discovery of chemical probes to further our understanding of the biology of leukemia harboring fusion proteins arising from chromosomal rearrangements, and to develop novel specifically targeted therapies. The NUP98-NSD1 fusion protein occurs in a highly aggressive subtype of acute myeloid leukemia after rearrangement of the genes NUP98 and NSD1. The methyltransferase activity of NSD1 is retained in the fusion, and it gives rise to abnormally high levels of methylation at lysine 36 on histone 3, enforcing oncogene activation. Therefore, inhibition of the methyltransferase activity of NUP98-NSD1 may be considered a viable therapeutic strategy. Here, we report the development and validation of a highly sensitive and robust luminescence-based assay for NSD1 and other methyltransferases that use S-adenosylmethionine (SAM) as a methyl donor. The assay quantifies S-adenosylhomocysteine (SAH), which is produced during methyl transfer from SAM. SAH is converted enzymatically to adenosine monophosphate (AMP); in the process, adenosine triphosphate (ATP) is consumed and the amount of ATP remaining is measured using a luminescent assay kit. The assay was validated by pilot high-throughput screening (HTS), dose-response confirmation of hits, and elimination of artifacts through counterscreening against SAH detection in the absence of NSD1. The known methyltransferase inhibitor suramin was identified, and profiled for selectivity against the histone methyltransferases EZH2, SETD7, and PRMT1. HTS using the luminescent NSD1 assay described here has the potential to deliver selective NSD1 inhibitors that may serve as leads in the development of targeted therapies for NUP98-NSD1-driven leukemias.
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Affiliation(s)
- Katherine M Drake
- High-Throughput Screening and Drug Discovery Lab, Nemours Center for Childhood Cancer Research, A I duPont Hospital for Children , Wilmington, Delaware
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64
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Abstract
In this issue of Blood, Ostronoff et al report a low remission rate in acute myeloid leukemia (AML) patients coexpressing FLT3/ITD and cryptic translocation t(5;11)(q35;p15.5), known as NUP98/NSD1.
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Shen C, Vakoc CR. Gain-of-function mutation of chromatin regulators as a tumorigenic mechanism and an opportunity for therapeutic intervention. Curr Opin Oncol 2015; 27:57-63. [PMID: 25402979 PMCID: PMC4355016 DOI: 10.1097/cco.0000000000000151] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Somatic gain-of-function mutations that drive cancer pathogenesis are well established opportunities for therapeutic intervention, as demonstrated by the clinical efficacy of kinase inhibitors in kinase-mutant malignancies. Here, we discuss the recently discovered gain-of-function mutations in chromatin-regulatory machineries that promote the pathogenesis of cancer. The current understanding of the underlying molecular mechanisms and the therapeutic potential for direct chemical inhibition will be reviewed. RECENT FINDINGS Point mutations that increase the catalytic activity of EZH2 and NSD2 histone methyltransferases are found in distinct subsets of B-cell neoplasms, which promote cell transformation by elevating the global level of H3K27 tri-methylation or H3K36 di-methylation, respectively. In addition, mutations in histone H3 have been identified in certain pediatric cancers which cause reprogramming of H3K27 and H3K36 methylation by interfering with the histone methyltransferase activity. Finally, chromosomal translocations involving chromatin regulator genes can lead to the formation of fusion oncoproteins that directly modify chromatin as their mechanism of action. SUMMARY Although relatively rare in aggregate, gain-of-function mutations in chromatin regulators represent compelling therapeutic targets in genetically defined subsets of cancer patients. However, a broader clinical impact for epigenetic therapies in oncology will require an increased understanding of how nonmutated chromatin regulators function as cancer-specific dependencies.
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Affiliation(s)
- Chen Shen
- aCold Spring Harbor Laboratory, Cold Spring Harbor, New York bMolecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA
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Chopra M, Bohlander SK. Disturbing the histone code in leukemia: translocations and mutations affecting histone methyl transferases. Cancer Genet 2014; 208:192-205. [PMID: 25592767 DOI: 10.1016/j.cancergen.2014.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/01/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
Abstract
Leukemia is characterized by increased numbers of blasts originating from transformed early hematopoietic stem and progenitor cells. Genetic alterations are widely recognized as the main drivers of oncogenic transformation. Of considerable interest are mutations affecting the writers of epigenetic marks. In this review, we focus on histone methyltransferases--enzymes that catalyze the methylation of lysine residues in core histones. Histone methylation is a tightly controlled mechanism that is responsible for both activating as well as repressing gene expression in a site-specific manner, depending on which lysine residue is methylated. Histone methyltransferases, including MLL1, DOT1L, EZH2, and SETD2 are recurrently deregulated in human leukemia, either directly by gene mutations or balanced translocations, or indirectly as components of protein complexes that are disturbed in leukemia due to alterations of the other components in these complexes. Several small molecule inhibitors of histone methyltransferases are currently being clinically evaluated for their therapeutic potential in human leukemia. These drugs reverse some of the adverse effects of aberrant histone methylation, and can induce differentiation and cell death in leukemic blasts.
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Affiliation(s)
- Martin Chopra
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
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Kjeldsen E. A novel insertion ins(18;5)(q21.1;q31.2q35.1) in acute myeloid leukemia associated with microdeletions at 5q31.2, 5q35.1q35.2 and 18q12.3q21.1 detected by oligobased array comparative genomic hybridization. Mol Cytogenet 2014; 7:63. [PMID: 25279000 PMCID: PMC4180307 DOI: 10.1186/s13039-014-0063-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/28/2014] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Nonrandom clonal chromosomal aberrations can be detected in approximately 55% of adult patients with acute myeloid leukemia (AML). Recurrent cytogenetic abnormalities play an important role in diagnosis, classification and prognosis of AML. However, several chromosomal abnormalities have not been completely determined or characterized, primarily because of their low incidence and limited amount of data. RESULTS We characterized an AML patient with a novel apparently balanced insertion ins(18;5)(q21;q31.2q35.1) that was cryptic by G-banding. The rearrangement was further examined by molecular cytogenetic methods and oligobased high-resolution array CGH (oaCGH) analysis. We show that an approximately 31.8 Mb large segment from chromosome 5 bands q31.2 to q35.1 has been inserted, by a direct mechanism, into chromosome 18 between bands q12.3 and q21.1. The insertion was unbalanced with concurrent submicroscopic deletions at 5q31.2 (approximately 0.37 Mb in size), 5q35.1q35.2 (approximately 1.98 Mb in size), and 18q12.3q21.1 (approximately 2.07 Mb in size). The microdeletions affect genes on 5q and 18q that have been associated with hematological malignancy and other cancers. A novel juxtaposition of the genes NPM1 and HAUS1 at 5q35.1 and 18q21.1, respectively, was detected by FISH analysis. Searching the literature and the Mitelman database revealed no previously reported ins(18;5) cases. Interestingly, however, two AML patients with translocation t(5;18)(q35;q21) encompassing the 5q35 and 18q21 breakpoint regions as detected in our present ins(18;5) patient have been reported. CONCLUSIONS It is well-known that cytogenetic abnormalities on the long arm of chromosome 5 affect hematopoiesis. However, the precise mechanism of their involvement in myeloid transformation is elusive. Our present data shed new light onto the frequent abnormalities on 5q as well as to the less frequent abnormalities observed on 18q in myeloid malignancies. In addition, we show that oaCGH analysis is a useful adjunct to revealing submicroscopic aberrations in regions of clinical importance. Reporting rare and nonrandom chromosomal abnormalities contribute to the identification of the whole spectrum of cytogenetic abnormalities in AML and their prognostic significance.
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Affiliation(s)
- Eigil Kjeldsen
- Department of Hematology, HemoDiagnostic Laboratory, Cancer Cytogenetics Section, Aarhus University Hospital, Tage-Hansens Gade 2, Ent. 4A, DK-8000 Aarhus C, Denmark
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Role of NSD1 in H2O2-induced GSTM3 suppression. Cell Signal 2014; 26:2757-64. [PMID: 25193115 DOI: 10.1016/j.cellsig.2014.08.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/06/2014] [Accepted: 08/26/2014] [Indexed: 11/23/2022]
Abstract
Nuclear receptor-binding SET domain-containing protein 1 (NSD1) has been proved to act as a histone methyltransferase and a transcription co-factor to regulate gene expression. However, the role of NSD1 in oxidative stress remains poorly understood. In the present study, we focused on the NSD1 regulation of antioxidant enzyme gene glutathione S-transferase M3 (GSTM3) expression in response to oxidative stress. H2O2 treatment caused the decrease of both NSD1 and GSTM3 expression, and the depletion of NSD1 expression by specific siRNA reversed the H2O2-reduced GSTM3 expression. Furthermore, we investigated NSD1 modulating the transcription of GSTM3 promoter with -63A/C polymorphism closed to TATA box in response to H2O2 by luciferase and in vitro or in vivo DNA-protein binding assays. The promoter activity of GSTM3 with -63A was higher than -63C, and was increased or decreased by the overexpression or depletion of NSD1, but -63C was not influenced. H2O2 repressed the promoter activity of GSTM3 with -63A more than -63C, and the depletion of NSD1 expression weakened H2O2 inhibition on the -63A promoter, but augmented H2O2 inhibition on the -63C promoter. In addition, NSD1 interacted with RNAPII and bound to GSTM3 -63A/C TATA box, with higher binding affinity to -63A than to -63C. These data indicated that NSD1 implicated in H2O2-induced oxidative stress, and H2O2-induced NSD1 suppression resulted in the decrease of GSTM3 expression through the -63A/C TATA box.
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NUP98/NSD1 and FLT3/ITD coexpression is more prevalent in younger AML patients and leads to induction failure: a COG and SWOG report. Blood 2014; 124:2400-7. [PMID: 25145343 DOI: 10.1182/blood-2014-04-570929] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NUP98/NSD1 has recently been reported in association with poor outcome in acute myeloid leukemia (AML). Previous studies also observed a high overlap between NUP98/NSD1 and FLT3/ITD, raising the question as to whether the reported poor outcome is due to NUP98/NSD1 or caused by the co-occurrence of these 2 genetic lesions. We aimed to determine the prognostic significance of NUP98/NSD1 in the context of FLT3/ITD AML. A total of 1421 patients enrolled in 5 consecutive Children's Oncology Group/Children's Cancer Group and SWOG trials were evaluated. NUP98/NSD1 was found in 15% of FLT3/ITD and 7% of cytogenetically normal (CN)-AML. Those with dual FLT3/ITD and NUP98/NSD1 (82% of NUP98/NSD1 patients) had a complete remission rate of 27% vs 69% in FLT3/ITD without NUP98/NSD1 (P < .001). The corresponding 3-year overall survival was 31% vs 48% (P = .011), respectively. In CN-AML, patients with concomitant NUP98/NSD1 and FLT3/ITD had a worse outcome than those harboring NUP98/NSD1 only. In multivariate analysis, the dual NUP98/NSD1 and FLT3/ITD remained an independent predictor of poor outcome, and NUP98/NSD1 without FLT3/ITD lost its prognostic significance. Our study demonstrates that it is the interaction between NUP98/NSD1 and FLT3/ITD that determines the poor outcome of patients with NUP98/NSD1 disease.
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Thanasopoulou A, Tzankov A, Schwaller J. Potent co-operation between the NUP98-NSD1 fusion and the FLT3-ITD mutation in acute myeloid leukemia induction. Haematologica 2014; 99:1465-71. [PMID: 24951466 DOI: 10.3324/haematol.2013.100917] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The NUP98-NSD1 fusion, product of the t(5;11)(q35;p15.5) chromosomal translocation, is one of the most prevalent genetic alterations in cytogenetically normal pediatric acute myeloid leukemias and is associated with poor prognosis. Co-existence of an FLT3-ITD activating mutation has been found in more than 70% of NUP98-NSD1-positive patients. To address functional synergism, we determined the transforming potential of retrovirally expressed NUP98-NSD1 and FLT3-ITD in the mouse. Expression of NUP98-NSD1 provided mouse strain-dependent, aberrant self-renewal potential to bone marrow progenitor cells. Co-expression of FLT3-ITD increased proliferation and maintained self-renewal in vitro. Transplantation of immortalized progenitors co-expressing NUP98-NSD1 and FLT3-ITD into mice resulted in acute myeloid leukemia after a short latency. In contrast, neither NUP98-NSD1 nor FLT3-ITD single transduced cells were able to initiate leukemia. Interestingly, as reported for patients carrying NUP98-NSD1, an increased Flt3-ITD to wild-type Flt3 mRNA expression ratio with increased FLT3-signaling was associated with rapidly induced disease. In contrast, there was no difference in the expression levels of the NUP98-NSD1 fusion or its proposed targets HoxA5, HoxA7, HoxA9 or HoxA10 between animals with different latencies to develop disease. Finally, leukemic cells co-expressing NUP98-NSD1 and FLT3-ITD were very sensitive to a small molecule FLT3 inhibitor, which underlines the significance of aberrant FLT3 signaling for NUP98-NSD1-positive leukemias and suggests new therapeutic approaches that could potentially improve patient outcome.
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Affiliation(s)
| | | | - Juerg Schwaller
- Department of Biomedicine, University Children's Hospital of Basel (UKBB), Switzerland
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Abstract
Nuclear pore complexes (NPCs) are the sole gateways between the nucleus and the cytoplasm of eukaryotic cells and they mediate all macromolecular trafficking between these cellular compartments. Nucleocytoplasmic transport is highly selective and precisely regulated and as such an important aspect of normal cellular function. Defects in this process or in its machinery have been linked to various human diseases, including cancer. Nucleoporins, which are about 30 proteins that built up NPCs, are critical players in nucleocytoplasmic transport and have also been shown to be key players in numerous other cellular processes, such as cell cycle control and gene expression regulation. This review will focus on the three nucleoporins Nup98, Nup214, and Nup358. Common to them is their significance in nucleocytoplasmic transport, their multiple other functions, and being targets for chromosomal translocations that lead to haematopoietic malignancies, in particular acute myeloid leukaemia. The underlying molecular mechanisms of nucleoporin-associated leukaemias are only poorly understood but share some characteristics and are distinguished by their poor prognosis and therapy outcome.
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Luscan A, Laurendeau I, Malan V, Francannet C, Odent S, Giuliano F, Lacombe D, Touraine R, Vidaud M, Pasmant E, Cormier-Daire V. Mutations in SETD2 cause a novel overgrowth condition. J Med Genet 2014; 51:512-7. [PMID: 24852293 DOI: 10.1136/jmedgenet-2014-102402] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Overgrowth conditions are a heterogeneous group of disorders characterised by increased growth and variable features, including macrocephaly, distinctive facial appearance and various degrees of learning difficulties and intellectual disability. Among them, Sotos and Weaver syndromes are clinically well defined and due to heterozygous mutations in NSD1 and EZH2, respectively. NSD1 and EZH2 are both histone-modifying enzymes. These two epigenetic writers catalyse two specific post-translational modifications of histones: methylation of histone 3 lysine 36 (H3K36) and lysine 27 (H3K27). We postulated that mutations in writers of these two chromatin marks could cause overgrowth conditions, resembling Sotos or Weaver syndromes, in patients with no NSD1 or EZH2 abnormalities. METHODS We analysed the coding sequences of 14 H3K27 methylation-related genes and eight H3K36 methylation-related genes using a targeted next-generation sequencing approach in three Sotos, 11 'Sotos-like' and two Weaver syndrome patients. RESULTS We identified two heterozygous mutations in the SETD2 gene in two patients with 'Sotos-like' syndrome: one missense p.Leu1815Trp de novo mutation in a boy and one nonsense p.Gln274* mutation in an adopted girl. SETD2 is non-redundantly responsible for H3K36 trimethylation. The two probands shared similar clinical features, including postnatal overgrowth, macrocephaly, obesity, speech delay and advanced carpal ossification. CONCLUSIONS Our results illustrate the power of targeted next-generation sequencing to identify rare disease-causing variants. We provide a compelling argument for Sotos and Sotos-like syndromes as epigenetic diseases caused by loss-of-function mutations of epigenetic writers of the H3K36 histone mark.
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Affiliation(s)
- Armelle Luscan
- EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France Service de Biochimie et de Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Ingrid Laurendeau
- EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France Service de Biochimie et de Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Valérie Malan
- Service d'Histo-Embryo-Cytogénétique, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Sylvie Odent
- Université de Rennes 1, CNRS UMR6290, Service de Génétique Clinique, CHU Hôpital Sud, Rennes, France
| | | | - Didier Lacombe
- Service de Génétique Médicale, CHU de Bordeaux et EA4576, Université de Bordeaux, Bordeaux, France
| | - Renaud Touraine
- Service de Génétique, CHU de Saint-Etienne, hôpital Nord, Saint-Etienne, France
| | - Michel Vidaud
- EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France Service de Biochimie et de Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Eric Pasmant
- EA7331, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France Service de Biochimie et de Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Valérie Cormier-Daire
- INSERM UMR_1163, Département de génétique, Université Paris Descartes Sorbonne Paris Cité, Institut Imagine, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
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Braekeleer ED, Douet-Guilbert N, Basinko A, Bris MJL, Morel F, Braekeleer MD. Hox gene dysregulation in acute myeloid leukemia. Future Oncol 2014; 10:475-95. [DOI: 10.2217/fon.13.195] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT: In humans, class I homeobox genes (HOX genes) are distributed in four clusters. Upstream regulators include transcriptional activators and members of the CDX family of transcription factors. HOX genes encode proteins and need cofactor interactions, to increase their specificity and selectivity. HOX genes contribute to the organization and regulation of hematopoiesis by controlling the balance between proliferation and differentiation. Changes in HOX gene expression can be associated with chromosomal rearrangements generating fusion genes, such as those involving MLL and NUP98, or molecular defects, such as mutations in NPM1 and CEBPA for example. Several miRNAs are involved in the control of HOX gene expression and their expression correlates with HOX gene dysregulation. HOX genes dysregulation is a dominant mechanism of leukemic transformation. A better knowledge of their target genes and the mechanisms by which their dysregulated expression contributes to leukemogenesis could lead to the development of new drugs.
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Affiliation(s)
- Etienne De Braekeleer
- Laboratoire d’Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Brest, Brest, France
| | - Nathalie Douet-Guilbert
- Laboratoire d’Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Brest, Brest, France
| | - Audrey Basinko
- Laboratoire d’Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Brest, Brest, France
| | - Marie-Josée Le Bris
- Service de Cytogénétique, Cytologie et Biologie de la Reproduction, Hôpital Morvan, CHRU Brest, Brest, France
| | - Frédéric Morel
- Laboratoire d’Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Brest, Brest, France
| | - Marc De Braekeleer
- Laboratoire d’Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Brest, Brest, France
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Tian X, Zhang S, Liu HM, Zhang YB, Blair CA, Mercola D, Sassone-Corsi P, Zi X. Histone lysine-specific methyltransferases and demethylases in carcinogenesis: new targets for cancer therapy and prevention. Curr Cancer Drug Targets 2014; 13:558-79. [PMID: 23713993 DOI: 10.2174/1568009611313050007] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 09/27/2012] [Accepted: 02/12/2013] [Indexed: 12/14/2022]
Abstract
Aberrant histone lysine methylation that is controlled by histone lysine methyltransferases (KMTs) and demethylases (KDMs) plays significant roles in carcinogenesis. Infections by tumor viruses or parasites and exposures to chemical carcinogens can modify the process of histone lysine methylation. Many KMTs and KDMs contribute to malignant transformation by regulating the expression of human telomerase reverse transcriptase (hTERT), forming a fused gene, interacting with proto-oncogenes or being up-regulated in cancer cells. In addition, histone lysine methylation participates in tumor suppressor gene inactivation during the early stages of carcinogenesis by regulating DNA methylation and/or by other DNA methylation independent mechanisms. Furthermore, recent genetic discoveries of many mutations in KMTs and KDMs in various types of cancers highlight their numerous roles in carcinogenesis and provide rare opportunities for selective and tumor-specific targeting of these enzymes. The study on global histone lysine methylation levels may also offer specific biomarkers for cancer detection, diagnosis and prognosis, as well as for genotoxic and non-genotoxic carcinogenic exposures and risk assessment. This review summarizes the role of histone lysine methylation in the process of cellular transformation and carcinogenesis, genetic alterations of KMTs and KDMs in different cancers and recent progress in discovery of small molecule inhibitors of these enzymes.
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Affiliation(s)
- Xuejiao Tian
- Department of Urology, University of California, Irvine, Orange CA 92868, USA
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75
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Abstract
The significance of epigenomic aberrations in cancer development has been underscored by the discovery of mutations in key chromatin modifiers, most notably in hematological malignancies. A new study of pediatric acute lymphoblastic leukemia (ALL) demonstrates the usefulness of mapping global epigenetic signatures and applying these data in a framework to identify and characterize underlying somatic genetic alterations in human cancers.
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76
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Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhsng CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45:1134-40. [PMID: 24071852 PMCID: PMC3966983 DOI: 10.1038/ng.2760] [Citation(s) in RCA: 1307] [Impact Index Per Article: 118.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed in 37% of cancers, was associated with higher rates of every other type of SCNA, TP53 mutations, CCNE1 amplifications and alterations of the PPP2R complex. SCNAs that were internal to chromosomes tended to be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their generation. Significantly recurrent focal SCNAs were observed in 140 regions, including 102 without known oncogene or tumor suppressor gene targets and 50 with significantly mutated genes. Amplified regions without known oncogenes were enriched for genes involved in epigenetic regulation. When levels of genomic disruption were accounted for, 7% of region pairs were anticorrelated, and these regions tended to encompass genes whose proteins physically interact, suggesting related functions. These results provide insights into mechanisms of generation and functional consequences of cancer-related SCNAs.
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Affiliation(s)
- Travis I Zack
- Broad Institute, Cambridge, Massachusetts, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Biophysics Program, Harvard University, Boston, Massachusetts, USA
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Akiki S, Dyer SA, Grimwade D, Ivey A, Abou-Zeid N, Borrow J, Jeffries S, Caddick J, Newell H, Begum S, Tawana K, Mason J, Velangi M, Griffiths M. NUP98-NSD1 fusion in association with FLT3-ITD mutation identifies a prognostically relevant subgroup of pediatric acute myeloid leukemia patients suitable for monitoring by real time quantitative PCR. Genes Chromosomes Cancer 2013; 52:1053-64. [PMID: 23999921 DOI: 10.1002/gcc.22100] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/10/2013] [Indexed: 12/26/2022] Open
Abstract
The cytogenetically cryptic t(5;11)(q35;p15) leading to the NUP98-NSD1 fusion is a rare but recurrent gene rearrangement recently reported to identify a group of young AML patients with poor prognosis. We used reverse transcription polymerase chain reaction (PCR) to screen retrospectively diagnostic samples from 54 unselected pediatric AML patients and designed a real time quantitative PCR assay to track individual patient response to treatment. Four positive cases (7%) were identified; three arising de novo and one therapy related AML. All had intermediate risk cytogenetic markers and a concurrent FLT3-ITD but lacked NPM1 and CEBPA mutations. The patients had a poor response to therapy and all proceeded to hematopoietic stem cell transplant. These data lend support to the adoption of screening for NUP98-NSD1 in pediatric AML without otherwise favorable genetic markers. The role of quantitative PCR is also highlighted as a potential tool for managing NUP98-NSD1 positive patients post-treatment.
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Affiliation(s)
- Susanna Akiki
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS foundation Trust, Birmingham, UK; School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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Napper AD, Watson VG. Targeted drug discovery for pediatric leukemia. Front Oncol 2013; 3:170. [PMID: 23847761 PMCID: PMC3703567 DOI: 10.3389/fonc.2013.00170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/13/2013] [Indexed: 12/31/2022] Open
Abstract
Despite dramatic advances in the treatment of pediatric leukemia over the past 50 years, there remain subsets of patients who respond poorly to treatment. Many of the high-risk cases of childhood leukemia with the poorest prognosis have been found to harbor specific genetic signatures, often resulting from chromosomal rearrangements. With increased understanding of the genetic and epigenetic makeup of high-risk pediatric leukemia has come the opportunity to develop targeted therapies that promise to be both more effective and less toxic than current chemotherapy. Of particular importance is an understanding of the interconnections between different targets within the same cancer, and observations of synergy between two different targeted therapies or between a targeted drug and conventional chemotherapy. It has become clear that many cancers are able to circumvent a single specific blockade, and pediatric leukemias are no exception in this regard. This review highlights the most promising approaches to new drugs and drug combinations for high-risk pediatric leukemia. Key biological evidence supporting selection of molecular targets is presented, together with a critical survey of recent progress toward the discovery, pre-clinical development, and clinical study of novel molecular therapeutics.
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Affiliation(s)
- Andrew D Napper
- High-Throughput Screening and Drug Discovery Laboratory, Nemours Center for Childhood Cancer Research, A.I. duPont Hospital for Children , Wilmington, DE , USA
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79
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Abstract
Systematic studies of the cancer genome have exploded in recent years. These studies have revealed scores of new cancer genes, including many in processes not previously known to be causal targets in cancer. The genes affect cell signaling, chromatin, and epigenomic regulation; RNA splicing; protein homeostasis; metabolism; and lineage maturation. Still, cancer genomics is in its infancy. Much work remains to complete the mutational catalog in primary tumors and across the natural history of cancer, to connect recurrent genomic alterations to altered pathways and acquired cellular vulnerabilities, and to use this information to guide the development and application of therapies.
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Affiliation(s)
- Levi A Garraway
- Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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80
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Shiba N, Ichikawa H, Taki T, Park MJ, Jo A, Mitani S, Kobayashi T, Shimada A, Sotomatsu M, Arakawa H, Adachi S, Tawa A, Horibe K, Tsuchida M, Hanada R, Tsukimoto I, Hayashi Y. NUP98-NSD1 gene fusion and its related gene expression signature are strongly associated with a poor prognosis in pediatric acute myeloid leukemia. Genes Chromosomes Cancer 2013; 52:683-93. [PMID: 23630019 DOI: 10.1002/gcc.22064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/15/2013] [Indexed: 12/17/2022] Open
Abstract
The cryptic t(5;11)(q35;p15.5) creates a fusion gene between the NUP98 and NSD1 genes. To ascertain the significance of this gene fusion, we explored its frequency, clinical impact, and gene expression pattern using DNA microarray in pediatric acute myeloid leukemia (AML) patients. NUP98-NSD1 fusion transcripts were detected in 6 (4.8%) of 124 pediatric AML patients. Supervised hierarchical clustering analyses using probe sets that were differentially expressed in these patients detected a characteristic gene expression pattern, including 18 NUP98-NSD1-negative patients (NUP98-NSD1-like patients). In total, a NUP98-NSD1-related gene expression signature (NUP98-NSD1 signature) was found in 19% (24/124) and in 58% (15/26) of cytogenetically normal cases. Their 4-year overall survival (OS) and event-free survival (EFS) were poor (33.3% in NUP98-NSD1-positive and 38.9% in NUP98-NSD1-like patients) compared with 100 NUP98-NSD1 signature-negative patients (4-year OS: 86.0%, 4-year EFS: 72.0%). Interestingly, t(7;11)(p15;p15)/NUP98-HOXA13, t(6;11)(q27;q23)/MLL-MLLT4 and t(6;9)(p22;q34)/DEK-NUP214, which are known as poor prognostic markers, were found in NUP98-NSD1-like patients. Furthermore, another type of NUP98-NSD1 fusion transcript was identified by additional RT-PCR analyses using other primers in a NUP98-NSD1-like patient, revealing the significance of this signature to detect NUP98-NSD1 gene fusions and to identify a new poor prognostic subgroup in AML.
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Affiliation(s)
- Norio Shiba
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa, Japan
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81
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Sarova I, Brezinova J, Zemanova Z, Bystricka D, Krejcik Z, Soukup P, Vydra J, Cermak J, Jonasova A, Michalova K. Characterization of chromosome 11 breakpoints and the areas of deletion and amplification in patients with newly diagnosed acute myeloid leukemia. Genes Chromosomes Cancer 2013; 52:619-35. [PMID: 23580398 DOI: 10.1002/gcc.22058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 02/24/2013] [Indexed: 01/08/2023] Open
Abstract
Chromosome 11 abnormalities are found in many hematological malignancies. In acute myeloid leukemia (AML), a proto-oncogene MLL (11q23.3) is frequently altered. However, rearrangements involving other regions of chromosome 11 have been reported. Therefore, we have characterized the chromosome 11 breakpoints and common deleted and amplified areas in the bone marrow or peripheral blood cells of newly diagnosed patients with AML. Using molecular-cytogenetic methods (multicolor fluorescence in situ hybridization (mFISH), multicolor banding (mBAND), microarrays, and FISH with bacterial artificial chromosome (BAC) probes, chromosome 11 abnormalities were delineated in 54 out of 300 (18%) newly diagnosed AML patients. At least 36 different chromosome 11 breakpoints were identified; two were recurrent (11p15.4 in the NUP98 gene and 11q23.3 in the MLL gene), and three were possibly nonrandom: 11p13 (ch11:29.31-31.80 Mb), 11p12 (ch11:36.75-37.49 Mb) and 11q13.2 (68.31-68.52 Mb). One new MLL gene rearrangement is also described. No commonly deleted region of chromosome 11 was identified. However, some regions were affected more often: 11pter-11p15.5 (n = 4; ch11:0-3.52 Mb), 11p14.1-11p13 (n = 4; ch11:28.00-31.00 Mb) and 11p13 (n = 4; ch11:31.00-31.50 Mb). One commonly duplicated (3 copies) region was identified in chromosomal band 11q23.3-11q24 (n = 9; ch11:118.35-125.00 Mb). In all eight cases of 11q amplification (>3 copies), only the 5' part of the MLL gene was affected. This study highlights several chromosome 11 loci that might be important for the leukemogeneic process in AML.
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Affiliation(s)
- Iveta Sarova
- Cytogenetic Department, Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
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82
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Daraki A, Bourantas LK, Manola KN. Translocation t(5;18)(q35;q21) as a rare nonrandom abnormality in acute myeloid leukemia. Cytogenet Genome Res 2013; 139:289-94. [PMID: 23548668 DOI: 10.1159/000348786] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2012] [Indexed: 12/16/2023] Open
Abstract
Cytogenetic abnormalities play an important role in diagnosis, classification and prognosis in acute myeloid leukemia (AML). Nevertheless, several chromosome abnormalities have not been completely determined, and their prognostic significance is currently unknown due to their low incidence and the sporadic limited data. We report a case of AML-M2 with a novel, nonrandom translocation t(5;18)(q35;q21) in order to clarify the clinical features and outcome of these patients which could be advisable for prognostic and therapeutic purposes. This translocation has been reported only once in AML. Our patient received intensive chemotherapy, but he achieved a complete remission only initially. Eighteen months post diagnosis, t(3;12)(p23;p13) was detected as a secondary abnormality to t(5;18)(q35;q21) in the progression of the disease. FISH studies confirmed the reciprocal t(5;18)(q35;q21) and demonstrated a rearrangement of ETV6 gene as a consequence of t(3;12)(p23;p13). The patient died a few days later. In conclusion, t(5;18)(q35;q21) is a rare but nonrandom abnormality in AML, found in FAB M2 subtype, possibly associated with a rather poor prognosis, while t(3;12)(p23;p13) seems to contribute to the progression of the disease. The publication of rare, nonrandom chromosome abnormalities such as t(5;18)(q35;q21) contribute to the identification of the whole spectrum of cytogenetic abnormalities in AML and their prognostic significance.
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MESH Headings
- Aged
- Chromosomes, Human, Pair 18/genetics
- Chromosomes, Human, Pair 5/genetics
- Disease Progression
- Fatal Outcome
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Male
- Metaphase
- Prognosis
- Proto-Oncogene Proteins c-ets/genetics
- Repressor Proteins/genetics
- Translocation, Genetic
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- A Daraki
- Department of Cytogenetics, Laboratory of Health Physics and Environmental Health, NCSR Demokritos, Athens, Greece
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83
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Sarris M, Nikolaou K, Talianidis I. Context-specific regulation of cancer epigenomes by histone and transcription factor methylation. Oncogene 2013; 33:1207-17. [PMID: 23503463 DOI: 10.1038/onc.2013.87] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 02/01/2013] [Indexed: 12/18/2022]
Abstract
Altered expression or activity of histone lysine methylases and demethylases in cancer lead to aberrant chromatin modification patterns, which contribute to uncontrolled cell proliferation via cancer-specific deregulation of gene expression programs or the induction of genome instability. Several transcription factors that regulate growth-associated genes undergo lysine methylation, expanding the repertoire of regulatory targets modulated by histone-methylating enzymes during tumorigenesis. In certain specific tumor types or specific physiological conditions, these enzymes may trigger chromatin structure and/or transcription factor activity changes that result in opposite effects on cancer initiation or progression. The mechanisms of such context-specific dual functions and those involved in the crosstalk between factor and histone modifications are subject to extensive research, which is beginning to shed light into this novel level of complexity of cancer-related epigenetic pathways.
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Affiliation(s)
- M Sarris
- Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - K Nikolaou
- Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | - I Talianidis
- Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
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84
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Andreu-Vieyra CV, Liang G. Nucleosome occupancy and gene regulation during tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:109-34. [PMID: 22956498 DOI: 10.1007/978-1-4419-9967-2_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the basic structural units of eukaryotic chromatin. In recent years, it has become evident that nucleosomes and their position, in concert with other epigenetic mechanisms (such as DNA methylation, histone modifications, changes in histone variants, as well as small noncoding regulatory RNAs) play essential roles in the control of gene expression. Here, we discuss the mechanisms and factors that regulate nucleosome position and gene expression in normal and cancer cells.
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85
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Asangani IA, Ateeq B, Cao Q, Dodson L, Pandhi M, Kunju LP, Mehra R, Lonigro RJ, Siddiqui J, Palanisamy N, Wu YM, Cao X, Kim JH, Zhao M, Qin ZS, Iyer MK, Maher CA, Kumar-Sinha C, Varambally S, Chinnaiyan AM. Characterization of the EZH2-MMSET histone methyltransferase regulatory axis in cancer. Mol Cell 2012; 49:80-93. [PMID: 23159737 DOI: 10.1016/j.molcel.2012.10.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/10/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Histone methyltransferases (HMTases), as chromatin modifiers, regulate the transcriptomic landscape in normal development as well in diseases such as cancer. Here, we molecularly order two HMTases, EZH2 and MMSET, that have established genetic links to oncogenesis. EZH2, which mediates histone H3K27 trimethylation and is associated with gene silencing, was shown to be coordinately expressed and function upstream of MMSET, which mediates H3K36 dimethylation and is associated with active transcription. We found that the EZH2-MMSET HMTase axis is coordinated by a microRNA network and that the oncogenic functions of EZH2 require MMSET activity. Together, these results suggest that the EZH2-MMSET HMTase axis coordinately functions as a master regulator of transcriptional repression, activation, and oncogenesis and may represent an attractive therapeutic target in cancer.
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Affiliation(s)
- Irfan A Asangani
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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86
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Braoudaki M, Tzortzatou-Stathopoulou F. Clinical Cytogenetics in Pediatric Acute Leukemia: An Update. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2012; 12:230-7. [DOI: 10.1016/j.clml.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 12/25/2011] [Accepted: 04/13/2012] [Indexed: 12/28/2022]
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87
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A transposon-based analysis of gene mutations related to skin cancer development. J Invest Dermatol 2012; 133:239-48. [PMID: 22832494 DOI: 10.1038/jid.2012.245] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nonmelanoma skin cancer (NMSC) is by far the most frequent type of cancer in humans. NMSC includes several types of malignancies with different clinical outcomes, the most frequent being basal and squamous cell carcinomas. We have used the Sleeping Beauty transposon/transposase system to identify somatic mutations associated with NMSC. Transgenic mice bearing multiple copies of a mutagenic Sleeping Beauty transposon T2Onc2 and expressing the SB11 transposase under the transcriptional control of regulatory elements from the keratin K5 promoter were treated with TPA, either in wild-type or Ha-ras mutated backgrounds. After several weeks of treatment, mice with transposition developed more malignant tumors with decreased latency compared with control mice. Transposon/transposase animals also developed basal cell carcinomas. Genetic analysis of the transposon integration sites in the tumors identified several genes recurrently mutated in different tumor samples, which may represent novel candidate cancer genes. We observed alterations in the expression levels of some of these genes in human tumors. Our results show that inactivating mutations in Notch1 and Nsd1, among others, may have an important role in skin carcinogenesis.
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88
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Abstract
Histone side chains are post-translationally modified at multiple sites, including at Lys36 on histone H3 (H3K36). Several enzymes from yeast and humans, including the methyltransferases SET domain-containing 2 (Set2) and nuclear receptor SET domain-containing 1 (NSD1), respectively, alter the methylation status of H3K36, and significant progress has been made in understanding how they affect chromatin structure and function. Although H3K36 methylation is most commonly associated with the transcription of active euchromatin, it has also been implicated in diverse processes, including alternative splicing, dosage compensation and transcriptional repression, as well as DNA repair and recombination. Disrupted placement of methylated H3K36 within the chromatin landscape can lead to a range of human diseases, underscoring the importance of this modification.
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89
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Krishnan S, Mali RS, Koehler KR, Vemula S, Chatterjee A, Ghosh J, Ramdas B, Ma P, Hashino E, Kapur R. Class I(A) PI3Kinase regulatory subunit, p85α, mediates mast cell development through regulation of growth and survival related genes. PLoS One 2012; 7:e28979. [PMID: 22238586 PMCID: PMC3251560 DOI: 10.1371/journal.pone.0028979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 11/18/2011] [Indexed: 12/04/2022] Open
Abstract
Stem cell factor (SCF) mediated KIT receptor activation plays a pivotal role in mast cell growth, maturation and survival. However, the signaling events downstream from KIT are poorly understood. Mast cells express multiple regulatory subunits of class 1A PI3Kinase (PI3K) including p85α, p85β, p50α, and p55α. While it is known that PI3K plays an essential role in mast cells; the precise mechanism by which these regulatory subunits impact specific mast cell functions including growth, survival and cycling are not known. We show that loss of p85α impairs the growth, survival and cycling of mast cell progenitors (MCp). To delineate the molecular mechanism (s) by which p85α regulates mast cell growth, survival and cycling, we performed microarray analyses to compare the gene expression profile of MCps derived from WT and p85α-deficient mice in response to SCF stimulation. We identified 151 unique genes exhibiting altered expression in p85α-deficient cells in response to SCF stimulation compared to WT cells. Functional categorization based on DAVID bioinformatics tool and Ingenuity Pathway Analysis (IPA) software relates the altered genes due to lack of p85α to transcription, cell cycle, cell survival, cell adhesion, cell differentiation, and signal transduction. Our results suggest that p85α is involved in mast cell development through regulation of expression of growth, survival and cell cycle related genes.
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Affiliation(s)
- Subha Krishnan
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Raghuveer Singh Mali
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Karl R. Koehler
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sasidhar Vemula
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Anindya Chatterjee
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Joydeep Ghosh
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Baskar Ramdas
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Peilin Ma
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Eri Hashino
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Reuben Kapur
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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90
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Abstract
Cancer genome analyses have revealed that the enzymes involved in epigenetic gene regulation are frequently deregulated in cancer. Here we describe the enzymes that control the epigenetic state of the cell, how they are affected in cancer and how this knowledge can be exploited to treat cancer with a new arsenal of selective therapies.
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Affiliation(s)
- E-J Geutjes
- Division of Molecular Carcinogenesis, Centre for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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91
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Abstract
Structural chromosomal rearrangements of the Nucleoporin 98 gene (NUP98), primarily balanced translocations and inversions, are associated with a wide array of hematopoietic malignancies. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. NUP98 gene fusions typically encode a fusion protein that retains the amino terminus of NUP98; in this context, it is important to note that several recent studies have demonstrated that the amino-terminal portion of NUP98 exhibits transcription activation potential. Approximately half of the NUP98 fusion partners encode homeodomain proteins, and at least 5 NUP98 fusions involve known histone-modifying genes. Several of the NUP98 fusions, including NUP98-homeobox (HOX)A9, NUP98-HOXD13, and NUP98-JARID1A, have been used to generate animal models of both lymphoid and myeloid malignancy; these models typically up-regulate HOXA cluster genes, including HOXA5, HOXA7, HOXA9, and HOXA10. In addition, several of the NUP98 fusion proteins have been shown to inhibit differentiation of hematopoietic precursors and to increase self-renewal of hematopoietic stem or progenitor cells, providing a potential mechanism for malignant transformation.
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92
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NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood 2011; 118:3645-56. [PMID: 21813447 DOI: 10.1182/blood-2011-04-346643] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Translocations involving nucleoporin 98kD (NUP98) on chromosome 11p15 occur at relatively low frequency in acute myeloid leukemia (AML) but can be missed with routine karyotyping. In this study, high-resolution genome-wide copy number analyses revealed cryptic NUP98/NSD1 translocations in 3 of 92 cytogenetically normal (CN)-AML cases. To determine their exact frequency, we screened > 1000 well-characterized pediatric and adult AML cases using a NUP98/NSD1-specific RT-PCR. Twenty-three cases harbored the NUP98/NSD1 fusion, representing 16.1% of pediatric and 2.3% of adult CN-AML patients. NUP98/NSD1-positive AML cases had significantly higher white blood cell counts (median, 147 × 10⁹/L), more frequent FAB-M4/M5 morphology (in 63%), and more CN-AML (in 78%), FLT3/internal tandem duplication (in 91%) and WT1 mutations (in 45%) than NUP98/NSD1-negative cases. NUP98/NSD1 was mutually exclusive with all recurrent type-II aberrations. Importantly, NUP98/NSD1 was an independent predictor for poor prognosis; 4-year event-free survival was < 10% for both pediatric and adult NUP98/NSD1-positive AML patients. NUP98/NSD1-positive AML showed a characteristic HOX-gene expression pattern, distinct from, for example, MLL-rearranged AML, and the fusion protein was aberrantly localized in nuclear aggregates, providing insight into the leukemogenic pathways of these AMLs. Taken together, NUP98/NSD1 identifies a previously unrecognized group of young AML patients, with distinct characteristics and dismal prognosis, for whom new treatment strategies are urgently needed.
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93
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Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD. Role of the nuclear envelope in genome organization and gene expression. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 3:147-66. [PMID: 21305702 DOI: 10.1002/wsbm.101] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although often depicted as a static structure upon which proteinaceous factors bind to control gene expression, the genome is actually highly mobile and capable of exploring the complex domain architecture of the nucleus, which in turn controls genome maintenance and gene expression. Numerous genes relocate from the nuclear periphery to the nuclear interior upon activation and are hypothesized to interact with pre-assembled sites of transcription. In contrast to the nuclear interior, the nuclear periphery is widely regarded as transcriptionally silent. This is reflected by the preferential association of heterochromatin with the nuclear envelope (NE). However, some activated genes are recruited to the nuclear periphery through interactions with nuclear pore complexes (NPCs), and NPC components are capable of preventing the spread of silent chromatin into adjacent regions of active chromatin, leading to the speculation that NPCs may facilitate the transition of chromatin between transcriptional states. Thus, the NE might better be considered as a discontinuous platform that promotes both gene activation and repression. As such, it is perhaps not surprising that many disease states are frequently associated with alterations in the NE. Here, we review the effects of the NE and its constituents on chromatin organization and gene expression.
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94
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Cheung N, So CWE. Transcriptional and epigenetic networks in haematological malignancy. FEBS Lett 2011; 585:2100-11. [DOI: 10.1016/j.febslet.2011.03.068] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 12/16/2022]
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95
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Qiao Q, Li Y, Chen Z, Wang M, Reinberg D, Xu RM. The structure of NSD1 reveals an autoregulatory mechanism underlying histone H3K36 methylation. J Biol Chem 2011; 286:8361-8368. [PMID: 21196496 PMCID: PMC3048720 DOI: 10.1074/jbc.m110.204115] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Indexed: 01/10/2023] Open
Abstract
The Sotos syndrome gene product, NSD1, is a SET domain histone methyltransferase that primarily dimethylates nucleosomal histone H3 lysine 36 (H3K36). To date, the intrinsic properties of NSD1 that determine its nucleosomal substrate selectivity and dimethyl H3K36 product specificity remain unknown. The 1.7 Å structure of the catalytic domain of NSD1 presented here shows that a regulatory loop adopts a conformation that prevents free access of H3K36 to the bound S-adenosyl-L-methionine. Molecular dynamics simulation and computational docking revealed that this normally inhibitory loop can adopt an active conformation, allowing H3K36 access to the active site, and that the nucleosome may stabilize the active conformation of the regulatory loop. Hence, our study reveals an autoregulatory mechanism of NSD1 and provides insight into the molecular mechanism of the nucleosomal substrate selectivity of this disease-related H3K36 methyltransferase.
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Affiliation(s)
- Qi Qiao
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China and
| | - Yan Li
- Department of Biochemistry, New York University School of Medicine, New York, New York 10016
| | - Zhi Chen
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China and
| | - Mingzhu Wang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China and
| | - Danny Reinberg
- Department of Biochemistry, New York University School of Medicine, New York, New York 10016; the Howard Hughes Medical Institute and
| | - Rui-Ming Xu
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China and.
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96
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Peters AHFM, Schwaller J. Epigenetic mechanisms in acute myeloid leukemia. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2011; 67:197-219. [PMID: 21141731 DOI: 10.1007/978-3-7643-8989-5_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Acute leukemia is characterized by clonal expansion of hematopoietic stem and progenitor cells with blocked differentiation. Clinical and experimental evidences suggest that acute myeloid leukemia (AML) is the product of several functionally cooperating genetic alterations including chromosomal translocations leading to expression of leukemogenic fusion proteins. Several AML-associated lesions target chromatin regulators like histone methyltransferases or histone acetyltransferases, including mixed-lineage leukemia 1 (MLL1) or CREB bindung protein/p300. Molecular and biochemical studies start to provide useful insights into the mechanisms of targeting and mode-of-action of such leukemogenic fusion proteins resulting in aberrant gene expression programs and AML. Chromatin modulating mechanisms are also mediating the transforming activity of key drivers of leukemogenesis by aberrant recruitment of corepressors. Recent large-scale screening efforts demonstrated that both aberrant DNA promoter methylation and aberrantly expressed microRNAs play an important role in the pathogenesis of AML as well. Current efforts to therapeutically exploit the potential reversibility of epigenetic mechanisms are focused on small molecules that inhibit DNA methyltransferases or histone deacetylases. Several phase I/II clinical trials using such compounds have reported promising, but mostly transient, clinical responses. This underscores the need to further dissect the molecular players of epigenetic mechanisms driving induction, maintenance, and potential reversibility of leukemic state to develop efficient and long-lasting targeted therapeutic strategies.
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Affiliation(s)
- Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.
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97
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Berdasco M, Esteller M. Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 2010; 19:698-711. [PMID: 21074720 DOI: 10.1016/j.devcel.2010.10.005] [Citation(s) in RCA: 411] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Appropriate patterns of DNA methylation and histone modifications are required to assure cell identity, and their deregulation can contribute to human diseases, such as cancer. Our aim here is to provide an overview of how epigenetic factors, including genomic DNA methylation, histone modifications, and microRNA regulation, contribute to normal development, paying special attention to their role in regulating tissue-specific genes. In addition, we summarize how these epigenetic patterns go awry during human cancer development. The possibility of "resetting" the abnormal cancer epigenome by applying pharmacological or genetic strategies is also discussed.
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Affiliation(s)
- María Berdasco
- Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, 08907 Barcelona, Catalonia, Spain
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98
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Varier RA, Timmers HTM. Histone lysine methylation and demethylation pathways in cancer. Biochim Biophys Acta Rev Cancer 2010; 1815:75-89. [PMID: 20951770 DOI: 10.1016/j.bbcan.2010.10.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 12/21/2022]
Abstract
The genetic changes leading to the development of human cancer are accompanied by alterations in the structure and modification status of chromatin, which represent powerful regulatory mechanisms for gene expression and genome stability. These epigenetic alterations have sparked interest into deciphering the regulatory pathways and function of post-translational modifications of histones during the initiation and progression of cancer. In this review we describe and summarize the current knowledge of several histone lysine methyltransferase and demethylase pathways relevant to cancer. Mechanistic insight into histone modifications will pave the way for the development and therapeutic application of "epidrugs" in cancer.
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Affiliation(s)
- Radhika A Varier
- Department of Physiological Chemistry, University Medical Centre, Utrecht, The Netherlands
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99
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Abstract
Three general approaches have been used to model myelodysplastic syndrome (MDS) in mice, including treatment with mutagens or carcinogens, xenotransplantation of human MDS cells, and genetic engineering of mouse hematopoietic cells. This article discusses the phenotypes observed in available mouse models for MDS with a concentration on a model that leads to aberrant expression of conserved homeobox genes that are important regulators of normal hematopoiesis. Using these models of MDS should allow a more complete understanding of the disease process and provide a platform for preclinical testing of therapeutic approaches.
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Affiliation(s)
- Sarah H Beachy
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 8901 Wisconsin Avenue, Bethesda, MD 20889-5105, USA
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100
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Wang Y, Xue Y, Chen S, Wu Y, Pan J, Zhang J, Shen J. A novel t(5;11)(q31;p15) involving the NUP98 gene on 11p15 is associated with a loss of the EGR1 gene on 5q31 in a patient with acute myeloid leukemia. ACTA ACUST UNITED AC 2010; 199:9-14. [PMID: 20417862 DOI: 10.1016/j.cancergencyto.2010.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Revised: 01/07/2010] [Accepted: 01/12/2010] [Indexed: 11/26/2022]
Abstract
To date, at least 25 translocations involving the NUP98 gene and different partner genes have been reported in the literature. Here, we describe a novel reciprocal t(5;11)(q31;p15) involving NUP98, as revealed by conventional karyotypic analysis using R-banding technique and fluorescence in situ hybridization (FISH) using a BAC RP11-120E20 probe and whole chromosome paint probes for chromosomes 5 and 11 in a 77-year-old woman who was diagnosed as having de novo acute myeloid leukemia. The patient received two courses of intensive combined chemotherapy but did not reach complete remission. She eventually died from the progressive disease, surviving for only 1 month after diagnosis. FISH analysis using WCP5 together with BAC RP11-878F9 or RP11-155N22 demonstrated that the breakpoint of chromosome 5 is located on 5q31. In addition, the EGR1 gene was unexpectedly found to be lost in the FISH study using EGR1 (red)/D5S23, D5S721 (green) dual-color probe. We supposed that the fusion gene created by t(5;11)(q31;p15) consisting of the NUP98 and its partner gene, as well as the loss of the EGR1 gene, may play a cooperative role in leukemogenesis. The partner gene of NUP98 in t(5;11)(q31;p15) is unclear at this time. Further molecular study is required to identify this partner gene in our patient.
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Affiliation(s)
- Yong Wang
- The First Affiliated Hospital of Soochow University, Jiangsu Institutes of Hematology, Suzhou, PR China
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