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Guo X, Plank-Bazinet J, Krivega I, Dale RK, Dean A. Embryonic erythropoiesis and hemoglobin switching require transcriptional repressor ETO2 to modulate chromatin organization. Nucleic Acids Res 2020; 48:10226-10240. [PMID: 32960220 DOI: 10.1093/nar/gkaa736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/19/2020] [Accepted: 09/18/2020] [Indexed: 11/14/2022] Open
Abstract
The underlying mechanism of transcriptional co-repressor ETO2 during early erythropoiesis and hemoglobin switching is unclear. We find that absence of ETO2 in mice interferes with down-regulation of PU.1 and GATA2 in the fetal liver, impeding a key step required for commitment to erythroid maturation. In human β-globin transgenic Eto2 null mice and in human CD34+ erythroid progenitor cells with reduced ETO2, loss of ETO2 results in ineffective silencing of embryonic/fetal globin gene expression, impeding hemoglobin switching during erythroid differentiation. ETO2 occupancy genome-wide occurs virtually exclusively at LDB1-complex binding sites in enhancers and ETO2 loss leads to increased enhancer activity and expression of target genes. ETO2 recruits the NuRD nucleosome remodeling and deacetylation complex to regulate histone acetylation and nucleosome occupancy in the β-globin locus control region and γ-globin gene. Loss of ETO2 elevates LDB1, MED1 and Pol II in the locus and facilitates fetal γ-globin/LCR looping and γ-globin transcription. Absence of the ETO2 hydrophobic heptad repeat region impairs ETO2-NuRD interaction and function in antagonizing γ-globin/LCR looping. Our results reveal a pivotal role for ETO2 in erythropoiesis and globin gene switching through its repressive role in the LDB1 complex, affecting the transcription factor and epigenetic environment and ultimately restructuring chromatin organization.
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Affiliation(s)
- Xiang Guo
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Jennifer Plank-Bazinet
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ryan K Dale
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 50 South Drive, Building 50, Room 3154, Bethesda, MD 20892, USA
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Wang C, Qi X, Zhou X, Sun J, Cai D, Lu G, Chen X, Jiang Z, Yao YG, Chan WY, Zhao H. RNA-Seq analysis on ets1 mutant embryos of Xenopus tropicalis identifies microseminoprotein beta gene 3 as an essential regulator of neural crest migration. FASEB J 2020; 34:12726-12738. [PMID: 32713114 DOI: 10.1096/fj.202000603r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 11/11/2022]
Abstract
The proto-oncogene ets1 is highly expressed in the pre-migratory and migratory neural crest (NC), and has been implicated in the delamination and migration of the NC cells. To identify the downstream target genes of Ets1 in this process, we did RNA sequencing (RNA-Seq) on wild-type and ets1 mutant X. tropicalis embryos. A list of genes with significantly differential expression was obtained by analyzing the RNA-Seq data. We validated the RNA-Seq data by quantitative PCR, and examined the expression pattern of the genes identified from this assay with whole mount in situ hybridization. A majority of the identified genes showed expression in migrating NC. Among them, the expression of microseminoprotein beta gene 3 (msmb3) was positively regulated by Ets1 in both X. laevis and X. tropicalis. Knockdown of msmb3 with antisense morpholino oligonucleotides or disruption of msmb3 by CRISPR/Cas9 both impaired the migratory streams of NC. Our study identified msmb3 as an Ets1 target gene and uncovered its function in maintaining neural crest migration pattern.
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Affiliation(s)
- Chengdong Wang
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xufeng Qi
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jianmin Sun
- Department of Pathogen Biology and Immunology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou, China
| | - Gang Lu
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiongfong Chen
- Advanced Biomedical Computing Center, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases
| | - Wai Yee Chan
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.,Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hui Zhao
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.,Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China
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Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L, Yew CCK, Waters JL, Leung ML, Rogers K, Rogers SM, McNoe LA, Selvanesan L, Navin N, Jenkins NA, Copeland NG, Mann MB. Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. Nat Biotechnol 2016; 34:962-72. [PMID: 27479497 PMCID: PMC6124494 DOI: 10.1038/nbt.3637] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/20/2016] [Indexed: 02/03/2023]
Abstract
A central challenge in oncology is how to kill tumors containing heterogeneous cell populations defined by different combinations of mutated genes. Identifying these mutated genes and understanding how they cooperate requires single-cell analysis, but current single-cell analytic methods, such as PCR-based strategies or whole-exome sequencing, are biased, lack sequencing depth or are cost prohibitive. Transposon-based mutagenesis allows the identification of early cancer drivers, but current sequencing methods have limitations that prevent single-cell analysis. We report a liquid-phase, capture-based sequencing and bioinformatics pipeline, Sleeping Beauty (SB) capture hybridization sequencing (SBCapSeq), that facilitates sequencing of transposon insertion sites from single tumor cells in a SB mouse model of myeloid leukemia (ML). SBCapSeq analysis of just 26 cells from one tumor revealed the tumor's major clonal subpopulations, enabled detection of clonal insertion events not detected by other sequencing methods and led to the identification of dominant subclones, each containing a unique pair of interacting gene drivers along with three to six cooperating cancer genes with SB-driven expression changes.
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Affiliation(s)
- Karen M Mann
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Justin Y Newberg
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Devin J Jones
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | | | - Liliana Guzman-Rojas
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Takahiro Kodama
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jerrold M Ward
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Alistair G Rust
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Louise van der Weyden
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Jill L Waters
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marco L Leung
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keith Rogers
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Susan M Rogers
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Leslie A McNoe
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Nicholas Navin
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nancy A Jenkins
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Neal G Copeland
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
| | - Michael B Mann
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA
- Institute of Molecular and Cell Biology, Singapore, Republic of Singapore
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Transposon mutagenesis reveals cooperation of ETS family transcription factors with signaling pathways in erythro-megakaryocytic leukemia. Proc Natl Acad Sci U S A 2013; 110:6091-6. [PMID: 23533276 DOI: 10.1073/pnas.1304234110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To define genetic lesions driving leukemia, we targeted cre-dependent Sleeping Beauty (SB) transposon mutagenesis to the blood-forming system using a hematopoietic-selective vav 1 oncogene (vav1) promoter. Leukemias of diverse lineages ensued, most commonly lymphoid leukemia and erythroleukemia. The inclusion of a transgenic allele of Janus kinase 2 (JAK2)V617F resulted in acceleration of transposon-driven disease and strong selection for erythroleukemic pathology with transformation of bipotential erythro-megakaryocytic cells. The genes encoding the E-twenty-six (ETS) transcription factors Ets related gene (Erg) and Ets1 were the most common sites for transposon insertion in SB-induced JAK2V617F-positive erythroleukemias, present in 87.5% and 65%, respectively, of independent leukemias examined. The role of activated Erg was validated by reproducing erythroleukemic pathology in mice transplanted with fetal liver cells expressing translocated in liposarcoma (TLS)-ERG, an activated form of ERG found in human leukemia. Via application of SB mutagenesis to TLS-ERG-induced erythroid transformation, we identified multiple loci as likely collaborators with activation of Erg. Jak2 was identified as a common transposon insertion site in TLS-ERG-induced disease, strongly validating the cooperation between JAK2V617F and transposon insertion at the Erg locus in the JAK2V617F-positive leukemias. Moreover, loci expressing other regulators of signal transduction pathways were conspicuous among the common transposon insertion sites in TLS-ERG-driven leukemia, suggesting that a key mechanism in erythroleukemia may be the collaboration of lesions disturbing erythroid maturation, most notably in genes of the ETS family, with mutations that reduce dependence on exogenous signals.
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Suresh PS, Venkatesh T. Computational interrogation of cis-regulatory elements of genes that are common targets of luteotropin and luteolysin in the primate corpus luteum. Gene 2013; 515:403-9. [DOI: 10.1016/j.gene.2012.12.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
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Meng FK, Sun HY, Tan XY, Li CR, Zhou JF, Liu WL. Negative regulation of cyclin D3 expression by transcription factor c-Ets1 in umbilical cord hematopoietic cells. Acta Pharmacol Sin 2011; 32:1159-64. [PMID: 21841808 DOI: 10.1038/aps.2011.41] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
AIM To investigate the role of transcription factor c-Ets1 in cyclin D3 expression and its effects on the proliferation of umbilical cord hematopoietic cells. METHODS Cyclin D3 promoter deletion constructs were generated and transfected into CD34(+) cells. Dual luciferase reporter assays and TFSEARCH software were used to identify negative regulatory domains and to predict putative transcription factors involved in cyclin D3 downregulation. Expression of c-Ets1 in CD34(+) cells was detected using electrophoretic mobility shift and super shift assays. Point mutants of c-Ets1 binding sites were constructed. The wild-type c-Ets1 and the mutant promoter constructs were co-transfected into CD34(+) cells to determine the promoter activity. The impact of c-Ets1 expression on the proliferation of CD34(+) cells was assessed using MTT assay. RESULTS Nine cyclin D3 promoter deletion constructs were generated. A negative regulatory domain containing c-Ets1 binding sites was identified between -439 bp and -362 bp. Transfection of the promoter deletion constructs containing mutant c-Ets1 binding sites enhanced cyclin D3 promoter activity. However, the opposite results were observed when CD34(+) cells were co-transfected with wildtype c-Ets1 and its promoter deletion constructs. The overexpression of c-Ets1 could suppress cyclin D3 mRNA and protein levels. In addition, it inhibits the proliferation of CD34(+) cells. CONCLUSION c-Ets1 functions as a negative transcription factor, down-regulating the expression of cyclin D3, which leads to inhibition of CD34(+) cell proliferation.
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Uehara T, Kondo C, Yamate J, Torii M, Maruyama T. A toxicogenomic approach for identifying biomarkers for myelosuppressive anemia in rats. Toxicology 2011; 282:139-45. [DOI: 10.1016/j.tox.2011.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 01/27/2023]
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Seeger FH, Chen L, Spyridopoulos I, Altschmied J, Aicher A, Haendeler J. Downregulation of ETS rescues diabetes-induced reduction of endothelial progenitor cells. PLoS One 2009; 4:e4529. [PMID: 19225563 PMCID: PMC2639694 DOI: 10.1371/journal.pone.0004529] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2008] [Accepted: 01/23/2009] [Indexed: 01/09/2023] Open
Abstract
Background Transplantation of vasculogenic progenitor cells (VPC) improves neovascularization after ischemia. However, patients with type 2 diabetes mellitus show a reduced VPC number and impaired functional activity. Previously, we demonstrated that p38 kinase inhibition prevents the negative effects of glucose on VPC number by increasing proliferation and differentiation towards the endothelial lineage in vitro. Moreover, the functional capacity of progenitor cells is reduced in a mouse model of metabolic syndrome including type 2 diabetes (Leprdb) in vivo. Findings The aim of this study was to elucidate the underlying signalling mechanisms in vitro and in vivo. Therefore, we performed DNA-protein binding arrays in the bone marrow of mice with metabolic syndrome, in blood-derived progenitor cells of diabetic patients as well as in VPC ex vivo treated with high levels of glucose. The transcriptional activation of ETS transcription factors was increased in all samples analyzed. Downregulation of ETS1 expression by siRNA abrogated the reduction of VPC number induced by high-glucose treatment. In addition, we observed a concomitant suppression of the non-endothelial ETS-target genes matrix metalloproteinase 9 (MMP9) and CD115 upon short term lentiviral delivery of ETS-specific shRNAs. Long term inhibition of ETS expression by lentiviral infection increased the number of cells with the endothelial markers CD144 and CD105. Conclusion These data demonstrate that diabetes leads to dysregulated activation of ETS, which blocks the functional activity of progenitor cells and their commitment towards the endothelial cell lineage.
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Affiliation(s)
- Florian Hartmut Seeger
- Molecular Cardiology, Department of Internal Medicine III, University of Frankfurt, Frankfurt, Germany
| | - Linping Chen
- Molecular Cardiology, Department of Internal Medicine III, University of Frankfurt, Frankfurt, Germany
| | - Ioakim Spyridopoulos
- Molecular Cardiology, Department of Internal Medicine III, University of Frankfurt, Frankfurt, Germany
| | - Joachim Altschmied
- Cell Biology & Molecular Aging Research, IUF (Institut für Umweltmedizinische Forschung) at the University of Duesseldorf gGmbH, Duesseldorf, Germany
| | - Alexandra Aicher
- Molecular Cardiology, Department of Internal Medicine III, University of Frankfurt, Frankfurt, Germany
| | - Judith Haendeler
- Molecular Cardiology, Department of Internal Medicine III, University of Frankfurt, Frankfurt, Germany
- Cell Biology & Molecular Aging Research, IUF (Institut für Umweltmedizinische Forschung) at the University of Duesseldorf gGmbH, Duesseldorf, Germany
- * E-mail:
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Hu JH, Navas P, Cao H, Stamatoyannopoulos G, Song CZ. Systematic RNAi studies on the role of Sp/KLF factors in globin gene expression and erythroid differentiation. J Mol Biol 2006; 366:1064-73. [PMID: 17224162 PMCID: PMC1907364 DOI: 10.1016/j.jmb.2006.12.047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Revised: 12/04/2006] [Accepted: 12/18/2006] [Indexed: 12/12/2022]
Abstract
Sp/KLF family of factors regulates gene expression by binding to the CACCC/GC/GT boxes in the DNA through their highly conserved three zinc finger domains. To investigate the role of this family of factors in erythroid differentiation and globin gene expression, we first measured the expression levels of selected Sp/KLF factors in primary cells of fetal and adult stages of erythroid development. This quantitative analysis revealed that their expression levels vary significantly in cells of either stages of the erythroid development. Significant difference in their expression levels was observed between fetal and adult erythroid cells for some Sp/KLF factors. Functional studies using RNA interference revealed that the silencing of Sp1 and KLF8 resulted in elevated level of gamma globin expression in K562 cells. In addition, K562 cells become visibly red after Sp1 knockdown. Benzidine staining revealed significant hemoglobinization of these cells, indicating erythroid differentiation. Moreover, the expression of PU.1, ETS1 and Notch1 is significantly down-regulated in the cells that underwent erythroid differentiation following Sp1 knockdown. Overexpression of PU.1 or ETS1 efficiently blocked the erythroid differentiation caused by Sp1 knockdown in K562 cells. The expression of c-Kit, however, was significantly up-regulated. These data indicate that Sp1 may play an important role in erythroid differentiation.
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Affiliation(s)
| | | | | | | | - Chao-Zhong Song
- *Corresponding author: Chao-Zhong Song, Tel. 206 616-2814; Fax. 206 606-4527; E-mail:
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