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Yamamoto K, Matsumoto H, Matsumoto S, Sakai R, Kitao A, Watanabe M, Goto H, Sugimoto T, Yano Y, Yakushijin K, Minami H. Unexpected appearance of KMT2A::MLLT10 fusion transcript in acute myeloid leukemia with t(5;11)(q31;q23.3). Cancer Genet 2023; 272-273:41-46. [PMID: 36774707 DOI: 10.1016/j.cancergen.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/06/2023]
Abstract
As an uncommon but nonrandom translocation in acute myeloid leukemia (AML) t(5;11)(q31;q23) results in fusion between KMT2A at 11q23 and ARHGAP26 at 5q31. The 5q31 region has another KMT2A partner, AFF4, which was identified in acute lymphoblastic leukemia harboring ins(5;11)(q31;q13q23). We report here a 65-year-old woman with AML M5b. G-banding and spectral karyotyping demonstrated 46,XX,t(5;11)(q31;q23.3). Fluorescence in situ hybridization revealed not only separated 5' and 3' KMT2A signals but a faint 5' KMT2A signal. Reverse transcription polymerase chain reaction (RT-PCR), using a KMT2A sense primer and ARHGAP26 antisense primer, detected no band whereas RT-PCR with a AFF4 antisense primer revealed an amplified band. However, sequence analysis unexpectedly disclosed that KMT2A exon 6 was connected with MLLT10 exons 15 to 18. This may be due to cross-hybridization between MLLT10 exon 18 and AFF4 antisense primer derived from AFF4 exon 10 since both exons had eight identical bases (AAGCAGCT). The MLLT10 gene is located at 10p12.31; a faint 5' KMT2A signal was probably present at this locus. These findings indicate that in AML the 5' KMT2A fragment containing exons 1 to 6 may be cryptically inserted into MLLT10 intron 14 when a reciprocal translocation t(5;11)(q31;q23.3) involving KMT2A occurred.
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Affiliation(s)
- Katsuya Yamamoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Hisayuki Matsumoto
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Sakuya Matsumoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rina Sakai
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akihito Kitao
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Marika Watanabe
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hideaki Goto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Hematology and Oncology, Kita-Harima Medical Center, Ono, Japan
| | - Takeshi Sugimoto
- Department of Hematology and Oncology, Kita-Harima Medical Center, Ono, Japan
| | - Yoshihiko Yano
- Department of Clinical Laboratory, Kobe University Hospital, Kobe, Japan
| | - Kimikazu Yakushijin
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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2
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Komatsu K, Sakaguchi K, Shimizu D, Yamoto K, Kato F, Miyairi I, Ogata T, Saitsu H. Characterization of KMT2A::MATR3 fusion in a patient with acute lymphoblastic leukemia and monitoring of minimal residual disease by nanoplate digital PCR. Pediatr Blood Cancer 2023; 70:e30120. [PMID: 36468647 DOI: 10.1002/pbc.30120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/31/2022] [Accepted: 11/05/2022] [Indexed: 12/11/2022]
Affiliation(s)
- Kazuyuki Komatsu
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kimiyoshi Sakaguchi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daisuke Shimizu
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Fumiko Kato
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Isao Miyairi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
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3
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The role of GTPase-activating protein ARHGAP26 in human cancers. Mol Cell Biochem 2021; 477:319-326. [PMID: 34716859 PMCID: PMC8755663 DOI: 10.1007/s11010-021-04274-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 10/07/2021] [Indexed: 12/11/2022]
Abstract
Rho GTPases are molecular switches that play an important role in regulating the behavior of a variety of tumor cells. RhoA GTPase-activating protein 26 (ARHGAP26) is a GTPase-activating protein and inhibits the activity of Rho GTPases by promoting the hydrolytic ability of Rho GTPases. It also affects tumorigenesis and progression of various tumors through several methods, including formation of abnormal fusion genes and circular RNA. This review summarizes the biological functions and molecular mechanisms of ARHGAP26 in different tumors, proposes the potential clinical value of ARHGAP26 in cancer treatment, and discusses current issues that need to be addressed.
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Frenkel-Morgenstern M, Gorohovski A, Tagore S, Sekar V, Vazquez M, Valencia A. ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer. Nucleic Acids Res 2017; 45:7094-7105. [PMID: 28549153 PMCID: PMC5499553 DOI: 10.1093/nar/gkx423] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 05/07/2017] [Indexed: 12/20/2022] Open
Abstract
Fusion proteins, comprising peptides deriving from the translation of two parental genes, are produced in cancer by chromosomal aberrations. The expressed fusion protein incorporates domains of both parental proteins. Using a methodology that treats discrete protein domains as binding sites for specific domains of interacting proteins, we have cataloged the protein interaction networks for 11 528 cancer fusions (ChiTaRS-3.1). Here, we present our novel method, chimeric protein–protein interactions (ChiPPI) that uses the domain–domain co-occurrence scores in order to identify preserved interactors of chimeric proteins. Mapping the influence of fusion proteins on cell metabolism and pathways reveals that ChiPPI networks often lose tumor suppressor proteins and gain oncoproteins. Furthermore, fusions often induce novel connections between non-interactors skewing interaction networks and signaling pathways. We compared fusion protein PPI networks in leukemia/lymphoma, sarcoma and solid tumors finding distinct enrichment patterns for each disease type. While certain pathways are enriched in all three diseases (Wnt, Notch and TGF β), there are distinct patterns for leukemia (EGFR signaling, DNA replication and CCKR signaling), for sarcoma (p53 pathway and CCKR signaling) and solid tumors (FGFR and EGFR signaling). Thus, the ChiPPI method represents a comprehensive tool for studying the anomaly of skewed cellular networks produced by fusion proteins in cancer.
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Affiliation(s)
| | | | - Somnath Tagore
- Faculty of Medicine, Bar-Ilan-University, Henrietta Szold 8, Safed 1311502, Israel
| | - Vaishnovi Sekar
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), M.F.Almagro 3, 28029 Madrid, Spain
| | - Miguel Vazquez
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), M.F.Almagro 3, 28029 Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), M.F.Almagro 3, 28029 Madrid, Spain
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Kim S, Nahm M, Kim N, Kwon Y, Kim J, Choi S, Choi EY, Shim J, Lee C, Lee S. Graf regulates hematopoiesis through GEEC endocytosis of EGFR. Development 2017; 144:4159-4172. [PMID: 28993397 DOI: 10.1242/dev.153288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/02/2017] [Indexed: 12/24/2022]
Abstract
GTPase regulator associated with focal adhesion kinase 1 (GRAF1) is an essential component of the GPI-enriched endocytic compartment (GEEC) endocytosis pathway. Mutations in the human GRAF1 gene are associated with acute myeloid leukemia, but its normal role in myeloid cell development remains unclear. We show that Graf, the Drosophila ortholog of GRAF1, is expressed and specifically localizes to GEEC endocytic membranes in macrophage-like plasmatocytes. We also find that loss of Graf impairs GEEC endocytosis, enhances EGFR signaling and induces a plasmatocyte overproliferation phenotype that requires the EGFR signaling cascade. Mechanistically, Graf-dependent GEEC endocytosis serves as a major route for EGFR internalization at high, but not low, doses of the predominant Drosophila EGFR ligand Spitz (Spi), and is indispensable for efficient EGFR degradation and signal attenuation. Finally, Graf interacts directly with EGFR in a receptor ubiquitylation-dependent manner, suggesting a mechanism by which Graf promotes GEEC endocytosis of EGFR at high Spi. Based on our findings, we propose a model in which Graf functions to downregulate EGFR signaling by facilitating Spi-induced receptor internalization through GEEC endocytosis, thereby restraining plasmatocyte proliferation.
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Affiliation(s)
- Sungdae Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul 08826, Korea
| | - Minyeop Nahm
- Department of Cell and Developmental Biology and Dental Research Institute, Seoul National University, Seoul 08826, Korea
| | - Najin Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul 08826, Korea
| | - Yumi Kwon
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Joohyung Kim
- Department of Brain and Cognitive Sciences, Seoul National University, Seoul 08826, Korea
| | - Sukwoo Choi
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Eun Young Choi
- Department of Biomedical Sciences, Seoul National University, Seoul 08826, Korea
| | - Jiwon Shim
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Seungbok Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul 08826, Korea .,Department of Cell and Developmental Biology and Dental Research Institute, Seoul National University, Seoul 08826, Korea.,Department of Brain and Cognitive Sciences, Seoul National University, Seoul 08826, Korea
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Panagopoulos I, Gorunova L, Brandal P, Garnes M, Tierens A, Heim S. Myeloid leukemia with t(7;21)(p22;q22) and 5q deletion. Oncol Rep 2013; 30:1549-52. [PMID: 23877199 PMCID: PMC3810351 DOI: 10.3892/or.2013.2623] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/29/2013] [Indexed: 11/24/2022] Open
Abstract
The rare but recurrent RUNX1-USP42 fusion gene is the result of a t(7;21)(p22;q22) chromosomal translocation and has been described in 6 cases of acute myeloid leukemia (AML) and one case of refractory anemia with excess of blast. In the present study, we present the molecular genetic analysis and the clinical features of a t(7;21)(p22;q22)-positive AML case. PCR amplified two RUNX1-USP42 cDNA fragments but no reciprocal USP42-RUNX1 fragment indicating that the RUNX1-USP42 is the leukemogenic fusion gene. Sequencing of the two amplified fragments showed that exon 6 or exon 7 of RUNX1 (accession number NM_001754 version 3) was fused to exon 3 of USP42 (accession number NM_032172 version 2). The predicted RUNX1-USP42 fusion protein would contain the Runt homology domain (RHD), which is responsible for heterodimerization with CBFB and for DNA binding, and the catalytic UCH (ubiquitin carboxyl terminal hydroxylase) domain of the USP42 protein. The bone marrow cells in the present case also had a 5q deletion, and it was revealed that 5 out of the 8 reported cases (including the present case) with t(7;21)(p22;q22)/RUNX1-USP42 also had cytogenetic abnormalities of 5q. The fact that t(7;21) and 5q- occur together much more often than chance would allow seems to be unquestionable, although the pathogenetic connection between the two aberrations remains unknown.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Medical Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.
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De Braekeleer E, Meyer C, Douet-Guilbert N, Morel F, Le Bris MJ, Berthou C, Arnaud B, Marschalek R, Férec C, De Braekeleer M. Complex and cryptic chromosomal rearrangements involving the MLL gene in acute leukemia: A study of 7 patients and review of the literature. Blood Cells Mol Dis 2010; 44:268-74. [DOI: 10.1016/j.bcmd.2010.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 02/03/2010] [Indexed: 11/30/2022]
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Abstract
The role of endocytosis in controlling a multitude of cell biological events is well established. Molecular and mechanistic characterization of endocytosis has predominantly focused on CME (clathrin-mediated endocytosis), although many other endocytic pathways have been described. It was recently shown that the BAR (Bin/amphiphysin/Rvs) and Rho GAP (GTPase-activating protein) domain-containing protein GRAF1 (GTPase regulator associated with focal adhesion kinase-1) is found on prevalent, pleiomorphic endocytic membranes, and is essential for the major, clathrin-independent endocytic pathway that these membranes mediate. This pathway is characterized by its ability to internalize GPI (glycosylphosphatidylinositol)-anchored proteins, bacterial toxins and large amounts of extracellular fluid. These membrane carriers are highly dynamic and associated with the activity of the small G-protein Cdc42 (cell division cycle 42). In the present paper, we review the role of GRAF1 in this CLIC (clathrin-independent carrier)/GEEC (GPI-anchored protein-enriched early endocytic compartment) endocytic pathway and discuss the current understanding regarding how this multidomain protein functions at the interface between membrane sculpting, small G-protein signalling and endocytosis.
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Soler G, Radford I, Meyer C, Marschalek R, Brouzes C, Ghez D, Romana S, Berger R. MLL insertion with MLL-MLLT3 gene fusion in acute leukemia: case report and review of the literature. ACTA ACUST UNITED AC 2008; 183:53-9. [DOI: 10.1016/j.cancergencyto.2008.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 01/16/2008] [Accepted: 01/28/2008] [Indexed: 11/27/2022]
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10
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Miremadi A, Oestergaard MZ, Pharoah PDP, Caldas C. Cancer genetics of epigenetic genes. Hum Mol Genet 2007; 16 Spec No 1:R28-49. [PMID: 17613546 DOI: 10.1093/hmg/ddm021] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cancer epigenome is characterised by specific DNA methylation and chromatin modification patterns. The proteins that mediate these changes are encoded by the epigenetics genes here defined as: DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins, histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (HMT) and histone demethylases. We review the evidence that these genes can be targeted by mutations and expression changes in human cancers.
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Affiliation(s)
- Ahmad Miremadi
- Cancer Genomics Program, Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
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Tirado C, Meloni-Ehrig A, Edwards T, Scheerle J, Burks K, Repetti C, Christacos N, Kelly J, Greenberg J, Murphy C, Croft C, Heritage D, Mowrey P. Cryptic ins(4;11)(q21;q23q23) detected by fluorescence in situ hybridization: a variant of t(4;11)(q21;q23) in an infant with a precursor B-cell acute lymphoblastic leukemia report of a second case. ACTA ACUST UNITED AC 2007; 174:166-9. [DOI: 10.1016/j.cancergencyto.2006.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 11/20/2006] [Accepted: 11/21/2006] [Indexed: 11/28/2022]
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12
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Bojesen SE, Ammerpohl O, Weinhäusl A, Haas OA, Mettal H, Bohle RM, Borkhardt A, Fuchs U. Characterisation of the GRAF gene promoter and its methylation in patients with acute myeloid leukaemia and myelodysplastic syndrome. Br J Cancer 2006; 94:323-32. [PMID: 16404424 PMCID: PMC2361128 DOI: 10.1038/sj.bjc.6602939] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report the isolation of the 5' flanking region of GRAF (GTPase regulator associated with the focal adhesion kinase), previously described as a putative tumour suppressor gene of acute myelogenous leukaemia and myelodysplastic syndrome, and demonstrate its promoter activity in reporter gene assays. Two putative protein-binding sites are identified of which one was sensitive to CpG methylation. The suppressed GRAF expression could be restored in leukaemia cell lines by treatment with a demethylating agent and an inhibitor of histone deacetylases. In contrast to normal tissues, which tested negative for GRAF promoter methylation, 11 of 29 (38%) bone marrow samples from patients with acute myeloid leukaemia or myelodysplastic syndrome were positive.
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Affiliation(s)
- S E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Herlev, Denmark
| | - O Ammerpohl
- University Hospital of Schleswig-Holstein, Clinic for General Surgery and Thoracic Surgery, Kiel, Germany
| | - A Weinhäusl
- ARCS, Austrian Research Center, Seibersdorf, Austria
| | | | - H Mettal
- University Hospital of Tübingen, Clinic for Anaesthesiology and transfusion medicine, Tübingen, Germany
| | - R M Bohle
- University Hospital of Giessen, Institute of Pathology, Giessen, Germany
| | - A Borkhardt
- Dr von Haunersches Kinderspital, Department of Haematology/Oncology, Munich, Germany
| | - U Fuchs
- Dr von Haunersches Kinderspital, Department of Haematology/Oncology, Munich, Germany
- Dr von Haunersches Kinderspital, Department of Haematology/Oncology, Lindwurmstrasse 2a, 80337 Munich, Germany; E-mail:
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Abstract
In all organisms, cell proliferation is orchestrated by coordinated patterns of gene expression. Transcription results from the activity of the RNA polymerase machinery and depends on the ability of transcription activators and repressors to access chromatin at specific promoters. During the last decades, increasing evidence supports aberrant transcription regulation as contributing to the development of human cancers. In fact, transcription regulatory proteins are often identified in oncogenic chromosomal rearrangements and are overexpressed in a variety of malignancies. Most transcription regulators are large proteins, containing multiple structural and functional domains some with enzymatic activity. These activities modify the structure of the chromatin, occluding certain DNA regions and exposing others for interaction with the transcription machinery. Thus, chromatin modifiers represent an additional level of transcription regulation. In this review we focus on several families of transcription activators and repressors that catalyse histone post-translational modifications (acetylation, methylation, phosphorylation, ubiquitination and SUMOylation); and how these enzymatic activities might alter the correct cell proliferation program, leading to cancer.
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Affiliation(s)
- Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology, University of Cambridge, Cambridge, UK
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Wilda M, Perez AV, Bruch J, Woessmann W, Metzler M, Fuchs U, Borkhardt A. Use of MLL/GRAF fusion mRNA for measurement of minimal residual disease during chemotherapy in an infant with acute monoblastic leukemia (AML-M5). Genes Chromosomes Cancer 2005; 43:424-6. [PMID: 15852479 DOI: 10.1002/gcc.20182] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Cytarabine/administration & dosage
- DNA-Binding Proteins/genetics
- Etoposide/administration & dosage
- GTPase-Activating Proteins/genetics
- Histone-Lysine N-Methyltransferase
- Humans
- Idarubicin/administration & dosage
- In Situ Hybridization, Fluorescence
- Infant
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Male
- Mitoxantrone/administration & dosage
- Myeloid-Lymphoid Leukemia Protein
- Neoplasm, Residual
- Oncogene Proteins, Fusion/genetics
- Proto-Oncogenes/genetics
- RNA, Messenger/genetics
- Transcription Factors/genetics
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