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Liu L, Patnana PK, Xie X, Frank D, Nimmagadda SC, Su M, Zhang D, Koenig T, Rosenbauer F, Liebmann M, Klotz L, Xu W, Vorwerk J, Neumann F, Hüve J, Unger A, Okun JG, Opalka B, Khandanpour C. GFI1B acts as a metabolic regulator in hematopoiesis and acute myeloid leukemia. Leukemia 2022; 36:2196-2207. [PMID: 35804097 PMCID: PMC9417998 DOI: 10.1038/s41375-022-01635-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Recent studies highlighted the role of transcription factors in metabolic regulation during hematopoiesis and leukemia development. GFI1B is a transcriptional repressor that plays a critical role in hematopoiesis, and its expression is negatively related to the prognosis of acute myeloid leukemia (AML) patients. We earlier reported a change in the metabolic state of hematopoietic stem cells upon Gfi1b deletion. Here we explored the role of Gfi1b in metabolism reprogramming during hematopoiesis and leukemogenesis. We demonstrated that Gfi1b deletion remarkably activated mitochondrial respiration and altered energy metabolism dependence toward oxidative phosphorylation (OXPHOS). Mitochondrial substrate dependency was shifted from glucose to fatty acids upon Gfi1b deletion via upregulating fatty acid oxidation (FAO). On a molecular level, Gfi1b epigenetically regulated multiple FAO-related genes. Moreover, we observed that metabolic phenotypes evolved as cells progressed from preleukemia to leukemia, and the correlation between Gfi1b expression level and metabolic phenotype was affected by genetic variations in AML cells. FAO or OXPHOS inhibition significantly impeded leukemia progression of Gfi1b-KO MLL/AF9 cells. Finally, we showed that Gfi1b-deficient AML cells were more sensitive to metformin as well as drugs implicated in OXPHOS and FAO inhibition, opening new potential therapeutic strategies.
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Affiliation(s)
- Longlong Liu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Pradeep Kumar Patnana
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany.,Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Xiaoqing Xie
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Daria Frank
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany.,Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Subbaiah Chary Nimmagadda
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Minhua Su
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 300052, Tianjin, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Thorsten Koenig
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, Faculty of Medicine, University of Muenster, 48149, Muenster, Germany
| | - Marie Liebmann
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149, Muenster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Muenster, 48149, Muenster, Germany
| | - Wendan Xu
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Jan Vorwerk
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany
| | - Felix Neumann
- Fluorescence Microscopy Facility Muenster (FM)2, Institute of Medical Physics and Biophysics, University of Muenster, 48149, Muenster, Germany.,evorion biotechnologies GmbH, 48149, Muenster, Germany
| | - Jana Hüve
- Fluorescence Microscopy Facility Muenster (FM)2, Institute of Medical Physics and Biophysics, University of Muenster, 48149, Muenster, Germany
| | - Andreas Unger
- Institute of Physiology II, University of Muenster, 48149, Muenster, Germany
| | - Jürgen Günther Okun
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, Dietmar-Hopp-Metabolic Center, 69120, Heidelberg, Germany
| | - Bertram Opalka
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, 45147, Essen, Germany
| | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, 48149, Muenster, Germany. .,Department of Hematology and Oncology, University Hospital of Schleswig-Holstein, University of Luebeck, 23538, Luebeck, Germany.
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2
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Characterization of a genomic region 8 kb downstream of GFI1B associated with myeloproliferative neoplasms. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166259. [PMID: 34450246 DOI: 10.1016/j.bbadis.2021.166259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022]
Abstract
A genomic locus 8 kb downstream of the transcription factor GFI1B (Growth Factor Independence 1B) predisposes to clonal hematopoiesis and myeloproliferative neoplasms. One of the most significantly associated polymorphisms in this region is rs621940-G. GFI1B auto-represses GFI1B, and altered GFI1B expression contributes to myeloid neoplasms. We studied whether rs621940-G affects GFI1B expression and growth of immature cells. GFI1B ChIP-seq showed clear binding to the rs621940 locus. Preferential binding of various hematopoietic transcription factors to either the rs621940-C or -G allele was observed, but GFI1B showed no preference. In gene reporter assays the rs621940 region inhibited GFI1B promoter activity with the G-allele having less suppressive effects compared to the C-allele. However, CRISPR-Cas9 mediated deletion of the locus in K562 cells did not alter GFI1B expression nor auto-repression. In healthy peripheral blood mononuclear cells GFI1B expression did not differ consistently between the rs621940 alleles. Long range and targeted deep sequencing did not detect consistent effects of rs621940-G on allelic GFI1B expression either. Finally, we observed that myeloid colony formation was not significantly affected by either rs621940 allele in 193 healthy donors. Together, these findings show no evidence that rs621940 or its locus affect GFI1B expression, auto-repression or growth of immature myeloid cells.
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Zhang L, Xin M, Wang P. Identification of a novel snoRNA expression signature associated with overall survival in patients with lung adenocarcinoma: A comprehensive analysis based on RNA sequencing dataset. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:7837-7860. [PMID: 34814278 DOI: 10.3934/mbe.2021389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Since multiple studies have reported that small nucleolar RNAs (snoRNAs) can be serve as prognostic biomarkers for cancers, however, the prognostic values of snoRNAs in lung adenocarcinoma (LUAD) remain unclear. Therefore, the main work of this study is to identify the prognostic snoRNAs of LUAD and conduct a comprehensive analysis. The Cancer Genome Atlas LUAD cohort whole-genome RNA-sequencing dataset is included in this study, prognostic analysis and multiple bioinformatics approaches are used for comprehensive analysis and identification of prognostic snoRNAs. There were seven LUAD prognostic snoRNAs were screened in current study. We also constructed a novel expression signature containing five LUAD prognostic snoRNAs (snoU109, SNORA5A, SNORA70, SNORD104 and U3). Survival analysis of this expression signature reveals that LUAD patients with high risk score was significantly related to an unfavourable overall survival (adjusted P = 0.01, adjusted hazard ratio = 1.476, 95% confidence interval = 1.096-1.987). Functional analysis indicated that LUAD patients with different risk score phenotypes had significant differences in cell cycle, apoptosis, integrin, transforming growth factor beta, ErbB, nuclear factor kappa B, mitogen-activated protein kinase, phosphatidylinositol-3-kinase and toll like receptor signaling pathway. Immune microenvironment analysis also indicated that there were significant differences in immune microenvironment scores among LUAD patients with different risk score. In conclusion, this study identified an novel expression signature containing five LUAD prognostic snoRNAs, which may be serve as an independent prognostic indicator for LUAD patients.
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Affiliation(s)
- Linbo Zhang
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
| | - Mei Xin
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
| | - Peng Wang
- Department of Health Management and Division of Physical Examination, The First Affiliated Hospital of Guangxi Medical University, Shuang Yong Road 6, Nanning 530021, China
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4
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The transcription factors GFI1 and GFI1B as modulators of the innate and acquired immune response. Adv Immunol 2021; 149:35-94. [PMID: 33993920 DOI: 10.1016/bs.ai.2021.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GFI1 and GFI1B are small nuclear proteins of 45 and 37kDa, respectively, that have a simple two-domain structure: The first consists of a group of six c-terminal C2H2 zinc finger motifs that are almost identical in sequence and bind to very similar, specific DNA sites. The second is an N-terminal 20 amino acid SNAG domain that can bind to the pocket of the histone demethylase KDM1A (LSD1) near its active site. When bound to DNA, both proteins act as bridging factors that bring LSD1 and associated proteins into the vicinity of methylated substrates, in particular histone H3 or TP53. GFI1 can also bring methyl transferases such as PRMT1 together with its substrates that include the DNA repair proteins MRE11 and 53BP1, thereby enabling their methylation and activation. While GFI1B is expressed almost exclusively in the erythroid and megakaryocytic lineage, GFI1 has clear biological roles in the development and differentiation of lymphoid and myeloid immune cells. GFI1 is required for lymphoid/myeloid and monocyte/granulocyte lineage decision as well as the correct nuclear interpretation of a number of important immune-signaling pathways that are initiated by NOTCH1, interleukins such as IL2, IL4, IL5 or IL7, by the pre TCR or -BCR receptors during early lymphoid differentiation or by T and B cell receptors during activation of lymphoid cells. Myeloid cells also depend on GFI1 at both stages of early differentiation as well as later stages in the process of activation of macrophages through Toll-like receptors in response to pathogen-associated molecular patterns. The knowledge gathered on these factors over the last decades puts GFI1 and GFI1B at the center of many biological processes that are critical for both the innate and acquired immune system.
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5
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Faleschini M, Papa N, Morel-Kopp MC, Marconi C, Giangregorio T, Melazzini F, Bozzi V, Seri M, Noris P, Pecci A, Savoia A, Bottega R. Dysregulation of oncogenic factors by GFI1B p32: investigation of a novel GFI1B germline mutation. Haematologica 2021; 107:260-267. [PMID: 33472357 PMCID: PMC8719102 DOI: 10.3324/haematol.2020.267328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Indexed: 11/10/2022] Open
Abstract
GFI1B is a transcription factor essential for the regulation of erythropoiesis and megakaryopoiesis, and pathogenic variants have been associated with thrombocytopenia and bleeding. Analysing thrombocytopenic families by whole exome sequencing, we identified a novel GFI1B variant (c.648+5G>A), which causes exon 9 skipping and overexpression of a shorter p32 isoform. We report the clinical data of our patients and critically review the phenotype observed in individuals with different GFI1B variants leading to the same effect on the p32 expression. Since p32 is increased in acute and chronic leukemia cells, we tested the expression level of genes playing a role in various type of cancers, including hematological tumors and found that they are significantly dysregulated, suggesting a potential role for GFI1B in carcinogenesis regulation. Increasing the detection of individuals with GFI1B variants will allow us to better characterize this rare disease and determine whether it is associated with an increased risk of developing malignancies.
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Affiliation(s)
| | - Nicole Papa
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
| | - Marie-Christine Morel-Kopp
- Department of Haematology and Transfusion Medicine, Royal North Shore Hospital and Northern Blood Research Centre, Kolling Institute, University of Sydney, Sydney
| | - Caterina Marconi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna
| | | | - Federica Melazzini
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Valeria Bozzi
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, Bologna
| | - Patrizia Noris
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Alessandro Pecci
- Biotechnology Research Laboratories, IRCCS Policlinico San Matteo Foundation, Pavia
| | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy; Department of Medical Sciences, University of Trieste, Trieste.
| | - Roberta Bottega
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste
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6
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Beauchemin H, Möröy T. Multifaceted Actions of GFI1 and GFI1B in Hematopoietic Stem Cell Self-Renewal and Lineage Commitment. Front Genet 2020; 11:591099. [PMID: 33193732 PMCID: PMC7649360 DOI: 10.3389/fgene.2020.591099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 12/15/2022] Open
Abstract
Growth factor independence 1 (GFI1) and the closely related protein GFI1B are small nuclear proteins that act as DNA binding transcriptional repressors. Both recognize the same consensus DNA binding motif via their C-terminal zinc finger domains and regulate the expression of their target genes by recruiting chromatin modifiers such as histone deacetylases (HDACs) and demethylases (LSD1) by using an N-terminal SNAG domain that comprises only 20 amino acids. The only region that is different between both proteins is the region that separates the zinc finger domains and the SNAG domain. Both proteins are co-expressed in hematopoietic stem cells (HSCs) and, to some extent, in multipotent progenitors (MPPs), but expression is specified as soon as early progenitors and show signs of lineage bias. While expression of GFI1 is maintained in lymphoid primed multipotent progenitors (LMPPs) that have the potential to differentiate into both myeloid and lymphoid cells, GFI1B expression is no longer detectable in these cells. By contrast, GFI1 expression is lost in megakaryocyte precursors (MKPs) and in megakaryocyte-erythrocyte progenitors (MEPs), which maintain a high level of GFI1B expression. Consequently, GFI1 drives myeloid and lymphoid differentiation and GFI1B drives the development of megakaryocytes, platelets, and erythrocytes. How such complementary cell type- and lineage-specific functions of GFI1 and GFI1B are maintained is still an unresolved question in particular since they share an almost identical structure and very similar biochemical modes of actions. The cell type-specific accessibility of GFI1/1B binding sites may explain the fact that very similar transcription factors can be responsible for very different transcriptional programming. An additional explanation comes from recent data showing that both proteins may have additional non-transcriptional functions. GFI1 interacts with a number of proteins involved in DNA repair and lack of GFI1 renders HSCs highly susceptible to DNA damage-induced death and restricts their proliferation. In contrast, GFI1B binds to proteins of the beta-catenin/Wnt signaling pathway and lack of GFI1B leads to an expansion of HSCs and MKPs, illustrating the different impact that GFI1 or GFI1B has on HSCs. In addition, GFI1 and GFI1B are required for endothelial cells to become the first blood cells during early murine development and are among those transcription factors needed to convert adult endothelial cells or fibroblasts into HSCs. This role of GFI1 and GFI1B bears high significance for the ongoing effort to generate hematopoietic stem and progenitor cells de novo for the autologous treatment of blood disorders such as leukemia and lymphoma.
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Affiliation(s)
| | - Tarik Möröy
- Institut de recherches cliniques de Montréal, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
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7
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Hautin M, Mornet C, Chauveau A, Bernard DG, Corcos L, Lippert E. Splicing Anomalies in Myeloproliferative Neoplasms: Paving the Way for New Therapeutic Venues. Cancers (Basel) 2020; 12:E2216. [PMID: 32784800 PMCID: PMC7464941 DOI: 10.3390/cancers12082216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
Since the discovery of spliceosome mutations in myeloid malignancies, abnormal pre-mRNA splicing, which has been well studied in various cancers, has attracted novel interest in hematology. However, despite the common occurrence of spliceosome mutations in myelo-proliferative neoplasms (MPN), not much is known regarding the characterization and mechanisms of splicing anomalies in MPN. In this article, we review the current scientific literature regarding "splicing and myeloproliferative neoplasms". We first analyse the clinical series reporting spliceosome mutations in MPN and their clinical correlates. We then present the current knowledge about molecular mechanisms by which these mutations participate in the pathogenesis of MPN or other myeloid malignancies. Beside spliceosome mutations, splicing anomalies have been described in myeloproliferative neoplasms, as well as in acute myeloid leukemias, a dreadful complication of these chronic diseases. Based on splicing anomalies reported in chronic myelogenous leukemia as well as in acute leukemia, and the mechanisms presiding splicing deregulation, we propose that abnormal splicing plays a major role in the evolution of myeloproliferative neoplasms and may be the target of specific therapeutic strategies.
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Affiliation(s)
- Marie Hautin
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Clélia Mornet
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Aurélie Chauveau
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
| | - Delphine G. Bernard
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Laurent Corcos
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
| | - Eric Lippert
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; (M.H.); (A.C.); (D.G.B.); (L.C.)
- Laboratoire d’Hématologie, CHU de Brest, F-29200 Brest, France;
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8
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Ashour N, Angulo JC, González-Corpas A, Orea MJ, Lobo MVT, Colomer R, Colás B, Esteller M, Ropero S. Epigenetic Regulation of Gfi1 in Endocrine-Related Cancers: a Role Regulating Tumor Growth. Int J Mol Sci 2020; 21:ijms21134687. [PMID: 32630147 PMCID: PMC7370116 DOI: 10.3390/ijms21134687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023] Open
Abstract
Prostate and breast cancer constitute the most common cancers among men and women worldwide. The aging population is one of the main risk factors for prostate and breast cancer development and accumulating studies link aging with epigenetic changes. Growth factor independence-1 (Gfi1) is a transcriptional repressor with an important role in human malignancies, including leukemia, colorectal carcinoma, and lung cancer, but its role in prostate and breast cancer is unknown. We have found that Gfi1 epigenetic silencing is a common event in prostate and breast cancer. Gfi1 re-expression in prostate and breast cancer cell lines displaying Gfi1 epigenetic silencing decreases cell proliferation, reduced colony formation density, and tumor growth in nude mice xenografts. In addition, we found that Gfi1 repress alpha 1-anti-trypsin (AAT) and alpha 1-anti-chymotrypsin (ACT) expression, two genes with important functions in cancer development, suggesting that Gfi1 silencing promotes tumor growth by increasing AAT and ACT expression in our system. Finally, Gfi1 epigenetic silencing could be a promising biomarker for prostate cancer progression because it is associated with shorter disease-free survival. In conclusion, our findings strongly indicate that Gfi1 epigenetic silencing in prostate and breast cancer could be a crucial step in the development of these two-well characterized endocrine related tumors.
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Affiliation(s)
- Nadia Ashour
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - Javier C. Angulo
- Servicio de Urología, Hospital Universitario de Getafe, Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Universidad Europea de Madrid, Getafe, 28905 Madrid, Spain;
| | - Ana González-Corpas
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - María J. Orea
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - María V. T. Lobo
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá; Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), 28054 Madrid, Spain;
| | - Ramón Colomer
- Medical Oncology Department, Instituto De Investigación Sanitaria La Princesa, HU La Princesa, 28029 Madrid, Spain;
- Department of Medicine, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Begoña Colás
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Catalonia, Spain;
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28040 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - Santiago Ropero
- Departamento de Biología de Sistemas, Unidad Docente de Bioquímica y Biología Molecular, Universidad de Alcalá, Alcalá de Henares, 28054 Madrid, Spain; (N.A.); (A.G.-C.); (M.J.O.); (B.C.)
- Correspondence:
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9
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Chen XX, Zhu JH, Li ZP, Xiao HT, Zhou H. Comprehensive Characterization of the Prognosis Value of Alternative Splicing Events in Acute Myeloid Leukemia. DNA Cell Biol 2020; 39:1243-1255. [PMID: 32543226 DOI: 10.1089/dna.2020.5534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Increasing evidence have demonstrated that dysregulated alternative splicing (AS) events promoted tumor development and was correlated with worse prognosis in the context of certain malignancies. Nevertheless, a comprehensive examination of the prognosis role of AS events in acute myeloid leukemia (AML) has not yet been illuminated. In this study, univariate and multivariate Cox regression analysis were used to identify survival-related AS events and independent prognostic predictors. The interaction between splicing factors (SFs) and AS events was visualized by Cytoscape. A total of 3013 survival-associated AS events in 1977 genes were screened in 151 AML patients. Interestingly, the majority (2031 events) were revealed to be protective factors. Furthermore, the prediction models were constructed for each type of AS and all of them displayed good performance in predicting prognosis, considering their area under curve values of the receiver operating characteristic were all above 0.7. Notably, the splicing regulatory network displayed the underlying interaction networks between SFs and AS events. Taken together, our study demonstrated the survival-related AS events in AML and uncovered the possible association between SFs and prognostic AS events, which provide new prognostic biomarkers and aid to develop novel targets for AML therapy.
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Affiliation(s)
- Xue-Xing Chen
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Hua Zhu
- Laboratory of Clinical Immunology, Wuhan No. 1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Ping Li
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Tao Xiao
- Department of Anatomy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Zhou
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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10
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Lee CJ, Ahn H, Jeong D, Pak M, Moon JH, Kim S. Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer. BMC Med Genomics 2020; 13:27. [PMID: 32093698 PMCID: PMC7038532 DOI: 10.1186/s12920-020-0659-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background In cancer, mutations of DNA methylation modification genes have crucial roles for epigenetic modifications genome-wide, which lead to the activation or suppression of important genes including tumor suppressor genes. Mutations on the epigenetic modifiers could affect the enzyme activity, which would result in the difference in genome-wide methylation profiles and, activation of downstream genes. Therefore, we investigated the effect of mutations on DNA methylation modification genes such as DNMT1, DNMT3A, MBD1, MBD4, TET1, TET2 and TET3 through a pan-cancer analysis. Methods First, we investigated the effect of mutations in DNA methylation modification genes on genome-wide methylation profiles. We collected 3,644 samples that have both of mRNA and methylation data from 12 major cancer types in The Cancer Genome Atlas (TCGA). The samples were divided into two groups according to the mutational signature. Differentially methylated regions (DMR) that overlapped with the promoter region were selected using minfi and differentially expressed genes (DEG) were identified using EBSeq. By integrating the DMR and DEG results, we constructed a comprehensive DNA methylome profiles on a pan-cancer scale. Second, we investigated the effect of DNA methylations in the promoter regions on downstream genes by comparing the two groups of samples in 11 cancer types. To investigate the effects of promoter methylation on downstream gene activations, we performed clustering analysis of DEGs. Among the DEGs, we selected highly correlated gene set that had differentially methylated promoter regions using graph based sub-network clustering methods. Results We chose an up-regulated DEGs cluster where had hypomethylated promoter in acute myeloid leukemia (LAML) and another down-regulated DEGs cluster where had hypermethylated promoter in colon adenocarcinoma (COAD). To rule out effects of gene regulation by transcription factor (TF), if differentially expressed TFs bound to the promoter of DEGs, that DEGs did not included to the gene set that effected by DNA methylation modifiers. Consequently, we identified 54 hypomethylated promoter DMR up-regulated DEGs in LAML and 45 hypermethylated promoter DMR down-regulated DEGs in COAD. Conclusions Our study on DNA methylation modification genes in mutated vs. non-mutated groups could provide useful insight into the epigenetic regulation of DEGs in cancer.
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Affiliation(s)
- Chai-Jin Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Hongryul Ahn
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Dabin Jeong
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea
| | - Ji Hwan Moon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea. .,Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Korea. .,Bioinformatics Institute, Seoul National University, Seoul, 08826, Korea.
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11
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van Bergen MGJM, van der Reijden BA. Targeting the GFI1/1B-CoREST Complex in Acute Myeloid Leukemia. Front Oncol 2019; 9:1027. [PMID: 31649884 PMCID: PMC6794713 DOI: 10.3389/fonc.2019.01027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022] Open
Abstract
One of the hallmarks of acute myeloid leukemia (AML) is a block in cellular differentiation. Recent studies have shown that small molecules targeting Lysine Specific Demethylase 1A (KDM1A) may force the malignant cells to terminally differentiate. KDM1A is a core component of the chromatin binding CoREST complex. Together with histone deacetylases CoREST regulates gene expression by histone 3 demethylation and deacetylation. The transcription factors GFI1 and GFI1B (for growth factor independence) are major interaction partners of KDM1A and recruit the CoREST complex to chromatin in myeloid cells. Recent studies show that the small molecules that target KDM1A disrupt the GFI1/1B-CoREST interaction and that this is key to inducing terminal differentiation of leukemia cells.
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Affiliation(s)
| | - Bert A. van der Reijden
- Laboratory of Hematology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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12
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Growth Factor Independence 1B-Mediated Transcriptional Repression and Lineage Allocation Require Lysine-Specific Demethylase 1-Dependent Recruitment of the BHC Complex. Mol Cell Biol 2019; 39:MCB.00020-19. [PMID: 30988160 DOI: 10.1128/mcb.00020-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
Growth factor independence 1B (GFI1B) coordinates assembly of transcriptional repressor complexes comprised of corepressors and histone-modifying enzymes to control gene expression programs governing lineage allocation in hematopoiesis. Enforced expression of GFI1B in K562 erythroleukemia cells favors erythroid over megakaryocytic differentiation, providing a platform to define molecular determinants of binary fate decisions triggered by GFI1B. We deployed proteome-wide proximity labeling to identify factors whose inclusion in GFI1B complexes depends upon GFI1B's obligate effector, lysine-specific demethylase 1 (LSD1). We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin-remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1, ZMYM2, and ZNF217) in an LSD1-dependent manner to control acquisition of erythroid traits by K562 cells. Among these elements, depletion of both HMG20A and HMG20B or of GSE1 blocks GFI1B-mediated erythroid differentiation, phenocopying impaired differentiation brought on by LSD1 depletion or disruption of GFI1B-LSD1 binding. These findings demonstrate the central role of the GFI1B-LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.
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13
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Thivakaran A, Botezatu L, Hönes JM, Schütte J, Vassen L, Al-Matary YS, Patnana P, Zeller A, Heuser M, Thol F, Gabdoulline R, Olberding N, Frank D, Suslo M, Köster R, Lennartz K, Görgens A, Giebel B, Opalka B, Dührsen U, Khandanpour C. Gfi1b: a key player in the genesis and maintenance of acute myeloid leukemia and myelodysplastic syndrome. Haematologica 2018; 103:614-625. [PMID: 29326122 PMCID: PMC5865438 DOI: 10.3324/haematol.2017.167288] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
Differentiation of hematopoietic stem cells is regulated by a concert of different transcription factors. Disturbed transcription factor function can be the basis of (pre)malignancies such as myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Growth factor independence 1b (Gfi1b) is a repressing transcription factor regulating quiescence of hematopoietic stem cells and differentiation of erythrocytes and platelets. Here, we show that low expression of Gfi1b in blast cells is associated with an inferior prognosis of MDS and AML patients. Using different models of human MDS or AML, we demonstrate that AML development was accelerated with heterozygous loss of Gfi1b, and latency was further decreased when Gfi1b was conditionally deleted. Loss of Gfi1b significantly increased the number of leukemic stem cells with upregulation of genes involved in leukemia development. On a molecular level, we found that loss of Gfi1b led to epigenetic changes, increased levels of reactive oxygen species, as well as alteration in the p38/Akt/FoXO pathways. These results demonstrate that Gfi1b functions as an oncosuppressor in MDS and AML development.
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Affiliation(s)
- Aniththa Thivakaran
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lacramioara Botezatu
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judith M Hönes
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Judith Schütte
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lothar Vassen
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Yahya S Al-Matary
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Pradeep Patnana
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amos Zeller
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Heuser
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Felicitas Thol
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Razif Gabdoulline
- Department of Haematology, Haemostaseology, Oncology, and Stem Cell Transplantation, Medical University of Hannover, Germany
| | - Nadine Olberding
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daria Frank
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Marina Suslo
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Renata Köster
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Klaus Lennartz
- Institute for Cell Biology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Andre Görgens
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Bertram Opalka
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Cyrus Khandanpour
- Department of Haematology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany .,Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Münster, Germany
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14
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Rabbolini DJ, Morel-Kopp MC, Chen Q, Gabrielli S, Dunlop LC, Chew LP, Blair N, Brighton TA, Singh N, Ng AP, Ward CM, Stevenson WS. Thrombocytopenia and CD34 expression is decoupled from α-granule deficiency with mutation of the first growth factor-independent 1B zinc finger. J Thromb Haemost 2017; 15:2245-2258. [PMID: 28880435 DOI: 10.1111/jth.13843] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Indexed: 01/23/2023]
Abstract
Essentials The phenotypes of different growth factor-independent 1B (GFI1B) variants are not established. GFI1B variants produce heterogeneous clinical phenotypes dependent on the site of mutation. Mutation of the first non-DNA-binding zinc-finger causes a mild platelet and clinical phenotype. GFI1B regulates the CD34 promoter; platelet CD34 expression is an indicator of GFI1B mutation. SUMMARY Background Mutation of the growth factor-independent 1B (GFI1B) fifth DNA-binding zinc-finger domain causes macrothrombocytopenia and α-granule deficiency leading to clinical bleeding. The phenotypes associated with GFI1B variants disrupting non-DNA-binding zinc-fingers remain uncharacterized. Objectives To determine the functional and phenotypic consequences of GFI1B variants disrupting non-DNA-binding zinc-finger domains. Methods The GFI1B C168F variant and a novel GFI1B c.2520 + 1_2520 + 8delGTGGGCAC splice variant were identified in four unrelated families. Phenotypic features, DNA-binding properties and transcriptional effects were determined and compared with those in individuals with a GFI1B H294 fs mutation of the fifth DNA-binding zinc-finger. Patient-specific induced pluripotent stem cell (iPSC)-derived megakaryocytes were generated to facilitate disease modeling. Results The DNA-binding GFI1B variant C168F, which is predicted to disrupt the first non-DNA-binding zinc-finger domain, is associated with macrothrombocytopenia without α-granule deficiency or bleeding symptoms. A GFI1B splice variant, c.2520 + 1_2520 + 8delGTGGGCAC, which generates a short GFI1B isoform that lacks non-DNA-binding zinc-fingers 1 and 2, is associated with increased platelet CD34 expression only, without quantitative or morphologic platelet abnormalities. GFI1B represses the CD34 promoter, and this repression is attenuated by different GFI1B zinc-finger mutations, suggesting that deregulation of CD34 expression occurs at a direct transcriptional level. Patient-specific iPSC-derived megakaryocytes phenocopy these observations. Conclusions Disruption of GFI1B non-DNA-binding zinc-finger 1 is associated with mild to moderate thrombocytopenia without α-granule deficiency or bleeding symptomatology, indicating that the site of GFI1B mutation has important phenotypic implications. Platelet CD34 expression appears to be a common feature of perturbed GFI1B function, and may have diagnostic utility.
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Affiliation(s)
- D J Rabbolini
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - M-C Morel-Kopp
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - Q Chen
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - S Gabrielli
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - L C Dunlop
- Department of Haematology, Liverpool Hospital, Sydney, Australia
| | - L P Chew
- Department of Haematology, Sarawak General Hospital, Sarawak, Malaysia
| | - N Blair
- Department of Neurogenetics, The Royal North Shore Hospital, Sydney, Australia
| | - T A Brighton
- Department of Haematology, Prince of Wales Hospital, Sydney, Australia
| | - N Singh
- Department of Haematology and Transfusion Medicine, Royal North Shore Hospital, Sydney, Australia
| | - A P Ng
- Department of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
| | - C M Ward
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
| | - W S Stevenson
- Northern Blood Research Centre, Kolling Institute of Medical Research, University of Sydney, Sydney, Australia
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15
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Prognostic significance of high GFI1 expression in AML of normal karyotype and its association with a FLT3-ITD signature. Sci Rep 2017; 7:11148. [PMID: 28894287 PMCID: PMC5593973 DOI: 10.1038/s41598-017-11718-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/29/2017] [Indexed: 01/09/2023] Open
Abstract
Growth Factor Independence 1 (GFI1) is a transcriptional repressor that plays a critical role during both myeloid and lymphoid haematopoietic lineage commitment. Several studies have demonstrated the involvement of GFI1 in haematological malignancies and have suggested that low expression of GFI1 is a negative indicator of disease progression for both myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). In this study, we have stratified AML patients into those defined as having a normal karyotype (CN-AML). Unlike the overall pattern in AML, those patients with CN-AML have a poorer survival rate when GFI1 expression is high. In this group, high GFI1 expression is paralleled by higher FLT3 expression, and, even when the FLT3 gene is not mutated, exhibit a FLT3-ITD signature of gene expression. Knock-down of GFI1 expression in the human AML Fujioka cell line led to a decrease in the level of FLT3 RNA and protein and to the down regulation of FLT3-ITD signature genes, thus linking two major prognostic indicators for AML.
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16
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Rabbolini DJ, Morel-Kopp MC, Ward CM, Stevenson WS. GFI1B variants associated with thrombocytopenia. Platelets 2017; 28:525-527. [PMID: 28580815 DOI: 10.1080/09537104.2017.1317734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- David J Rabbolini
- a Department of Haematology and Transfusion Medicine , Royal North Shore Hospital , Sydney , Australia.,b Northern Blood Research Centre , Kolling Institute of Medical Research, University of Sydney , Sydney , Australia
| | - Marie-Christine Morel-Kopp
- a Department of Haematology and Transfusion Medicine , Royal North Shore Hospital , Sydney , Australia.,b Northern Blood Research Centre , Kolling Institute of Medical Research, University of Sydney , Sydney , Australia
| | - Christopher M Ward
- a Department of Haematology and Transfusion Medicine , Royal North Shore Hospital , Sydney , Australia.,b Northern Blood Research Centre , Kolling Institute of Medical Research, University of Sydney , Sydney , Australia
| | - William S Stevenson
- a Department of Haematology and Transfusion Medicine , Royal North Shore Hospital , Sydney , Australia.,b Northern Blood Research Centre , Kolling Institute of Medical Research, University of Sydney , Sydney , Australia
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17
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Anguita E, Candel FJ, Chaparro A, Roldán-Etcheverry JJ. Transcription Factor GFI1B in Health and Disease. Front Oncol 2017; 7:54. [PMID: 28401061 PMCID: PMC5368270 DOI: 10.3389/fonc.2017.00054] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/13/2017] [Indexed: 12/13/2022] Open
Abstract
Many human diseases arise through dysregulation of genes that control key cell fate pathways. Transcription factors (TFs) are major cell fate regulators frequently involved in cancer, particularly in leukemia. The GFI1B gene, coding a TF, was identified by sequence homology with the oncogene growth factor independence 1 (GFI1). Both GFI1 and GFI1B have six C-terminal C2H2 zinc fingers and an N-terminal SNAG (SNAIL/GFI1) transcriptional repression domain. Gfi1 is essential for neutrophil differentiation in mice. In humans, GFI1 mutations are associated with severe congenital neutropenia. Gfi1 is also required for B and T lymphopoiesis. However, knockout mice have demonstrated that Gfi1b is required for development of both erythroid and megakaryocytic lineages. Consistent with this, human mutations of GFI1B produce bleeding disorders with low platelet count and abnormal function. Loss of Gfi1b in adult mice increases the absolute numbers of hematopoietic stem cells (HSCs) that are less quiescent than wild-type HSCs. In keeping with this key role in cell fate, GFI1B is emerging as a gene involved in cancer, which also includes solid tumors. In fact, abnormal activation of GFI1B and GFI1 has been related to human medulloblastoma and is also likely to be relevant in blood malignancies. Several pieces of evidence supporting this statement will be detailed in this mini review.
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Affiliation(s)
- Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Francisco J Candel
- Microbiology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC) , Madrid , Spain
| | - Alberto Chaparro
- Hematology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
| | - Juan J Roldán-Etcheverry
- Hematology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain; Department of Medicine, Universidad Complutense de Madrid (UCM), Madrid, Spain
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18
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Singh D, Upadhyay G, Sengupta A, Biplob MA, Chakyayil S, George T, Saleque S. Cooperative Stimulation of Megakaryocytic Differentiation by Gfi1b Gene Targets Kindlin3 and Talin1. PLoS One 2016; 11:e0164506. [PMID: 27768697 PMCID: PMC5074496 DOI: 10.1371/journal.pone.0164506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/26/2016] [Indexed: 11/18/2022] Open
Abstract
Understanding the production and differentiation of megakaryocytes from progenitors is crucial for realizing the biology and functions of these vital cells. Previous gene ablation studies demonstrated the essential role of the transcriptional repressor Gfi1b (growth factor independence 1b) in the generation of both erythroid and megakaryocytic cells. However, our recent work has demonstrated the down-regulation of this factor during megakaryocytic differentiation. In this study we identify two new gene targets of Gfi1b, the cytoskeletal proteins Kindlin3 and Talin1, and demonstrate the inverse expression and functions of these cytoskeletal targets relative to Gfi1b, during megakaryocytic differentiation. Both kindlin3 and talin1 promoters exhibit dose dependent Gfi1b and LSD1 (lysine specific demethylase 1; a Gfi1b cofactor) enrichment in megakaryocytes and repression in non-hematopoietic cells. Accordingly the expression of these genes is elevated in gfi1b mutant and LSD1 inhibited hematopoietic cells, while during megakaryocytic differentiation, declining Gfi1b levels fostered the reciprocal upregulation of these cytoskeletal factors. Concordantly, manipulation of Kindlin3 and Talin1 expression demonstrated positive correlation with megakaryocytic differentiation with over-expression stimulating, and inhibition diminishing, this process. Co-operativity between these factors and integrins in promoting differentiation was further underscored by physical interactions between them and integrinβ3/CD61 and by stimulation of differentiation by the Talin1 head domain, which is necessary and sufficient for integrin activation. Therefore this study demonstrates the significance of Gfi1b regulated Kindlin3-Talin1 expression in driving megakaryocytic differentiation and highlights the contribution of cytoskeletal agents in the developmental progression of these platelet progenitors.
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Affiliation(s)
- Divya Singh
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Ghanshyam Upadhyay
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Ananya Sengupta
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Mohammed A. Biplob
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Shaleen Chakyayil
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Tiji George
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
| | - Shireen Saleque
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY, 10031, United States of America
- * E-mail:
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19
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Polfus L, Khajuria R, Schick U, Pankratz N, Pazoki R, Brody J, Chen MH, Auer P, Floyd J, Huang J, Lange L, van Rooij F, Gibbs R, Metcalf G, Muzny D, Veeraraghavan N, Walter K, Chen L, Yanek L, Becker L, Peloso G, Wakabayashi A, Kals M, Metspalu A, Esko T, Fox K, Wallace R, Franceschini N, Matijevic N, Rice K, Bartz T, Lyytikäinen LP, Kähönen M, Lehtimäki T, Raitakari O, Li-Gao R, Mook-Kanamori D, Lettre G, van Duijn C, Franco O, Rich S, Rivadeneira F, Hofman A, Uitterlinden A, Wilson J, Psaty B, Soranzo N, Dehghan A, Boerwinkle E, Zhang X, Johnson A, O’Donnell C, Johnsen J, Reiner A, Ganesh S, Sankaran V. Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis. Am J Hum Genet 2016; 99:481-8. [PMID: 27486782 DOI: 10.1016/j.ajhg.2016.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/20/2016] [Indexed: 01/26/2023] Open
Abstract
Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10(-10)) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10(-27)). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.
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20
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Anguita E, Gupta R, Olariu V, Valk PJ, Peterson C, Delwel R, Enver T. A somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network. Dev Biol 2016; 411:277-286. [PMID: 26851695 DOI: 10.1016/j.ydbio.2016.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 01/22/2023]
Abstract
We identify a mutation (D262N) in the erythroid-affiliated transcriptional repressor GFI1B, in an acute myeloid leukemia (AML) patient with antecedent myelodysplastic syndrome (MDS). The GFI1B-D262N mutant functionally antagonizes the transcriptional activity of wild-type GFI1B. GFI1B-D262N promoted myelomonocytic versus erythroid output from primary human hematopoietic precursors and enhanced cell survival of both normal and MDS derived precursors. Re-analysis of AML transcriptome data identifies a distinct group of patients in whom expression of wild-type GFI1B and SPI1 (PU.1) have an inverse pattern. In delineating this GFI1B-SPI1 relationship we show that (i) SPI1 is a direct target of GFI1B, (ii) expression of GFI1B-D262N produces elevated expression of SPI1, and (iii) SPI1-knockdown restores balanced lineage output from GFI1B-D262N-expressing precursors. These results table the SPI1-GFI1B transcriptional network as an important regulatory axis in AML as well as in the development of erythroid versus myelomonocytic cell fate.
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Affiliation(s)
- Eduardo Anguita
- Hematology Department, Hospital Clínico San Carlos (IdISSC), Prof. Martín Lagos s/n, 28040 Madrid, Spain.
| | - Rajeev Gupta
- UCL Cancer Institute, Paul O'Gorman Building 72 Huntley St., London WC1E6BT, United Kingdom.
| | - Victor Olariu
- Computational Biology and Biological Physics Division, Lund University, Lund, Sweden.
| | - Peter J Valk
- Department of Hematology Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Carsten Peterson
- Computational Biology and Biological Physics Division, Lund University, Lund, Sweden.
| | - Ruud Delwel
- Department of Hematology Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Tariq Enver
- UCL Cancer Institute, Paul O'Gorman Building 72 Huntley St., London WC1E6BT, United Kingdom.
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Sengupta A, Upadhyay G, Sen S, Saleque S. Reciprocal regulation of alternative lineages by Rgs18 and its transcriptional repressor Gfi1b. J Cell Sci 2015; 129:145-54. [PMID: 26567214 DOI: 10.1242/jcs.177519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/05/2015] [Indexed: 12/19/2022] Open
Abstract
Appropriate diversification of cellular lineages from multi-potent progenitors is essential for normal development and homeostasis. The specification of erythroid and megakaryocytic lineages represents an especially vital developmental event whose molecular regulation remains incompletely defined. We now demonstrate the role of Rgs18, a GTPase-activating protein and transcriptional target of the repressor Gfi1b, in regulating these processes in mouse and human cells. Gfi1b stringently represses Rgs18 expression in erythroid cells, whereas, during megakaryocytic differentiation, declining Gfi1b levels facilitate a robust induction of Rgs18. Concordantly, alterations in Rgs18 expression produce disparate outcomes by augmenting megakaryocytic and potently suppressing erythroid differentiation and vice versa. These phenotypes reflect the differential impact of Rgs18 on signaling through p38 MAPK family proteins, and ERK1 and ERK2 (also known as MAPK3 and MAPK1, respectively) in the two lineages, which in turn alter the balance between the mutually antagonistic transcription factors Fli1 and Klf1. Overall, these results identify Rgs18 as a new and crucial effector of Gfi1b that regulates downstream signaling and gene expression programs to orchestrate erythro-megakaryocytic lineage choices. This dual role of Rgs18 in reciprocally regulating divergent lineages could exemplify generic mechanisms characteristic of multiple family members in different contexts.
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Affiliation(s)
- Ananya Sengupta
- Dept. of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Ghanshyam Upadhyay
- Dept. of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Sayani Sen
- Dept. of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Shireen Saleque
- Dept. of Biology, The City College of New York and The Graduate Center of The City University of New York, 160 Convent Avenue, New York, NY 10031, USA
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22
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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23
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Adamia S, Kriangkum J, Belch AR, Pilarski LM. Aberrant posttranscriptional processing of hyaluronan synthase 1 in malignant transformation and tumor progression. Adv Cancer Res 2015; 123:67-94. [PMID: 25081526 DOI: 10.1016/b978-0-12-800092-2.00003-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
It is becoming increasingly apparent that splicing defects play a key role in cancer, and that alterations in genomic splicing elements promote aberrant splicing. Alternative splicing increases the diversity of the human transcriptome and increases the numbers of functional gene products. However, dysregulation that leads to aberrant pre-mRNA splicing can contribute to cancer. Hyaluronan (HA), known to be an important component of cancer progression, is synthesized by hyaluronan synthases (HASs). In cancer cells, hyaluronan synthase 1 (HAS1) pre-mRNA is abnormally spliced to generate a family of aberrant splice variants (HAS1Vs) that synthesize extracellular and intracellular HA. HAS1Vs are clinically relevant, being found almost exclusively in malignant cells. Expression of aberrant HAS1Vs predicts poor survival in multiple myeloma. In this review, we summarize the unusual properties of HAS1Vs and their relationship to cancer. HAS1Vs form heterogeneous multimers with normally spliced HAS1 as well as with each other and with HAS3. Aberrant variants of HAS1 synthesize HA. Extracellular HA synthesized by HAS1Vs is likely to promote malignant spread. We speculate that synthesis of intracellular HA plays a fundamental and early role in oncogenesis by promoting genetic instability and the emergence of viable cancer variants that lead to aggressive disease.
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Affiliation(s)
- Sophia Adamia
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
| | - Jitra Kriangkum
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Andrew R Belch
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Linda M Pilarski
- Department of Oncology, University of Alberta and Cross Cancer Institute, Edmonton, Alberta, Canada
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24
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Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium BRIDGE, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HH, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. Transcriptional diversity during lineage commitment of human blood progenitors. Science 2014; 345:1251033. [PMID: 25258084 PMCID: PMC4254742 DOI: 10.1126/science.1251033] [Citation(s) in RCA: 215] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.
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Affiliation(s)
- Lu Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joost H.A. Martens
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Giovanni Canu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sara P. Garcia
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Iain C. Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ewa Bielczyk-Maczynska
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sophia Coe
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Pawan Poudel
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sjoert B.G. Jansen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - William J. Astle
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Antony Attwood
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tadbir Bariana
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Bernard de Bono
- CHIME Institute, University College London, Archway Campus, London, United Kingdom
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | - Alessandra Breschi
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - John C. Chambers
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | | | - Fizzah A. Choudry
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Coupland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Martijn van der Ent
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Wendy N. Erber
- Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Joop H. Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rémi Favier
- Assistance Publique-Hopitaux de Paris, Institut National de la Santé et de la Recherche Médicale U1009, Villejuif, France
| | - Matthew E. Fenech
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Nicola Foad
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kathleen Freson
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Chris van Geet
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Keith Gomez
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Roderic Guigo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Daniel Hampshire
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne M. Kelly
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Jaspal S. Kooner
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | - Michael Laffan
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Claire Lentaigne
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Charlotte Labalette
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tiphaine Martin
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Twin Research & Genetic Epidemiology, Genetics & Molecular Medicine Division, St Thomas’ Hospital, King’s College, London, United Kingdom
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Sylvia Nürnberg
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Emilio Palumbo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Bert A. van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen J. Sammut
- Department of Oncology, Addenbrooke’s Cambridge University Hospital NHS Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research United Kingdom, Cambridge Institute, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Greg Slodkowicz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Asif U. Tamuri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Louella Vasquez
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Katrin Voss
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Watt
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sarah Westbury
- School of Clinical Sciences, University of Bristol, United Kingdom
| | - Paul Flicek
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Remco Loos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sylvia Richardson
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
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25
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Gao P, Jin Z, Cheng Y, Cao X. RNA-Seq analysis identifies aberrant RNA splicing of TRIP12 in acute myeloid leukemia patients at remission. Tumour Biol 2014; 35:9585-90. [PMID: 24961348 DOI: 10.1007/s13277-014-2228-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/11/2014] [Indexed: 11/27/2022] Open
Abstract
Aberrant splicing events play important roles in the pathogenesis of acute myeloid leukemia (AML). To investigate the aberrant splicing events in AML during treatment, we carried out RNA sequencing in peripheral mononuclear cell samples from a patient with complete remission. In addition to the sequencing samples, selected splicing events were confirmed and validated with real-time quantitative RT-PCR in another seven pairs of samples. A total of 4.05 and 3.39 GB clean data of the AML and remission sample were generated, respectively, and 2,223 differentially expressed genes (DEGs) were identified. Integrated with gene expression profiling on T cells from AML patients compared with healthy donors, 82 DEGs were also differentially expressed in AML CD4 T cells and CD8 T cells. Twenty-three alternative splicing events were considered to be confidential, and they were involved in many biological processes, such as RNA processing, cellular macromolecule catabolic process, and DNA binding process. An exon3-skipping event in TRIP12 was detected in patients at remission and further validated in another three independent samples. TRIP12 is an ubiquitin ligase of ARF, which suppresses aberrant cell growth by activating p53 responses. The exon3-skipping isoform of TRIP12 increased significantly after treatment. Our results may provide new understanding of AML, and the confirmed alternative splicing event of TRIP12 may be used as potential target for future investigations.
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Affiliation(s)
- Panke Gao
- Department of Hematology, The Third Hospital Affiliated to Suzhou University, First People's Hospital of Changzhou, Changzhou, 213003, Jiangsu, China
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26
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Vassen L, Beauchemin H, Lemsaddek W, Krongold J, Trudel M, Möröy T. Growth factor independence 1b (gfi1b) is important for the maturation of erythroid cells and the regulation of embryonic globin expression. PLoS One 2014; 9:e96636. [PMID: 24800817 PMCID: PMC4011847 DOI: 10.1371/journal.pone.0096636] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/09/2014] [Indexed: 12/15/2022] Open
Abstract
Growth factor independence 1b (GFI1B) is a DNA binding repressor of transcription with vital functions in hematopoiesis. Gfi1b-null embryos die at midgestation very likely due to defects in erythro- and megakaryopoiesis. To analyze the full functionality of Gfi1b, we used conditionally deficient mice that harbor floxed Gfi1b alleles and inducible (Mx-Cre, Cre-ERT) or erythroid specific (EpoR-Cre) Cre expressing transgenes. In contrast to the germline knockout, EpoR-Cre mediated erythroid specific ablation of Gfi1b allows full gestation, but causes perinatal lethality with very few mice surviving to adulthood. Both the embryonic deletion of Gfi1b by EpoR-Cre and the deletion in adult mice by Mx-Cre or Cre-ERT leads to reduced numbers of erythroid precursors, perturbed and delayed erythroid maturation, anemia and extramedullary erythropoiesis. Global expression analyses showed that the Hba-x, Hbb-bh1 and Hbb-y embryonic globin genes were upregulated in Gfi1b deficient TER119+ fetal liver cells over the gestation period from day 12.5–17.5 p.c. and an increased level of Hbb-bh1 and Hbb-y embryonic globin gene expression was even maintained in adult Gfi1b deficient mice. While the expression of Bcl11a, a regulator of embryonic globin expression was not affected by Gfi1b deficiency, the expression of Gata1 was reduced and the expression of Sox6, also involved in globin switch, was almost entirely lost when Gfi1b was absent. These findings establish Gfi1b as a regulator of embryonic globin expression and embryonic and adult erythroid maturation.
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Affiliation(s)
- Lothar Vassen
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
| | - Hugues Beauchemin
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
| | - Wafaa Lemsaddek
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
| | - Joseph Krongold
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Marie Trudel
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, IRCM, Montréal, Québec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- * E-mail:
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27
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NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood 2014; 123:2816-25. [PMID: 24574459 DOI: 10.1182/blood-2013-02-481507] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous studies revealed an increase in alternative splicing of multiple RNAs in cells from patients with acute myeloid leukemia (AML) compared with CD34(+) bone marrow cells from normal donors. Aberrantly spliced genes included a number of oncogenes, tumor suppressor genes, and genes involved in regulation of apoptosis, cell cycle, and cell differentiation. Among the most commonly mis-spliced genes (>70% of AML patients) were 2, NOTCH2 and FLT3, that encode myeloid cell surface proteins. The splice variants of NOTCH2 and FLT3 resulted from complete or partial exon skipping and utilization of cryptic splice sites. Longitudinal analyses suggested that NOTCH2 and FLT3 aberrant splicing correlated with disease status. Correlation analyses between splice variants of these genes and clinical features of patients showed an association between NOTCH2-Va splice variant and overall survival of patients. Our results suggest that NOTCH2 and FLT3 mis-splicing is a common characteristic of AML and has the potential to generate transcripts encoding proteins with altered function. Thus, splice variants of these genes might provide disease markers and targets for novel therapeutics.
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28
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Adamia S, Haibe-Kains B, Pilarski PM, Bar-Natan M, Pevzner S, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Burke J, Galinsky I, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Stone R, Griffin JD. A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets. Clin Cancer Res 2013; 20:1135-45. [PMID: 24284058 DOI: 10.1158/1078-0432.ccr-13-0956] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE Despite new treatments, acute myeloid leukemia (AML) remains an incurable disease. More effective drug design requires an expanded view of the molecular complexity that underlies AML. Alternative splicing of RNA is used by normal cells to generate protein diversity. Growing evidence indicates that aberrant splicing of genes plays a key role in cancer. We investigated genome-wide splicing abnormalities in AML and based on these abnormalities, we aimed to identify novel potential biomarkers and therapeutic targets. EXPERIMENTAL DESIGN We used genome-wide alternative splicing screening to investigate alternative splicing abnormalities in two independent AML patient cohorts [Dana-Farber Cancer Institute (DFCI) (Boston, MA) and University Hospital de Nantes (UHN) (Nantes, France)] and normal donors. Selected splicing events were confirmed through cloning and sequencing analysis, and than validated in 193 patients with AML. RESULTS Our results show that approximately 29% of expressed genes genome-wide were differentially and recurrently spliced in patients with AML compared with normal donors bone marrow CD34(+) cells. Results were reproducible in two independent AML cohorts. In both cohorts, annotation analyses indicated similar proportions of differentially spliced genes encoding several oncogenes, tumor suppressor proteins, splicing factors, and heterogeneous-nuclear-ribonucleoproteins, proteins involved in apoptosis, cell proliferation, and spliceosome assembly. Our findings are consistent with reports for other malignances and indicate that AML-specific aberrations in splicing mechanisms are a hallmark of AML pathogenesis. CONCLUSIONS Overall, our results suggest that aberrant splicing is a common characteristic for AML. Our findings also suggest that splice variant transcripts that are the result of splicing aberrations create novel disease markers and provide potential targets for small molecules or antibody therapeutics for this disease.
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Affiliation(s)
- Sophia Adamia
- Authors' Affiliations: Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada; Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Center for Cancer Systems Biology and Department of Genetics, Harvard Medical School, Boston University School of Medicine and Biomedical Engineering Department, Boston University, Boston, Massachusetts; Unité de Génomique du Myélome, Laboratoire UGM, University Hospital, CHU Rangueil, Toulouse, France; Hematology Laboratory, University Hospital; and INSERM U892, Nantes, France; Molecular Diagnostics Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts; Biotique Systems Inc., www.biotiquesystems.com; Adult Leukemia Program, Dana Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
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Walter RB, Laszlo GS, Alonzo TA, Gerbing RB, Levy S, Fitzgibbon MP, Gudgeon CJ, Ries RE, Harrington KH, Raimondi SC, Hirsch BA, Gamis AS, McIntosh MW, Meshinchi S. Significance of expression of ITGA5 and its splice variants in acute myeloid leukemia: a report from the Children's Oncology Group. Am J Hematol 2013; 88:694-702. [PMID: 23686445 PMCID: PMC3757130 DOI: 10.1002/ajh.23486] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/06/2013] [Accepted: 05/13/2013] [Indexed: 12/25/2022]
Abstract
Acute myeloid leukemia (AML) encompasses a heterogeneous group of diseases, and novel biomarkers for risk refinement and stratification are needed to optimize patient care. To identify novel risk factors, we performed transcriptome sequencing on 68 diagnostic AML samples and identified 2 transcript variants (-E2 and -E2/3) of the α-subunit (ITGA5) of the very late antigen-5 integrin. We then quantified expression of ITGA5 and these splice variants in specimens from participants of the AAML03P1 trial. We found no association between ITGA5 expression and clinical outcome. In contrast, patients with the highest relative expression (Q4) of the -E2/3 ITGA5 splice variant less likely had low-risk disease than Q1-3 patients (21% vs. 38%, P = 0.027). Q4 patients had worse response to chemotherapy with a higher proportion having persistent minimal residual disease (50% vs. 23%, P = 0.003) and inferior overall survival (at 5 years: 48% vs. 67%, P = 0.015); the latter association was limited to low-risk patients (Q4 vs. Q1-3: 56% vs. 85%, P = 0.043) and was not seen in standard-risk (51% vs. 60%, P = 0.340) or high-risk (33% vs. 38%, P = 0.952) patients. Our exploratory studies indicate that transcriptome sequencing is useful for biomarker discovery, as exemplified by the identification of ITGA5 -E2/3 splice variant as potential novel adverse prognostic marker for low-risk AML that, if confirmed, could serve to further risk-stratify this patient subset.
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MESH Headings
- Adult
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Child
- Child, Preschool
- Disease-Free Survival
- Female
- Gene Expression Regulation, Leukemic/genetics
- Humans
- Infant
- Infant, Newborn
- Integrin alpha5/biosynthesis
- Integrin alpha5/genetics
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Male
- RNA Splicing/genetics
- Risk Factors
- Survival Rate
- Transcriptome/genetics
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Affiliation(s)
- Roland B. Walter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - George S. Laszlo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Todd A. Alonzo
- Department of Biostatistics, University of Southern California, Los Angeles, CA, USA
- Children's Oncology Group, Arcadia, CA, USA
| | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Matthew P. Fitzgibbon
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chelsea J. Gudgeon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rhonda E. Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Susana C. Raimondi
- Children's Oncology Group, Arcadia, CA, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Betsy A. Hirsch
- Children's Oncology Group, Arcadia, CA, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota Cancer Center, Minneapolis, MN, USA
| | - Alan S. Gamis
- Children's Oncology Group, Arcadia, CA, USA
- Division of Hematology-Oncology, Children's Mercy Hospitals and Clinics, Kansas City, MO, USA
| | - Martin W. McIntosh
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Children's Oncology Group, Arcadia, CA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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30
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Koldehoff M, Zakrzewski JL, Beelen DW, Elmaagacli AH. Additive antileukemia effects by GFI1B- and BCR–ABL-specific siRNA in advanced phase chronic myeloid leukemic cells. Cancer Gene Ther 2013; 20:421-7. [DOI: 10.1038/cgt.2013.31] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/15/2013] [Indexed: 11/09/2022]
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Chowdhury AH, Ramroop JR, Upadhyay G, Sengupta A, Andrzejczyk A, Saleque S. Differential transcriptional regulation of meis1 by Gfi1b and its co-factors LSD1 and CoREST. PLoS One 2013; 8:e53666. [PMID: 23308270 PMCID: PMC3538684 DOI: 10.1371/journal.pone.0053666] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 12/03/2012] [Indexed: 02/01/2023] Open
Abstract
Gfi1b (growth factor independence 1b) is a zinc finger transcription factor essential for development of the erythroid and megakaryocytic lineages. To elucidate the mechanism underlying Gfi1b function, potential downstream transcriptional targets were identified by chromatin immunoprecipitation and expression profiling approaches. The combination of these approaches revealed the oncogene meis1, which encodes a homeobox protein, as a direct and prominent target of Gfi1b. Examination of the meis1 promoter sequence revealed multiple Gfi1/1b consensus binding motifs. Distinct regions of the promoter were occupied by Gfi1b and its cofactors LSD1 and CoREST/Rcor1, in erythroid cells but not in the closely related megakaryocyte lineage. Accordingly, Meis1 was significantly upregulated in LSD1 inhibited erythroid cells, but not in megakaryocytes. This lineage specific upregulation in Meis1 expression was accompanied by a parallel increase in di-methyl histone3 lysine4 levels in the Meis1 promoter in LSD1 inhibited, erythroid cells. Meis1 was also substantially upregulated in gfi1b−/− fetal liver cells along with its transcriptional partners Pbx1 and several Hox messages. Elevated Meis1 message levels persisted in gfi1b mutant fetal liver cells differentiated along the erythroid lineage, relative to wild type. However, cells differentiated along the megakaryocytic lineage, exhibited no difference in Meis1 levels between controls and mutants. Transfection experiments further demonstrated specific repression of meis1 promoter driven reporters by wild type Gfi1b but neither by a SNAG domain mutant nor by a DNA binding deficient one, thus confirming direct functional regulation of this promoter by the Gfi1b transcriptional complex. Overall, our results demonstrate direct yet differential regulation of meis1 transcription by Gfi1b in distinct hematopoietic lineages thus revealing it to be a common, albeit lineage specific, target of both Gfi1b and its paralog Gfi1.
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Affiliation(s)
- Asif H. Chowdhury
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Johnny R. Ramroop
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Ghanshyam Upadhyay
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Ananya Sengupta
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Anna Andrzejczyk
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
| | - Shireen Saleque
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, New York, United States of America
- * E-mail:
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inv(16)/t(16;16) acute myeloid leukemia with non-type A CBFB-MYH11 fusions associate with distinct clinical and genetic features and lack KIT mutations. Blood 2012; 121:385-91. [PMID: 23160462 DOI: 10.1182/blood-2012-07-442772] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The inv(16)(p13q22)/t(16;16)(p13;q22) in acute myeloid leukemia results in multiple CBFB-MYH11 fusion transcripts, with type A being most frequent. The biologic and prognostic implications of different fusions are unclear. We analyzed CBFB-MYH11 fusion types in 208 inv(16)/t(16;16) patients with de novo disease, and compared clinical and cytogenetic features and the KIT mutation status between type A (n = 182; 87%) and non-type A (n = 26; 13%) patients. At diagnosis, non-type A patients had lower white blood counts (P = .007), and more often trisomies of chromosomes 8 (P = .01) and 21 (P < .001) and less often trisomy 22 (P = .02). No patient with non-type A fusion carried a KIT mutation, whereas 27% of type A patients did (P = .002). Among the latter, KIT mutations conferred adverse prognosis; clinical outcomes of non-type A and type A patients with wild-type KIT were similar. We also derived a fusion-type-associated global gene-expression profile. Gene Ontology analysis of the differentially expressed genes revealed-among others-an enrichment of up-regulated genes involved in activation of caspase activity, cell differentiation and cell cycle control in non-type A patients. We conclude that non-type A fusions associate with distinct clinical and genetic features, including lack of KIT mutations, and a unique gene-expression profile.
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Abstract
Leukemia progression and relapse is fueled by leukemia stem cells (LSC) that are resistant to current treatments. In the progression of chronic myeloid leukemia (CML), blast crisis progenitors are capable of adopting more primitive but deregulated stem cell features with acquired resistance to targeted therapies. This in turn promotes LSC behavior characterized by aberrant self-renewal, differentiation, and survival capacity. Multiple reports suggest that cell cycle alterations, activation of critical signaling pathways, aberrant microenvironmental cues from the hematopoietic niche, and aberrant epigenetic events and deregulation of RNA processing may facilitate the enhanced survival and malignant transformation of CML progenitors. Here we review the molecular evolution of CML LSC that promotes CML progression and relapse. Recent advances in these areas have identified novel targets that represent important avenues for future therapeutic approaches aimed at selectively eradicating the LSC population while sparing normal hematopoietic progenitors in patients suffering from chronic myeloid malignancies.
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Laurent B, Randrianarison-Huetz V, Frisan E, Andrieu-Soler C, Soler E, Fontenay M, Dusanter-Fourt I, Duménil D. A short Gfi-1B isoform controls erythroid differentiation by recruiting the LSD1-CoREST complex through the dimethylation of its SNAG domain. J Cell Sci 2012; 125:993-1002. [PMID: 22399799 DOI: 10.1242/jcs.095877] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Gfi-1B is a transcriptional repressor essential for the regulation of erythropoiesis and megakaryopoiesis. Here we identify Gfi-1B p32, a Gfi-1B isoform, as essential for erythroid differentiation. Gfi-1B p32 is generated by alternative splicing and lacks the two first zinc finger domains of the protein. Selective knock down of Gfi-1B p32 compromises erythroid differentiation, whereas its ectopic expression induces erythropoiesis in the absence of erythropoietin. Gfi-1B p32 isoform binds to Gfi-1B target gene promoters and associates with the LSD1-CoREST repressor complex more efficiently than the major Gfi-1B p37 isoform. Furthermore, we show that Gfi-1B includes a KSKK motif in its SNAG domain, which recruits the repressor complex only when dimethylated on lysine 8. Mutation of lysine 8 prevents Gfi-1B p32-induced erythroid development. Our results thus highlight a key role for the alternatively spliced Gfi-1B p32 isoform in erythroid development.
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Affiliation(s)
- Benoît Laurent
- Institut Cochin, Université Paris Descartes, Paris Sorbonne Cité, CNRS (UMR 8104), Paris, France
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Zhang XZ, Yin AH, Zhu XY, Ding Q, Wang CH, Chen YX. Using an exon microarray to identify a global profile of gene expression and alternative splicing in K562 cells exposed to sodium valproate. Oncol Rep 2011; 27:1258-65. [PMID: 22200904 PMCID: PMC3583465 DOI: 10.3892/or.2011.1601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/12/2011] [Indexed: 12/22/2022] Open
Abstract
To investigate the effect of valproate treatment on the K562 cell line, a model for chronic myelogenous leukaemia, the growth and survival of the K562 cell line were investigated using the Annexin-V/PI dual staining method, and global profiles of gene expression and alternative splicing in K562 cells were assessed using exon microarrays. A significant increase in cell apoptosis was observed in valproate-exposed K562 cells using flow cytometry. A total of 628 transcripts were identified as being significantly differentially expressed. The number of genes demonstrating increased expression levels was greater than the number of genes demonstrating decreased expression levels (445 genes vs. 183 genes, respectively). The significant enrichment analysis of GO terms for the differentially expressed genes revealed that these genes are involved in many important biological processes such as apoptosis. Six of the genes observed to be differentially expressed that might be involved in apoptosis were selected to undergo qRT-PCR validation. In total, 198 candidates of alternative splicing variants were identified. Among them, three alternative splicing events were selected for validation, and CBLC and TBX1 were confirmed to be alternatively spliced by semi-nested PCR. In conclusion, valproate exposure facilitated cell apoptosis, altered mRNA expression and alternative splicing events in the K562 cell line.
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Affiliation(s)
- Xiang-Zhong Zhang
- Department of Hematology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
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Möröy T, Khandanpour C. Growth factor independence 1 (Gfi1) as a regulator of lymphocyte development and activation. Semin Immunol 2011; 23:368-78. [PMID: 21920773 DOI: 10.1016/j.smim.2011.08.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
Abstract
T- and B-lymphocytes are important elements in the immune defense repertoire of higher organisms. The development and function of lymphoid cells is regulated at many levels one being the control of gene expression by transcription factors. The zinc finger transcriptional repressor Gfi1 has emerged as a factor that is critically implicated in the commitment of precursor cells for the lymphoid lineage. In addition, Gfi1 controls distinct stages of early T- or B-lymphoid development and is also critical for their maturation, activation and effector function. From many years of work, a picture emerges in which Gfi1 is part of a complicated, but well orchestrated network of interdependent regulators, most of which impinge on lymphoid development and activation by transcriptional regulation. Biochemical studies show that Gfi1 is part of a large DNA binding multi-protein complex that enables histone modifications, but may also control alternative pre mRNA splicing. Many insights into the biological role of Gfi1 have been gained through the study of gene deficient mice that have defects in B- and T-cell differentiation, in T-cell selection and polarization processes and in the response of mature B- and T-cells towards antigen. Most importantly, the defects seen in Gfi1 deficient mice also point to roles of Gfi1 in diseases of the immune system that involve auto-immune responses and acute lymphoid leukemia and lymphoma.
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Affiliation(s)
- Tarik Möröy
- Institut de recherches cliniques de Montréal - IRCM, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
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van der Meer LT, Jansen JH, van der Reijden BA. Gfi1 and Gfi1b: key regulators of hematopoiesis. Leukemia 2010; 24:1834-43. [DOI: 10.1038/leu.2010.195] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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38
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Hernández A, Villegas A, Anguita E. Human promoter mutations unveil Oct-1 and GATA-1 opposite action on Gfi1b regulation. Ann Hematol 2010; 89:759-65. [PMID: 20143233 DOI: 10.1007/s00277-009-0900-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 12/30/2009] [Indexed: 01/17/2023]
Abstract
Growth factor-independence 1b (Gfi1b) is a zinc finger transcription factor essential for erythroid and megakaryocytic development. To better understand Gfi1b regulation and to know the implication of the level of expression of this gene in human pathology, we have searched for promoter punctual sequence variations in 214 patients with different hematological diseases. We found two previously unknown congenital mutations at evolutionary conserved GATA and octamer-binding (Oct) transcription factor sites. The Oct site mutation was also found in five relatives of the patient. The GATA motif mutation reduced promoter activity by 50% in vitro, while homozygous patients with the octamer site mutation showed a four-to-five times increase of Gfi1b RNA in platelets. Electrophoretic mobility shift analyses demonstrated that different protein complexes bind to both sites and that binding is reduced by the mutations. Finally, we found that GATA-1 and Oct-1 are the main components of each complex. This study provides evidences of a new mechanism for Gfi1b repression. This is also the first report of Gfi1b mutations with a functional implication; further investigation and follow-up will clarify the involvement of these mutations in hematological disease.
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Affiliation(s)
- Aurora Hernández
- Hematology Department, Hospital Clinico San Carlos, University Complutense, Madrid, Spain
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Anguita E, Villegas A, Iborra F, Hernández A. GFI1B controls its own expression binding to multiple sites. Haematologica 2009; 95:36-46. [PMID: 19773260 DOI: 10.3324/haematol.2009.012351] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Transcription factors play essential roles in both normal and malignant hematopoiesis. This is the case for the growth factor independent 1b (GFI1B) transcription factor, which is required for erythroid and megakaryocytic differentiation and over-expressed in leukemic patients and cell lines. DESIGN AND METHODS To investigate GFI1B regulation, we searched for multispecies conserved non-coding elements between GFI1B and neighboring genes. We used a formaldehyde-assisted isolation of regulatory elements (FAIRE) assay and DNase1 hypersensitivity to assess the chromatin conformation of these sites. Next, we analyzed transcription factor binding and histone modifications at the GFI1B locus including the conserved non-coding elements by a chromatin immunoprecipitation assay. Finally, we studied the interaction of the GFI1B promoter and the conserved non-coding elements with the chromatin conformation capture technique and used immunofluorescence to evaluate GFI1B levels in individual cells. RESULTS We localized several conserved non-coding elements containing multiple erythroid specific transcription factor binding sites at the GFI1B locus. In GFI1B-expressing cells a subset of these conserved non-coding elements and the promoter adopt a close spatial conformation, localize with open chromatin sites, harbor chromatin modifications associated with gene activation and bind multiple transcription factors and co-repressors. Conclusions Our findings indicate that GFI1B regulatory elements behave as activators and repressors. Different protein levels within a cell population suggest that cells must activate and repress GFI1B continuously to control its final level. These data are consistent with a model of GFI1B regulation in which GFI1B binds to its own promoter and to the conserved non-coding elements as its levels rise. This would attract repressor complexes that progressively down-regulate the gene. GFI1B expression would decrease until a stage at which the activating complexes predominate and expression increases.
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Affiliation(s)
- Eduardo Anguita
- Hematology Department, Hospital Clinico San Carlos, 28040 Madrid, Spain.
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