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Zhang Y, Wen Y, Nie J, Wang T, Wang G, Gao Q, Cao Y, Wang H, Qi S, Xie S. MYEF2: an immune infiltration-related prognostic factor in IDH-wild-type glioblastoma. Aging (Albany NY) 2023; 15:7760-7780. [PMID: 37556355 PMCID: PMC10457068 DOI: 10.18632/aging.204939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/15/2023] [Indexed: 08/11/2023]
Abstract
Glioblastoma (GBM) is the most malignant and prevalent primary brain tumor. In this study, weighted gene coexpression network analysis (WGCNA) was performed to analyze RNA binding protein (RBP) expression data from The Cancer Genome Atlas (TCGA) for the IDH-wild type GBM cohort. The CIBERSORT algorithm quantified the cellular composition of immune cells and was used to identify key modules associated with CD8+ T cell infiltration. Coexpression networks analysis and protein-protein interaction (PPI) network analysis was used to filter out central RBP genes. Eleven RBP genes, including MYEF2, MAPT, NOVA1, MAP2, TUBB2B, CDH10, TTYH1, PTPRZ1, SOX2, NOVA2 and SCG3, were identified as candidate CD8+ T cell infiltration-associated central genes. A Cox proportional hazards regression model and Kaplan-Meier analysis were applied to identify candidate biomarkers. MYEF2 was selected as a prognostic biomarker based on the results of prognostic analysis. Flow Cytometric Analysis indicated that MYEF2 expression was negatively correlated with dysfunctional CD8+ T cell markers. Kaplan-Meier survival analysis (based on IHC staining) revealed that GBM patients with elevated MYEF2 expression have a better prognosis. Knockdown of MYEF2 in GBM cells via in vitro assays was observed to promote cell proliferation and migration. Our study suggests that MYEF2 expression negatively correlates with T cell exhaustion and tumor progression, rendering it a potentially valuable prognostic biomarker for GBM.
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Affiliation(s)
- Yunxiao Zhang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Yunyu Wen
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Jing Nie
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Tong Wang
- Department of Neurosurgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621000, Sichuan, PR China
| | - Gang Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Qiaoping Gao
- Department of Medical Quality Management, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Yongfu Cao
- Neurosurgery, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510700, Guangdong, PR China
| | - Hai Wang
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Songtao Qi
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Sidi Xie
- Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
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Zhang P, Zhao JH, Chen L, Bian ZL, Ju LL, Wang HX, Cai WH. Expression and function of myelin expression factor 2 in hepatocellular carcinoma. BMC Gastroenterol 2023; 23:20. [PMID: 36658471 PMCID: PMC9854206 DOI: 10.1186/s12876-023-02644-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is one of the most common malignant tumours in the world and has a high mortality rate. However, the pathogenesis of HCC remains unclear. This study aimed to investigate the potential biomarkers of HCC. METHODS ONCOMINE, HCCDB and THE HUMAN PROTEIN ATLAS were used to identify myelin expression factor 2 (MYEF2) as a potential biomarker for HCC. The Cancer Genome Atlas database was used to further validate and analyse the value of MYEF2. Kaplan-Meier Plotter was used for the prognostic analysis. The COX regression model and Kaplan-Meier method were used to investigate the clinical value of MYEF2 in the prognosis of HCC by reviewing the survival status of patients. Fluorescent quantitative polymerase chain reaction (qPCR) and immunohistochemistry were used to detect the expressions of the MYEF2 mRNA and protein in HCC tissues and cell lines. qPCR and Western blotting were used to validate the efficiency of MYEF2 knockout and overexpression in HCC cells. The invasion and migration abilities regulated by MYEF2 were detected by performing transwell and wound healing assays. RESULTS MYEF2 is significantly upregulated in HCC and is mainly located in the nucleus of HCC cells. MYEF2 expression is significantly associated with the tumour stage, histological grade and TNM stage. High MYEF2 expression is an independent prognostic factor for patients with HCC. Functionally, elevated MYEF2 facilitated cell migration and invasion in vitro. In contrast, decreased MYEF2 inhibited cell migration and invasion. CONCLUSIONS MYEF2 may be a novel biomarker with potential diagnosis and prognosis values and as a potential therapeutic target for HCC.
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Affiliation(s)
- Peng Zhang
- grid.260483.b0000 0000 9530 8833Medical School of Nantong University, Nantong Third People’s Hospital, Nantong, 226000 Jiangsu People’s Republic of China
| | - Jiang-Hua Zhao
- grid.260483.b0000 0000 9530 8833Medical School of Nantong University, Nantong Third People’s Hospital, Nantong, 226000 Jiangsu People’s Republic of China
| | - Lin Chen
- grid.260483.b0000 0000 9530 8833Nantong Institute of Liver Diseases, Nantong Third People’s Hospital, Nantong University, Nantong, 226000 Jiangsu People’s Republic of China
| | - Zhao-Lian Bian
- grid.260483.b0000 0000 9530 8833Nantong Institute of Liver Diseases, Nantong Third People’s Hospital, Nantong University, Nantong, 226000 Jiangsu People’s Republic of China
| | - Lin-Ling Ju
- grid.260483.b0000 0000 9530 8833Nantong Institute of Liver Diseases, Nantong Third People’s Hospital, Nantong University, Nantong, 226000 Jiangsu People’s Republic of China
| | - Hui-Xuan Wang
- grid.260483.b0000 0000 9530 8833Nantong Institute of Liver Diseases, Nantong Third People’s Hospital, Nantong University, Nantong, 226000 Jiangsu People’s Republic of China
| | - Wei-Hua Cai
- grid.260483.b0000 0000 9530 8833Nantong Institute of Liver Disease, Department of Hepatobiliary Surgery, Nantong Third People’s Hospital, Nantong University, Nantong, 226000 Jiangsu People’s Republic of China
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Rummukainen P, Tarkkonen K, Dudakovic A, Al-Majidi R, Nieminen-Pihala V, Valensisi C, Hawkins RD, van Wijnen AJ, Kiviranta R. Lysine-Specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation. PLoS One 2022; 17:e0265027. [PMID: 35255108 PMCID: PMC8901060 DOI: 10.1371/journal.pone.0265027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/18/2022] [Indexed: 02/03/2023] Open
Abstract
Epigenetic mechanisms regulate osteogenic lineage differentiation of mesenchymal stromal cells. Histone methylation is controlled by multiple lysine demethylases and is an important step in controlling local chromatin structure and gene expression. Here, we show that the lysine-specific histone demethylase Kdm1A/Lsd1 is abundantly expressed in osteoblasts and that its suppression impairs osteoblast differentiation and bone nodule formation in vitro. Although Lsd1 knockdown did not affect global H3K4 methylation levels, genome-wide ChIP-Seq analysis revealed high levels of Lsd1 at gene promoters and its binding was associated with di- and tri-methylation of histone 3 at lysine 4 (H3K4me2 and H3K4me3). Lsd1 binding sites in osteoblastic cells were enriched for the Runx2 consensus motif suggesting a functional link between the two proteins. Importantly, inhibition of Lsd1 activity decreased osteoblast activity in vivo. In support, mesenchymal-targeted knockdown of Lsd1 led to decreased osteoblast activity and disrupted primary spongiosa ossification and reorganization in vivo. Together, our studies demonstrate that Lsd1 occupies Runx2-binding cites at H3K4me2 and H3K4me3 and its activity is required for proper bone formation.
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Affiliation(s)
| | - Kati Tarkkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
| | - Rana Al-Majidi
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Cristina Valensisi
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - R. David Hawkins
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States of America
| | - Andre J. van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester, MN, United States of America
- Department of Biochemistry, University of Vermont, Burlington, VT, United States of America
- * E-mail: (AJW); (RK)
| | - Riku Kiviranta
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Endocrinology, Turku University Hospital, Turku, Finland
- * E-mail: (AJW); (RK)
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Fathi E, Ehsani A, Sanaat Z, Vandghanooni S, Farahzadi R, Montazersaheb S. Hematopoietic stem cells characteristics: from isolation to transplantation. Curr Stem Cell Res Ther 2022; 17:407-414. [DOI: 10.2174/1574888x17666220211160954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/05/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Hematopoietic stem cells (HSCs) have a self-renewal as well as pluripotency properties and are responsible to produce all types of blood cells. These cells are generated during embryonic development and transit through various anatomical niches (bone marrow microenvironment). Today, they are easily enriched from some sources including peripheral blood, bone marrow, and umbilical cord blood (UCB). HSCs have been used for many years to treat a variety of cancers and blood disorders such as various types of leukemia, lymphoma, myelodysplastic, myeloproliferative syndromes etc. Although almost 50 years have passed since the discovery of stem cells and many investigations have been done on cell therapy and regenerative medicine, further studies need to be conducted in this regard. This manuscript review the history, location, evolution, isolation, and therapeutic approaches of HSCs.
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Affiliation(s)
- Ezzatollah Fathi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Ali Ehsani
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zohreh Sanaat
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Somayeh Vandghanooni
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Raheleh Farahzadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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5
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Mulari S, Eskin A, Lampinen M, Nummi A, Nieminen T, Teittinen K, Ojala T, Kankainen M, Vento A, Laurikka J, Kupari M, Harjula A, Tuncbag N, Kankuri E. Ischemic Heart Disease Selectively Modifies the Right Atrial Appendage Transcriptome. Front Cardiovasc Med 2021; 8:728198. [PMID: 34926599 PMCID: PMC8674465 DOI: 10.3389/fcvm.2021.728198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Although many pathological changes have been associated with ischemic heart disease (IHD), molecular-level alterations specific to the ischemic myocardium and their potential to reflect disease severity or therapeutic outcome remain unclear. Currently, diagnosis occurs relatively late and evaluating disease severity is largely based on clinical symptoms, various imaging modalities, or the determination of risk factors. This study aims to identify IHD-associated signature RNAs from the atrial myocardium and evaluate their ability to reflect disease severity or cardiac surgery outcomes. Methods and Results: We collected right atrial appendage (RAA) biopsies from 40 patients with invasive coronary angiography (ICA)-positive IHD undergoing coronary artery bypass surgery and from 8 patients ICA-negative for IHD (non-IHD) undergoing valvular surgery. Following RNA sequencing, RAA transcriptomes were analyzed against 429 donors from the GTEx project without cardiac disease. The IHD transcriptome was characterized by repressed RNA expression in pathways for cell-cell contacts and mitochondrial dysfunction. Increased expressions of the CSRNP3, FUT10, SHD, NAV2-AS4, and hsa-mir-181 genes resulted in significance with the complexity of coronary artery obstructions or correlated with a functional cardiac benefit from bypass surgery. Conclusions: Our results provide an atrial myocardium-focused insight into IHD signature RNAs. The specific gene expression changes characterized here, pave the way for future disease mechanism-based identification of biomarkers for early detection and treatment of IHD.
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Affiliation(s)
- Severi Mulari
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Arda Eskin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | - Milla Lampinen
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Annu Nummi
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuomo Nieminen
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Teittinen
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Teija Ojala
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Kankainen
- Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Antti Vento
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jari Laurikka
- Department of Cardiothoracic Surgery, Heart Center, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markku Kupari
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ari Harjula
- Heart and Lung Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
- Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey
- School of Medicine, Koc University, Istanbul, Turkey
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Runx1 promotes murine erythroid progenitor proliferation and inhibits differentiation by preventing Pu.1 downregulation. Proc Natl Acad Sci U S A 2019; 116:17841-17847. [PMID: 31431533 DOI: 10.1073/pnas.1901122116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Pu.1 is an ETS family transcription factor (TF) that plays critical roles in erythroid progenitors by promoting proliferation and blocking terminal differentiation. However, the mechanisms controlling expression and down-regulation of Pu.1 during early erythropoiesis have not been defined. In this study, we identify the actions of Runx1 and Pu.1 itself at the Pu.1 gene Upstream Regulatory Element (URE) as major regulators of Pu.1 expression in Burst-Forming Unit erythrocytes (BFUe). During early erythropoiesis, Runx1 and Pu.1 levels decline, and chromatin accessibility at the URE is lost. Ectopic expression of Runx1 or Pu.1, both of which bind the URE, prevents Pu.1 down-regulation and blocks terminal erythroid differentiation, resulting in extensive ex vivo proliferation and immortalization of erythroid progenitors. Ectopic expression of Runx1 in BFUe lacking a URE fails to block terminal erythroid differentiation. Thus, Runx1, acting at the URE, and Pu.1 itself directly regulate Pu.1 levels in erythroid cells, and loss of both factors is critical for Pu.1 down-regulation during terminal differentiation. The molecular mechanism of URE inactivation in erythroid cells through loss of TF binding represents a distinct pattern of Pu.1 regulation from those described in other hematopoietic cell types such as T cells which down-regulate Pu.1 through active repression. The importance of down-regulation of Runx1 and Pu.1 in erythropoiesis is further supported by genome-wide analyses showing that their DNA-binding motifs are highly overrepresented in regions that lose chromatin accessibility during early erythroid development.
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7
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El-Athman R, Fuhr L, Relógio A. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine 2018; 33:68-81. [PMID: 29936137 PMCID: PMC6085510 DOI: 10.1016/j.ebiom.2018.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany.
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8
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H1.0 Linker Histone as an Epigenetic Regulator of Cell Proliferation and Differentiation. Genes (Basel) 2018; 9:genes9060310. [PMID: 29925815 PMCID: PMC6027317 DOI: 10.3390/genes9060310] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/18/2018] [Indexed: 12/16/2022] Open
Abstract
H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having a general structural role, H1 histones also have additional epigenetic functions related to DNA replication and repair, genome stability, and gene-specific expression regulation. Synthesis of the H1 subtypes is differentially regulated both in development and adult cells, thus suggesting that each protein has a more or less specific function. The somatic variant H1.0 is a linker histone that was recognized since long ago to be involved in cell differentiation. Moreover, it has been recently found to affect generation of epigenetic and functional intra-tumor heterogeneity. Interestingly, H1.0 or post-translational forms of it have been also found in extracellular vesicles (EVs) released from cancer cells in culture, thus suggesting that these cells may escape differentiation at least in part by discarding H1.0 through the EV route. In this review we will discuss the role of H1.0 in development, differentiation, and stem cell maintenance, also in relation with tumorigenesis, and EV production.
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Yamamoto R, Kawahara M, Ito S, Satoh J, Tatsumi G, Hishizawa M, Suzuki T, Andoh A. Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super-enhancer in erythroleukemia cells. Oncotarget 2018; 9:21007-21021. [PMID: 29765516 PMCID: PMC5940392 DOI: 10.18632/oncotarget.24774] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/24/2018] [Indexed: 12/22/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is a histone modifier for transcriptional repression involved in the regulation of hematopoiesis. We previously reported that a LSD1 inhibitor NCD38 induces transdifferentiation from erythroid lineage to granulomonocytic lineage and exerts anti-leukemia effect through de-repression of the specific super-enhancers of hematopoietic regulators including ERG in a human erythroleukemia cell line, HEL. However, the mechanistic basis for this specificity of NCD38 has remained unclear. Herein, we report major partners associated with LSD1 and clarify the mechanism in HEL cells. Proteome analysis identified 54 candidate proteins associated with LSD1, including several transcription factors such as GFI1B and RUNX1 as well as BRAF-histone deacetylase complex (BHC) components such as CoREST, HDAC1, and HDAC2. NCD38 selectively disrupted the interaction of LSD1 with GFI1B but not with RUNX1, CoREST, HDAC1 and HDAC2. Erg was downregulated in murine erythroid progenitors with prominent upregulation of Gfi1b. NCD38 induced ERG and attenuated an erythroid marker CD235a in HEL while this attenuation was mimicked by the lentiviral overexpression of ERG. The ERG super-enhancer contained the conserved binding motif of GFI1B and was actually occupied by GFI1B. NCD38 dissociated LSD1 and CoREST but not GFI1B from the ERG super-enhancer. Collectively, the selective separation of LSD1 from GFI1B by NCD38 restores the ERG super-enhancer activation and consequently upregulates ERG expression, inducing the transdifferentiation linked to the anti-leukemia effect.
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Affiliation(s)
- Ryusuke Yamamoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masahiro Kawahara
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan.,Department of Medicine, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Junko Satoh
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Goichi Tatsumi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Takayoshi Suzuki
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan.,CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Akira Andoh
- Department of Medicine, Shiga University of Medical Science, Otsu, Shiga, Japan
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10
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Yi X, Jiang X, Li X, Jiang DS. Histone lysine methylation and congenital heart disease: From bench to bedside (Review). Int J Mol Med 2017; 40:953-964. [PMID: 28902362 DOI: 10.3892/ijmm.2017.3115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/21/2017] [Indexed: 11/05/2022] Open
Abstract
Histone post-translational modifications (PTM) as one of the key epigenetic regulatory mechanisms that plays critical role in various biological processes, including regulating chromatin structure dynamics and gene expression. Histone lysine methyltransferase contributes to the establishment and maintenance of differential histone methylation status, which can recognize histone methylated sites and build an association between these modifications and their downstream processes. Recently, it was found that abnormalities in the histone lysine methylation level or pattern may lead to the occurrence of many types of cardiovascular diseases, such as congenital heart disease (CHD). In order to provide new theoretical basis and targets for the treatment of CHD from the view of developmental biology and genetics, this review discusses and elaborates on the association between histone lysine methylation modifications and CHD.
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Affiliation(s)
- Xin Yi
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xuejun Jiang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiaoyan Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Ding-Sheng Jiang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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11
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Draper JE, Sroczynska P, Leong HS, Fadlullah MZH, Miller C, Kouskoff V, Lacaud G. Mouse RUNX1C regulates premegakaryocytic/erythroid output and maintains survival of megakaryocyte progenitors. Blood 2017; 130:271-284. [PMID: 28490570 PMCID: PMC5833261 DOI: 10.1182/blood-2016-06-723635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 04/21/2017] [Indexed: 12/13/2022] Open
Abstract
RUNX1 is crucial for the regulation of megakaryocyte specification, maturation, and thrombopoiesis. Runx1 possesses 2 promoters: the distal P1 and proximal P2 promoters. The major protein isoforms generated by P1 and P2 are RUNX1C and RUNX1B, respectively, which differ solely in their N-terminal amino acid sequences. RUNX1C is the most abundantly expressed isoform in adult hematopoiesis, present in all RUNX1-expressing populations, including the cKit+ hematopoietic stem and progenitor cells. RUNX1B expression is more restricted, being highly expressed in the megakaryocyte lineage but downregulated during erythropoiesis. We generated a Runx1 P1 knock-in of RUNX1B, termed P1-MRIPV This mouse line lacks RUNX1C expression but has normal total RUNX1 levels, solely comprising RUNX1B. Using this mouse line, we establish a specific requirement for the P1-RUNX1C isoform in megakaryopoiesis, which cannot be entirely compensated for by RUNX1B overexpression. P1 knock-in megakaryocyte progenitors have reduced proliferative capacity and undergo increased cell death, resulting in thrombocytopenia. P1 knock-in premegakaryocyte/erythroid progenitors demonstrate an erythroid-specification bias, evident from increased erythroid colony-forming ability and decreased megakaryocyte output. At a transcriptional level, multiple erythroid-specific genes are upregulated and megakaryocyte-specific transcripts are downregulated. In addition, proapoptotic pathways are activated in P1 knock-in premegakaryocyte/erythroid progenitors, presumably accounting for the increased cell death in the megakaryocyte progenitor compartment. Unlike in the conditional adult Runx1 null models, megakaryocytic maturation is not affected in the P1 knock-in mice, suggesting that RUNX1B can regulate endomitosis and thrombopoiesis. Therefore, despite the high degree of structural similarity, RUNX1B and RUNX1C isoforms have distinct and specific roles in adult megakaryopoiesis.
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Affiliation(s)
- Julia E Draper
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Patrycja Sroczynska
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
- Biotech Research and Innovation Center and
- Center for Epigenetics, University of Copenhagen, Copenhagen, Denmark; and
| | - Hui Sun Leong
- Cancer Research UK Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute and
| | - Muhammad Z H Fadlullah
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Crispin Miller
- Cancer Research UK Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute and
| | - Valerie Kouskoff
- Division of Developmental Biology & Medicine, The University of Manchester, Manchester, United Kingdom
| | - Georges Lacaud
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
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12
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Johnston WL, Krizus A, Ramani AK, Dunham W, Youn JY, Fraser AG, Gingras AC, Dennis JW. C. elegans SUP-46, an HNRNPM family RNA-binding protein that prevents paternally-mediated epigenetic sterility. BMC Biol 2017; 15:61. [PMID: 28716093 PMCID: PMC5513350 DOI: 10.1186/s12915-017-0398-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/21/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history of ancestral stress that allows for adaptation and propagation of the species. In the nematode C. elegans, defective epigenetic transmission often manifests as progressive germline mortality. We previously isolated sup-46 in a screen for suppressors of the hexosamine pathway gene mutant, gna-2(qa705). In this study, we examine the role of SUP-46 in stress resistance and progressive germline mortality. RESULTS We identified SUP-46 as an HNRNPM family RNA-binding protein, and uncovered a highly novel role for SUP-46 in preventing paternally-mediated progressive germline mortality following mating. Proximity biotinylation profiling of human homologs (HNRNPM, MYEF2) identified proteins of ribonucleoprotein complexes previously shown to contain non-coding RNA. Like HNRNPM and MYEF2, SUP-46 was associated with multiple RNA granules, including stress granules, and also formed granules on active chromatin. SUP-46 depletion disrupted germ RNA granules and caused ectopic sperm, increased sperm transcripts, and chronic heat stress sensitivity. SUP-46 was also required for resistance to acute heat stress, and a conserved "MYEF2" motif was identified that was needed for stress resistance. CONCLUSIONS In mammals, non-coding RNA from the sperm of stressed males has been shown to recapitulate paternal stress phenotypes in the offspring. Our results suggest that HNRNPM family proteins enable stress resistance and paternally-mediated epigenetic transmission that may be conserved across species.
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Affiliation(s)
- Wendy L. Johnston
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Aldis Krizus
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Arun K. Ramani
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON Canada
| | - Wade Dunham
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Ji Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
| | - Andrew G. Fraser
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- The Donnelly Centre, University of Toronto, Toronto, ON Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - James W. Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
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13
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Kuvardina ON, Herkt S, Meyer A, Schneider L, Yillah J, Kohrs N, Bonig H, Seifried E, Müller-Tidow C, Lausen J. Hematopoietic transcription factors and differential cofactor binding regulate PRKACB isoform expression. Oncotarget 2017; 8:71685-71698. [PMID: 29069738 PMCID: PMC5641081 DOI: 10.18632/oncotarget.17386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/27/2017] [Indexed: 01/05/2023] Open
Abstract
Hematopoietic differentiation is controlled by key transcription factors, which regulate stem cell functions and differentiation. TAL1 is a central transcription factor for hematopoietic stem cell development in the embryo and for gene regulation during erythroid/megakaryocytic differentiation. Knowledge of the target genes controlled by a given transcription factor is important to understand its contribution to normal development and disease. To uncover direct target genes of TAL1 we used high affinity streptavidin/biotin-based chromatin precipitation (Strep-CP) followed by Strep-CP on ChIP analysis using ChIP promoter arrays. We identified 451 TAL1 target genes in K562 cells. Furthermore, we analysed the regulation of one of these genes, the catalytic subunit beta of protein kinase A (PRKACB), during megakaryopoiesis of K562 and primary human CD34+ stem cell/progenitor cells. We found that TAL1 together with hematopoietic transcription factors RUNX1 and GATA1 binds to the promoter of the isoform 3 of PRKACB (Cβ3). During megakaryocytic differentiation a coactivator complex on the Cβ3 promoter, which includes WDR5 and p300, is replaced with a corepressor complex. In this manner, activating chromatin modifications are removed and expression of the PRKACB-Cβ3 isoform during megakaryocytic differentiation is reduced. Our data uncover a role of the TAL1 complex in controlling differential isoform expression of PRKACB. These results reveal a novel function of TAL1, RUNX1 and GATA1 in the transcriptional control of protein kinase A activity, with implications for cellular signalling control during differentiation and disease.
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Affiliation(s)
- Olga N Kuvardina
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Stefanie Herkt
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Annekarin Meyer
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Lucas Schneider
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Jasmin Yillah
- Georg-Speyer-Haus, Institute for Tumorbiology and experimental Therapy, Frankfurt, Germany
| | - Nicole Kohrs
- Georg-Speyer-Haus, Institute for Tumorbiology and experimental Therapy, Frankfurt, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - Jörn Lausen
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
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14
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Thirant C, Ignacimouttou C, Lopez CK, Diop M, Le Mouël L, Thiollier C, Siret A, Dessen P, Aid Z, Rivière J, Rameau P, Lefebvre C, Khaled M, Leverger G, Ballerini P, Petit A, Raslova H, Carmichael CL, Kile BT, Soler E, Crispino JD, Wichmann C, Pflumio F, Schwaller J, Vainchenker W, Lobry C, Droin N, Bernard OA, Malinge S, Mercher T. ETO2-GLIS2 Hijacks Transcriptional Complexes to Drive Cellular Identity and Self-Renewal in Pediatric Acute Megakaryoblastic Leukemia. Cancer Cell 2017; 31:452-465. [PMID: 28292442 DOI: 10.1016/j.ccell.2017.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 12/22/2016] [Accepted: 02/09/2017] [Indexed: 12/17/2022]
Abstract
Chimeric transcription factors are a hallmark of human leukemia, but the molecular mechanisms by which they block differentiation and promote aberrant self-renewal remain unclear. Here, we demonstrate that the ETO2-GLIS2 fusion oncoprotein, which is found in aggressive acute megakaryoblastic leukemia, confers megakaryocytic identity via the GLIS2 moiety while both ETO2 and GLIS2 domains are required to drive increased self-renewal properties. ETO2-GLIS2 directly binds DNA to control transcription of associated genes by upregulation of expression and interaction with the ETS-related ERG protein at enhancer elements. Importantly, specific interference with ETO2-GLIS2 oligomerization reverses the transcriptional activation at enhancers and promotes megakaryocytic differentiation, providing a relevant interface to target in this poor-prognosis pediatric leukemia.
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Affiliation(s)
- Cécile Thirant
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Cathy Ignacimouttou
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France
| | - Cécile K Lopez
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | | | - Lou Le Mouël
- Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Clarisse Thiollier
- Gustave Roussy, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France
| | - Aurélie Siret
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Phillipe Dessen
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Zakia Aid
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Julie Rivière
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | | | | | | | | | | | | | - Hana Raslova
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | | | - Benjamin T Kile
- Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia
| | - Eric Soler
- INSERM UMR967, 92265 Fontenay-aux-Roses, France
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, IL 60611, USA
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany
| | | | - Jürg Schwaller
- University Children's Hospital Beider Basel (UKBB), Departement of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - William Vainchenker
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Camille Lobry
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Nathalie Droin
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France; INSERM U523, CNRS UMS3655, Gustave Roussy, 94800 Villejuif, France
| | - Olivier A Bernard
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris-Sud, 91405 Orsay, France
| | - Sébastien Malinge
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France
| | - Thomas Mercher
- INSERM U1170, Equipe Labellisée Ligue Contre le Cancer, Gustave Roussy Institute, 39 rue Camille Desmoulins, 94800 Villejuif, France; Gustave Roussy, 94800 Villejuif, France; Université Paris Diderot, 75013 Paris, France; Université Paris-Sud, 91405 Orsay, France.
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15
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Bonifer C, Levantini E, Kouskoff V, Lacaud G. Runx1 Structure and Function in Blood Cell Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 962:65-81. [PMID: 28299651 DOI: 10.1007/978-981-10-3233-2_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RUNX transcription factors belong to a highly conserved class of transcriptional regulators which play various roles in the development of the majority of metazoans. In this review we focus on the founding member of the family, RUNX1, and its role in the transcriptional control of blood cell development in mammals. We summarize data showing that RUNX1 functions both as activator and repressor within a chromatin environment, a feature that requires its interaction with multiple other transcription factors and co-factors. Furthermore, we outline how RUNX1 works together with other factors to reshape the epigenetic landscape and the three-dimensional structure of gene loci within the nucleus. Finally, we review how aberrant forms of RUNX1 deregulate blood cell development and cause hematopoietic malignancies.
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Affiliation(s)
- Constanze Bonifer
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Elena Levantini
- Beth Israel Diaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Richerche, Pisa, Italy
| | - Valerie Kouskoff
- Division of Developmental Biology & Medicine, The University of Manchester, Manchester, UK
| | - Georges Lacaud
- Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK
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16
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Smits AH, Borrmann A, Roosjen M, van Hest JC, Vermeulen M. Click-MS: Tagless Protein Enrichment Using Bioorthogonal Chemistry for Quantitative Proteomics. ACS Chem Biol 2016; 11:3245-3250. [PMID: 27643597 DOI: 10.1021/acschembio.6b00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Epitope-tagging is an effective tool to facilitate protein enrichment from crude cell extracts. Traditionally, N- or C-terminal fused tags are employed, which, however, can perturb protein function. Unnatural amino acids (UAAs) harboring small reactive handles can be site-specifically incorporated into proteins, thus serving as a potential alternative for conventional protein tags. Here, we introduce Click-MS, which combines the power of site-specific UAA incorporation, bioorthogonal chemistry, and quantitative mass spectrometry-based proteomics to specifically enrich a single protein of interest from crude mammalian cell extracts. By genetic encoding of p-azido-l-phenylalanine, the protein of interest can be selectively captured using copper-free click chemistry. We use Click-MS to enrich proteins that function in different cellular compartments, and we identify protein-protein interactions, showing the great potential of Click-MS for interaction proteomics workflows.
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Affiliation(s)
- Arne H. Smits
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Annika Borrmann
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Mark Roosjen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jan C.M. van Hest
- Department
of Bio-organic Chemistry, Faculty of Science, Institute for Molecules
and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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17
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Papageorgiou DN, Karkoulia E, Amaral-Psarris A, Burda P, Kolodziej K, Demmers J, Bungert J, Stopka T, Strouboulis J. Distinct and overlapping DNMT1 interactions with multiple transcription factors in erythroid cells: Evidence for co-repressor functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1515-1526. [PMID: 27693117 DOI: 10.1016/j.bbagrm.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 01/14/2023]
Abstract
DNMT1 is the maintenance DNA methyltransferase shown to be essential for embryonic development and cellular growth and differentiation in many somatic tissues in mammals. Increasing evidence has also suggested a role for DNMT1 in repressing gene expression through interactions with specific transcription factors. Previously, we identified DNMT1 as an interacting partner of the TR2/TR4 nuclear receptor heterodimer in erythroid cells, implicated in the developmental silencing of fetal β-type globin genes in the adult stage of human erythropoiesis. Here, we extended this work by using a biotinylation tagging approach to characterize DNMT1 protein complexes in mouse erythroleukemic cells. We identified novel DNMT1 interactions with several hematopoietic transcription factors with essential roles in erythroid differentiation, including GATA1, GFI-1b and FOG-1. We provide evidence for DNMT1 forming distinct protein subcomplexes with specific transcription factors and propose the existence of a "core" DNMT1 complex with the transcription factors ZBP-89 and ZNF143, which is also present in non-hematopoietic cells. Furthermore, we identified the short (17a.a.) PCNA Binding Domain (PBD) located near the N-terminus of DNMT1 as being necessary for mediating interactions with the transcription factors described herein. Lastly, we provide evidence for DNMT1 serving as a co-repressor of ZBP-89 and GATA1 acting through upstream regulatory elements of the PU.1 and GATA1 gene loci.
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Affiliation(s)
- Dimitris N Papageorgiou
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Elena Karkoulia
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Alexandra Amaral-Psarris
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Pavel Burda
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarzyna Kolodziej
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Tomas Stopka
- Biocev, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - John Strouboulis
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
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18
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Schiera G, Di Liegro CM, Puleo V, Colletta O, Fricano A, Cancemi P, Di Cara G, Di Liegro I. Extracellular vesicles shed by melanoma cells contain a modified form of H1.0 linker histone and H1.0 mRNA-binding proteins. Int J Oncol 2016; 49:1807-1814. [PMID: 27633859 PMCID: PMC5063456 DOI: 10.3892/ijo.2016.3692] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Extracellular vesicles (EVs) are now recognized as a fundamental way for cell-to-cell horizontal transfer of properties, in both physiological and pathological conditions. Most of EV-mediated cross-talk among cells depend on the exchange of proteins, and nucleic acids, among which mRNAs, and non-coding RNAs such as different species of miRNAs. Cancer cells, in particular, use EVs to discard molecules which could be dangerous to them (for example differentiation-inducing proteins such as histone H1.0, or antitumor drugs), to transfer molecules which, after entering the surrounding cells, are able to transform their phenotype, and even to secrete factors, which allow escaping from immune surveillance. Herein we report that melanoma cells not only secrete EVs which contain a modified form of H1.0 histone, but also transport the corresponding mRNA. Given the already known role in tumorigenesis of some RNA binding proteins (RBPs), we also searched for proteins of this class in EVs. This study revealed the presence in A375 melanoma cells of at least three RBPs, with apparent MW of about 65, 45 and 38 kDa, which are able to bind H1.0 mRNA. Moreover, we purified one of these proteins, which by MALDI-TOF mass spectrometry was identified as the already known transcription factor MYEF2.
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Affiliation(s)
- Gabriella Schiera
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Carlo Maria Di Liegro
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Veronica Puleo
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Oriana Colletta
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Anna Fricano
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Patrizia Cancemi
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), I-90128 Palermo, Italy
| | - Gianluca Di Cara
- Center of Experimental Oncobiology (C.OB.S.), La Maddalena Hospital III Level Oncological Dept., Palermo, Italy
| | - Italia Di Liegro
- Department of Experimental Biomedicine and Clinical Neurosciences (BIONEC), University of Palermo, I-90127 Palermo, Italy
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19
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Kohrs N, Kolodziej S, Kuvardina ON, Herglotz J, Yillah J, Herkt S, Piechatzek A, Salinas Riester G, Lingner T, Wichmann C, Bonig H, Seifried E, Platzbecker U, Medyouf H, Grez M, Lausen J. MiR144/451 Expression Is Repressed by RUNX1 During Megakaryopoiesis and Disturbed by RUNX1/ETO. PLoS Genet 2016; 12:e1005946. [PMID: 26990877 PMCID: PMC4798443 DOI: 10.1371/journal.pgen.1005946] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/01/2016] [Indexed: 01/22/2023] Open
Abstract
A network of lineage-specific transcription factors and microRNAs tightly regulates differentiation of hematopoietic stem cells along the distinct lineages. Deregulation of this regulatory network contributes to impaired lineage fidelity and leukemogenesis. We found that the hematopoietic master regulator RUNX1 controls the expression of certain microRNAs, of importance during erythroid/megakaryocytic differentiation. In particular, we show that the erythorid miR144/451 cluster is epigenetically repressed by RUNX1 during megakaryopoiesis. Furthermore, the leukemogenic RUNX1/ETO fusion protein transcriptionally represses the miR144/451 pre-microRNA. Thus RUNX1/ETO contributes to increased expression of miR451 target genes and interferes with normal gene expression during differentiation. Furthermore, we observed that inhibition of RUNX1/ETO in Kasumi1 cells and in RUNX1/ETO positive primary acute myeloid leukemia patient samples leads to up-regulation of miR144/451. RUNX1 thus emerges as a key regulator of a microRNA network, driving differentiation at the megakaryocytic/erythroid branching point. The network is disturbed by the leukemogenic RUNX1/ETO fusion product.
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Affiliation(s)
- Nicole Kohrs
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Stephan Kolodziej
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Olga N. Kuvardina
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Julia Herglotz
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jasmin Yillah
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Stefanie Herkt
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Alexander Piechatzek
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | | | - Thomas Lingner
- Medical-University Goettingen, Transcriptome Analysis Laboratory, Goettingen, Germany
| | - Christian Wichmann
- Department of Transfusion Medicine, Cell Therapeutics and Hemostaseology, Ludwig-Maximilian University Hospital, Munich, Germany
| | - Halvard Bonig
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Erhard Seifried
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
| | - Uwe Platzbecker
- Department of Hematology, Medical Clinic and Polyclinic I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Hind Medyouf
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Manuel Grez
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
| | - Jörn Lausen
- Georg-Speyer-Haus, Institute for Tumorbiology and Experimental Therapy, Frankfurt, Germany
- Institute for Transfusion Medicine and Immunohematology, Johann-Wolfgang-Goethe University and German Red Cross Blood Service, Frankfurt am Main, Germany
- * E-mail:
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20
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Draper JE, Sroczynska P, Tsoulaki O, Leong HS, Fadlullah MZH, Miller C, Kouskoff V, Lacaud G. RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PLoS Genet 2016; 12:e1005814. [PMID: 26808730 PMCID: PMC4726605 DOI: 10.1371/journal.pgen.1005814] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/23/2015] [Indexed: 12/11/2022] Open
Abstract
The Core Binding Factor (CBF) protein RUNX1 is a master regulator of definitive hematopoiesis, crucial for hematopoietic stem cell (HSC) emergence during ontogeny. RUNX1 also plays vital roles in adult mice, in regulating the correct specification of numerous blood lineages. Akin to the other mammalian Runx genes, Runx1 has two promoters P1 (distal) and P2 (proximal) which generate distinct protein isoforms. The activities and specific relevance of these two promoters in adult hematopoiesis remain to be fully elucidated. Utilizing a dual reporter mouse model we demonstrate that the distal P1 promoter is broadly active in adult hematopoietic stem and progenitor cell (HSPC) populations. By contrast the activity of the proximal P2 promoter is more restricted and its upregulation, in both the immature Lineage- Sca1high cKithigh (LSK) and bipotential Pre-Megakaryocytic/Erythroid Progenitor (PreMegE) populations, coincides with a loss of erythroid (Ery) specification. Accordingly the PreMegE population can be prospectively separated into "pro-erythroid" and "pro-megakaryocyte" populations based on Runx1 P2 activity. Comparative gene expression analyses between Runx1 P2+ and P2- populations indicated that levels of CD34 expression could substitute for P2 activity to distinguish these two cell populations in wild type (WT) bone marrow (BM). Prospective isolation of these two populations will enable the further investigation of molecular mechanisms involved in megakaryocytic/erythroid (Mk/Ery) cell fate decisions. Having characterized the extensive activity of P1, we utilized a P1-GFP homozygous mouse model to analyze the impact of the complete absence of Runx1 P1 expression in adult mice and observed strong defects in the T cell lineage. Finally, we investigated how the leukemic fusion protein AML1-ETO9a might influence Runx1 promoter usage. Short-term AML1-ETO9a induction in BM resulted in preferential P2 upregulation, suggesting its expression may be important to establish a pre-leukemic environment.
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Affiliation(s)
- Julia E. Draper
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Patrycja Sroczynska
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Olga Tsoulaki
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Hui Sun Leong
- Cancer Research UK Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Muhammad Z. H. Fadlullah
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Crispin Miller
- Cancer Research UK Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Valerie Kouskoff
- Cancer Research UK Stem Cell Haematopoiesis Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
| | - Georges Lacaud
- Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom
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21
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Genetic and Epigenetic Mechanisms That Maintain Hematopoietic Stem Cell Function. Stem Cells Int 2015; 2016:5178965. [PMID: 26798358 PMCID: PMC4699043 DOI: 10.1155/2016/5178965] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 09/09/2015] [Indexed: 01/15/2023] Open
Abstract
All hematopoiesis cells develop from multipotent progenitor cells. Hematopoietic stem cells (HSC) have the ability to develop into all blood lineages but also maintain their stemness. Different molecular mechanisms have been identified that are crucial for regulating quiescence and self-renewal to maintain the stem cell pool and for inducing proliferation and lineage differentiation. The stem cell niche provides the microenvironment to keep HSC in a quiescent state. Furthermore, several transcription factors and epigenetic modifiers are involved in this process. These create modifications that regulate the cell fate in a more or less reversible and dynamic way and contribute to HSC homeostasis. In addition, HSC respond in a unique way to DNA damage. These mechanisms also contribute to the regulation of HSC function and are essential to ensure viability after DNA damage. How HSC maintain their quiescent stage during the entire life is still matter of ongoing research. Here we will focus on the molecular mechanisms that regulate HSC function.
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22
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Abstract
Hematopoiesis is characterized by a lifelong balance between hematopoietic stem cell (HSC) self-renewal and differentiation into mature blood populations. Proper instruction of cell fate decisions requires tight homeostatic regulation of transcriptional programs through a combination of epigenetic modifications, management of cis-regulatory elements, and transcription factor activity. Recent work has focused on integrating biochemical, genetic, and evolutionary data sets to gain further insight into these regulatory components. Long noncoding RNA (lncRNA), post-translational modifications of transcription factors, and circadian rhythm add additional layers of complexity. These analyses have provided a wealth of information, much of which has been made available through public databases. Elucidating the regulatory processes that govern hematopoietic transcriptional programs is expected to provide useful insights into hematopoiesis that may be applied broadly across tissue types while enabling the discovery and implementation of therapeutics to treat human disease.
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Affiliation(s)
- David E Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
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23
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van Riel B, Rosenbauer F. Epigenetic control of hematopoiesis: the PU.1 chromatin connection. Biol Chem 2015; 395:1265-74. [PMID: 25205721 DOI: 10.1515/hsz-2014-0195] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 07/03/2014] [Indexed: 12/21/2022]
Abstract
Purine-rich box1 (PU.1) is a transcription factor that not only has a key role in the development of most hematopoietic cell lineages but also in the suppression of leukemia. To exert these functions, PU.1 can cross-talk with multiple different proteins by forming complexes in order to activate or repress transcription. Among its protein partners are chromatin remodelers, DNA methyltransferases, and a number of other transcription factors with important roles in hematopoiesis. While a great deal of knowledge has been acquired about PU.1 function over the years, it was the development of novel genome-wide technologies, which boosted our understanding of how PU.1 acts on the chromatin to drive its repertoire of target genes. This review summarizes current knowledge and ideas of molecular mechanisms by which PU.1 controls hematopoiesis and suppresses leukemia.
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24
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Soler E, Grosveld F. Targeting epigenetics to speed up repair. Cell Stem Cell 2014; 14:553-4. [PMID: 24792110 DOI: 10.1016/j.stem.2014.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this issue of Cell Stem Cell, Palii et al. reveal that TAL1 is a master regulator of adhesion and migration networks in human endothelial progenitors and that ex vivo treatment with the histone deacetylase inhibitor TSA enables their faster vascularization after ischemic injury.
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Affiliation(s)
- Eric Soler
- INSERM UMR967 CEA/DSV/iRCM, 92265 Fontenay-aux-Roses, France.
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
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25
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Giraud G, Stadhouders R, Conidi A, Dekkers DHW, Huylebroeck D, Demmers JAA, Soler E, Grosveld FG. NLS-tagging: an alternative strategy to tag nuclear proteins. Nucleic Acids Res 2014; 42:gku869. [PMID: 25260593 PMCID: PMC4245968 DOI: 10.1093/nar/gku869] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The characterization of transcription factor complexes and their binding sites in the genome by affinity purification has yielded tremendous new insights into how genes are regulated. The affinity purification requires either the use of antibodies raised against the factor of interest itself or by high-affinity binding of a C- or N-terminally added tag sequence to the factor. Unfortunately, fusing extra amino acids to the termini of a factor can interfere with its biological function or the tag may be inaccessible inside the protein. Here, we describe an effective solution to that problem by integrating the ‘tag’ close to the nuclear localization sequence domain of the factor. We demonstrate the effectiveness of this approach with the transcription factors Fli-1 and Irf2bp2, which cannot be tagged at their extremities without loss of function. This resulted in the identification of novel proteins partners and a new hypothesis on the contribution of Fli-1 to hematopoiesis.
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Affiliation(s)
- Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Ralph Stadhouders
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Laboratory of Molecular Biology (Celgen), Department of Development and Regeneration, KU Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Eric Soler
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Laboratory of Hematopoiesis and Leukemic Stem Cells (LSHL), CEA/INSERM U967, Fontenay-aux-Roses, France Center for Biomedical Genetics and Medical Epigenetics Consortium, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Center for Biomedical Genetics and Medical Epigenetics Consortium, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands Center for Biomedical Genetics, Erasmus Medical Center, Faculty building, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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26
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Ptasinska A, Assi SA, Martinez-Soria N, Imperato MR, Piper J, Cauchy P, Pickin A, James SR, Hoogenkamp M, Williamson D, Wu M, Tenen DG, Ott S, Westhead DR, Cockerill PN, Heidenreich O, Bonifer C. Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal. Cell Rep 2014; 8:1974-1988. [PMID: 25242324 PMCID: PMC4487811 DOI: 10.1016/j.celrep.2014.08.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/19/2014] [Accepted: 08/12/2014] [Indexed: 11/29/2022] Open
Abstract
Oncogenic transcription factors such as RUNX1/ETO, which is generated by the chromosomal translocation t(8;21), subvert normal blood cell development by impairing differentiation and driving malignant self-renewal. Here, we use digital footprinting and chromatin immunoprecipitation sequencing (ChIP-seq) to identify the core RUNX1/ETO-responsive transcriptional network of t(8;21) cells. We show that the transcriptional program underlying leukemic propagation is regulated by a dynamic equilibrium between RUNX1/ETO and RUNX1 complexes, which bind to identical DNA sites in a mutually exclusive fashion. Perturbation of this equilibrium in t(8;21) cells by RUNX1/ETO depletion leads to a global redistribution of transcription factor complexes within preexisting open chromatin, resulting in the formation of a transcriptional network that drives myeloid differentiation. Our work demonstrates on a genome-wide level that the extent of impaired myeloid differentiation in t(8;21) is controlled by the dynamic balance between RUNX1/ETO and RUNX1 activities through the repression of transcription factors that drive differentiation. RUNX1/ETO drives a t(8;21)-specific transcriptional network RUNX1/ETO and RUNX1 dynamically compete for the same genomic sites RUNX1/ETO targets transcription factor complexes that control differentiation RUNX1/ETO depletion activates a transcriptional network dominated by C/EBPα
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Affiliation(s)
- Anetta Ptasinska
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK; School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalia Martinez-Soria
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Rosaria Imperato
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Jason Piper
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - Pierre Cauchy
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Anna Pickin
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Sally R James
- Section of Experimental Haematology, Leeds Institute for Molecular Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Maarten Hoogenkamp
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Dan Williamson
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Mengchu Wu
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Republic of Singapore, Singapore 117456, Singapore
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Peter N Cockerill
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK
| | - Olaf Heidenreich
- Northern Institute for Cancer Research, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK.
| | - Constanze Bonifer
- School of Cancer Sciences, College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, UK.
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27
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García-González E, Recillas-Targa F. A regulatory element affects the activity and chromatin structure of the chicken α-globin 3' enhancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1233-41. [PMID: 25239823 DOI: 10.1016/j.bbagrm.2014.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 09/09/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022]
Abstract
Gene promoters are frequently insufficient to drive the spatiotemporal patterns of gene expression during cell differentiation and organism development. Enhancers convey these properties through diverse mechanisms, including long-distance interactions with target promoters via their association with specific transcription factors. Despite unprecedented progress in the knowledge of enhancer mechanisms of action, there are still many unanswered questions. In particular, the contribution of an enhancer's local chromatin configuration to its mechanism of action is not completely understood. Here we describe a novel regulatory element, the Upstream Enhancer Element (UEE), which modulates the activity of the chicken α-globin 3' enhancer by regulating its chromatin structure, specifically by positioning a nucleosome upstream of the core enhancer. This element binds nuclear factors and confers a more restricted activation on the α-globin 3' enhancer, suggesting a progressive/rheostatic model for enhancer activity. Our results suggest that the UEE activity contributes to the positioning of a nucleosome that is necessary for the α-globin 3' enhancer activation.
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Affiliation(s)
- Estela García-González
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico.
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28
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Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Davé UP. LMO2 induces T-cell leukemia with epigenetic deregulation of CD4. Exp Hematol 2014; 42:581-93.e5. [PMID: 24792354 PMCID: PMC4241760 DOI: 10.1016/j.exphem.2014.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 04/18/2014] [Accepted: 04/23/2014] [Indexed: 02/05/2023]
Abstract
In this study, we present a remarkable clonal cell line, 32080, derived from a CD2-Lmo2- transgenic T-cell leukemia with differentiation arrest at the transition from the intermediate single positive to double positive stages of T-cell development. We observed that 32080 cells had a striking variegated pattern in CD4 expression. There was cell-to-cell variability, with some cells expressing no CD4 and others expressing high CD4. The two populations were isogenic and yet differed in their rates of apoptosis and sensitivity to glucocorticoid. We sorted the 32080 line for CD4-positive or CD4-negative cells and observed them in culture. After 1 week, both sorted populations showed variegated CD4 expression, like the parental line, showing that the two populations could interconvert. We determined that cell replication was necessary to transit from CD4(+) to CD4(-) and CD4(-) to CD4(+). Lmo2 knockdown decreased CD4 expression, while inhibition of intracellular NOTCH1 or histone deacetylase activity induced CD4 expression. Enforced expression of RUNX1 repressed CD4 expression. We analyzed the CD4 locus by Histone 3 chromatin immunoprecipitation and found silencing marks in the CD4(-) cells and activating marks in the CD4(+) population. The 32080 cell line is a striking model of intermediate single positive to double positive T-cell plasticity and invokes a novel mechanism for LMO2's oncogenic functions.
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Affiliation(s)
- Susan M Cleveland
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Charnise Goodings
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Rati M Tripathi
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Natalina Elliott
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA
| | - Mary Ann Thompson
- Vanderbilt University Medical Center, Department of Pathology, Microbiology, and Immunology, Nashville, Tennessee, USA
| | - Yan Guo
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Utpal P Davé
- Tennessee Valley Healthcare System and the Vanderbilt University Medical Center, Departments of Medicine and Cancer Biology, Nashville, Tennessee, USA.
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29
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de Pater E, Kaimakis P, Vink CS, Yokomizo T, Yamada-Inagawa T, van der Linden R, Kartalaei PS, Camper SA, Speck N, Dzierzak E. Gata2 is required for HSC generation and survival. ACTA ACUST UNITED AC 2013; 210:2843-50. [PMID: 24297996 PMCID: PMC3865477 DOI: 10.1084/jem.20130751] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GATA2 function is essential for the generation of HSCs during the stage of endothelial-to-hematopoietic cell transition and thereafter for HSC survival Knowledge of the key transcription factors that drive hematopoietic stem cell (HSC) generation is of particular importance for current hematopoietic regenerative approaches and reprogramming strategies. Whereas GATA2 has long been implicated as a hematopoietic transcription factor and its dysregulated expression is associated with human immunodeficiency syndromes and vascular integrity, it is as yet unknown how GATA2 functions in the generation of HSCs. HSCs are generated from endothelial cells of the major embryonic vasculature (aorta, vitelline, and umbilical arteries) and are found in intra-aortic hematopoietic clusters. In this study, we find that GATA2 function is essential for the generation of HSCs during the stage of endothelial-to-hematopoietic cell transition. Specific deletion of Gata2 in Vec (Vascular Endothelial Cadherin)-expressing endothelial cells results in a deficiency of long-term repopulating HSCs and intra-aortic cluster cells. By specific deletion of Gata2 in Vav-expressing hematopoietic cells (after HSC generation), we further show that GATA2 is essential for HSC survival. This is in contrast to the known activity of the RUNX1 transcription factor, which functions only in the generation of HSCs, and highlights the unique requirement for GATA2 function in HSCs throughout all developmental stages.
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Affiliation(s)
- Emma de Pater
- Erasmus Medical Center, Erasmus Stem Cell Institute, 3000 CA Rotterdam, Netherlands
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30
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The C-terminus of CBFβ-SMMHC is required to induce embryonic hematopoietic defects and leukemogenesis. Blood 2012; 121:638-42. [PMID: 23152542 DOI: 10.1182/blood-2012-06-434688] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The C-terminus of CBFβ-SMMHC, the fusion protein produced by a chromosome 16 inversion in acute myeloid leukemia subtype M4Eo, contains domains for self-multimerization and transcriptional repression, both of which have been proposed to be important for leukemogenesis by CBFβ-SMMHC. To test the role of the fusion protein's C-terminus in vivo, we generated knock-in mice expressing a C-terminally truncated CBFβ-SMMHC (CBFβ-SMMHCΔC95). Embryos with a single copy of CBFβ-SMMHCΔC95 were viable and showed no defects in hematopoiesis, whereas embryos homozygous for the CBFβ-SMMHCΔC95 allele had hematopoietic defects and died in mid-gestation, similar to embryos with a single-copy of the full-length CBFβ-SMMHC. Importantly, unlike mice expressing full-length CBFβ-SMMHC, none of the mice expressing CBFβ-SMMHCΔC95 developed leukemia, even after treatment with a mutagen, although some of the older mice developed a nontransplantable myeloproliferative disease. Our data indicate that the CBFβ-SMMHC's C-terminus is essential to induce embryonic hematopoietic defects and leukemogenesis.
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