1
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Hopp MT, Vaidya SM, Grimmig KM, Strudthoff LJ, Clauser JC, Yuan X, Singh S, Müller J, Oldenburg J, Hamza I, Imhof D. Quantitative analysis of heme and hemoglobin for the detection of intravascular hemolysis. Anal Chim Acta 2024; 1312:342766. [PMID: 38834280 DOI: 10.1016/j.aca.2024.342766] [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: 11/15/2023] [Revised: 03/13/2024] [Accepted: 05/21/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Intravascular hemolysis is associated with massive release of hemoglobin and consequently labile heme into the blood, resulting in prothrombotic and proinflammatory events in patients. Though heme is well-known to participate in these adverse effects, it is not monitored. Instead, haptoglobin and hemoglobin serve as clinical biomarkers. The quantification of labile heme together with hemoglobin, however, should be considered in clinical diagnosis as well, to obtain a complete picture of the hemolytic state in patients. So far, quantification techniques for labile heme were not yet systematically analyzed and compared for their clinical application potential, especially in the presence of hemoglobin. RESULTS Two commercial assays (Heme Assay Kit®, Hemin Assay Kit®) and five common approaches (pyridine hemochromogen assay, apo-horseradish peroxidase-based assay, UV/Vis spectroscopy, HPLC, mass spectrometry) were analyzed concerning their linearity, accuracy, and precision, as well as their ability to distinguish between hemoglobin-bound heme and labile heme. Further, techniques for the quantification of hemoglobin (Harboe method, SLS method, Hemastix®) were included to study their selectivity for hemoglobin and potential interference by the presence of labile heme. Both, indirect and direct approaches were suitable for the determination of a wide concentration of heme (∼0.02-45 μM) and hemoglobin (∼0.002-17 μM). A clear distinction between hemoglobin-bound heme and labile heme with one method was not possible. Thus, a novel combined approach is presented and applied to human and porcine plasma samples for the determination of hemoglobin and labile heme. SIGNIFICANCE Our results demonstrate the need to develop improved techniques to differentiate labile and protein-bound heme for early detection of intravascular hemolysis. Here, we present a novel strategy by combining two spectroscopic methods, which is most reliable as an easy-to-use tool for the determination of hemoglobin and heme levels in plasma samples for the diagnosis of intravascular hemolysis and in basic biomedical research.
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Affiliation(s)
- Marie-T Hopp
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121, Bonn, Germany; Department of Chemistry, Institute for Integrated Natural Sciences, University of Koblenz, D-56070, Koblenz, Germany
| | - Sonali M Vaidya
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121, Bonn, Germany
| | - Karina M Grimmig
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121, Bonn, Germany
| | - Lasse J Strudthoff
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Medical Faculty RWTH Aachen University, D-52074, Aachen, Germany
| | - Johanna C Clauser
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Medical Faculty RWTH Aachen University, D-52074, Aachen, Germany
| | - Xiaojing Yuan
- Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, US-21201, Baltimore, MD, USA
| | - Sneha Singh
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, D-53127, Bonn, Germany
| | - Jens Müller
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, D-53127, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, D-53127, Bonn, Germany
| | - Iqbal Hamza
- Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, US-21201, Baltimore, MD, USA
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, D-53121, Bonn, Germany.
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2
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Liao R, Bresnick EH. Endogenous Small Molecule Effectors in GATA Transcription Factor Mechanisms Governing Biological and Pathological Processes. Exp Hematol 2024:104252. [PMID: 38876253 DOI: 10.1016/j.exphem.2024.104252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Transcriptional mechanisms establish and maintain complex genetic and protein networks to control cell state transitions. The hematopoietic transcription factor GATA1 is a master regulator of erythropoiesis and megakaryopoiesis, and human GATA1 genetic variants cause anemia and megakaryoblastic leukemia. Multiomic analyses revealed that GATA1 controls expression of transporters and metabolic enzymes that dictate intracellular levels of endogenous small molecules, including heme, metal ions, and sphingolipids. Besides its canonical function as a hemoglobin component, heme facilitates or antagonizes GATA1 function to regulate erythropoiesis via mechanisms dependent or independent of the heme-binding transcription factor BACH1. GATA1 regulates expression of genes encoding heme biosynthetic enzymes and BACH1. GATA1 maintains homeostasis of bioactive ceramides during erythroid differentiation by regulating genes encoding sphingolipid metabolic enzymes. Disrupting ceramide homeostasis impairs critical cytokine signaling and is detrimental to erythroid cells. During erythroid maturation, GATA1 induces a zinc transporter switch that favors export versus import, thus dictating the intracellular zinc level, erythroblast survival, and differentiation. In aggregate, these studies support an emerging paradigm in which GATA factor-dependent transcriptional mechanisms control the intracellular levels of endogenous small molecules and small molecule-dependent feedback loops that serve as vital effectors of transcription factor activity, genome function, and cell state transitions.
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Affiliation(s)
- Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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3
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Borg J, Loy C, Kim J, Buhagiar A, Chin C, Damle N, De Vlaminck I, Felice A, Liu T, Matei I, Meydan C, Muratani M, Mzava O, Overbey E, Ryon KA, Smith SM, Tierney BT, Trudel G, Zwart SR, Beheshti A, Mason CE, Borg J. Spatiotemporal expression and control of haemoglobin in space. Nat Commun 2024; 15:4927. [PMID: 38862545 PMCID: PMC11166948 DOI: 10.1038/s41467-024-49289-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
It is now widely recognised that the environment in space activates a diverse set of genes involved in regulating fundamental cellular pathways. This includes the activation of genes associated with blood homoeostasis and erythropoiesis, with a particular emphasis on those involved in globin chain production. Haemoglobin biology provides an intriguing model for studying space omics, as it has been extensively explored at multiple -omic levels, spanning DNA, RNA, and protein analyses, in both experimental and clinical contexts. In this study, we examined the developmental expression of haemoglobin over time and space using a unique suite of multi-omic datasets available on NASA GeneLab, from the NASA Twins Study, the JAXA CFE study, and the Inspiration4 mission. Our findings reveal significant variations in globin gene expression corresponding to the distinct spatiotemporal characteristics of the collected samples. This study sheds light on the dynamic nature of globin gene regulation in response to the space environment and provides valuable insights into the broader implications of space omics research.
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Affiliation(s)
- Josef Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Conor Loy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alfred Buhagiar
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta
| | - Christopher Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Iwijn De Vlaminck
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Alex Felice
- Department of Surgery, Faculty of Medicine and Surgery, University of Malta, Msida, MSD2080, Malta
| | - Tammy Liu
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Irina Matei
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Masafumi Muratani
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Omary Mzava
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Eliah Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Scott M Smith
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | - Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Guy Trudel
- Ottawa Hospital Research Institute, Department of Medicine, Ottawa, Ontario, Canada
| | - Sara R Zwart
- Biomedical Research and Environmental Sciences Division, Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
- University of Texas Medical Branch, Galveston, TX, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Joseph Borg
- Faculty of Health Sciences, University of Malta, Msida, MSD2080, Malta.
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4
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Tseng YJ, Kageyama Y, Murdaugh RL, Kitano A, Kim JH, Hoegenauer KA, Tiessen J, Smith MH, Uryu H, Takahashi K, Martin JF, Samee MAH, Nakada D. Increased iron uptake by splenic hematopoietic stem cells promotes TET2-dependent erythroid regeneration. Nat Commun 2024; 15:538. [PMID: 38225226 PMCID: PMC10789814 DOI: 10.1038/s41467-024-44718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Hematopoietic stem cells (HSCs) are capable of regenerating the blood system, but the instructive cues that direct HSCs to regenerate particular lineages lost to the injury remain elusive. Here, we show that iron is increasingly taken up by HSCs during anemia and induces erythroid gene expression and regeneration in a Tet2-dependent manner. Lineage tracing of HSCs reveals that HSCs respond to hemolytic anemia by increasing erythroid output. The number of HSCs in the spleen, but not bone marrow, increases upon anemia and these HSCs exhibit enhanced proliferation, erythroid differentiation, iron uptake, and TET2 protein expression. Increased iron in HSCs promotes DNA demethylation and expression of erythroid genes. Suppressing iron uptake or TET2 expression impairs erythroid genes expression and erythroid differentiation of HSCs; iron supplementation, however, augments these processes. These results establish that the physiological level of iron taken up by HSCs has an instructive role in promoting erythroid-biased differentiation of HSCs.
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Affiliation(s)
- Yu-Jung Tseng
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuki Kageyama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rebecca L Murdaugh
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ayumi Kitano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jong Hwan Kim
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kevin A Hoegenauer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan Tiessen
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mackenzie H Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hidetaka Uryu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - James F Martin
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Cardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX, 77030, USA
| | - Md Abul Hassan Samee
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daisuke Nakada
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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5
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Liao R, Babatunde A, Qiu S, Harikumar H, Coon JJ, Overmyer KA, Hannun YA, Luberto C, Bresnick EH. A transcriptional network governing ceramide homeostasis establishes a cytokine-dependent developmental process. Nat Commun 2023; 14:7262. [PMID: 37945603 PMCID: PMC10636182 DOI: 10.1038/s41467-023-42978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
Transcriptional mechanisms controlling developmental processes establish and maintain proteomic networks, which can govern the levels of intracellular small molecules. Although dynamic changes in bioactive small molecules can link transcription factor and genome activity with cell state transitions, many mechanistic questions are unresolved. Using quantitative lipidomics and multiomics, we discover that the hematopoietic transcription factor GATA1 establishes ceramide homeostasis during erythroid differentiation by regulating genes encoding sphingolipid metabolic enzymes. Inhibiting a GATA1-induced sphingolipid biosynthetic enzyme, delta(4)-desaturase, or disrupting ceramide homeostasis with cell-permeable dihydroceramide or ceramide is detrimental to erythroid, but not myeloid, progenitor activity. Coupled with genetic editing-based rewiring of the regulatory circuitry, we demonstrate that ceramide homeostasis commissions vital stem cell factor and erythropoietin signaling by opposing an inhibitory protein phosphatase 2A-dependent, dual-component mechanism. Integrating bioactive lipids as essential components of GATA factor mechanisms to control cell state transitions has implications for diverse cell and tissue types.
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Affiliation(s)
- Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Abiola Babatunde
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Stephanie Qiu
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Hamsini Harikumar
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, National Center for Quantitative Biology of Complex Systems, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, National Center for Quantitative Biology of Complex Systems, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Yusuf A Hannun
- Department of Medicine, Stony Book University, Stony Brook, NY, USA
- Northport Veterans Affairs Medical Center, Northport, NY, USA
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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6
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Jung MM, Shen S, Botten GA, Olender T, Katsumura KR, Johnson KD, Soukup AA, Liu P, Zhang Q, Jensvold ZD, Lewis PW, Beagrie RA, Low JK, Yang L, Mackay JP, Godley LA, Brand M, Xu J, Keles S, Bresnick EH. Pathogenic human variant that dislocates GATA2 zinc fingers disrupts hematopoietic gene expression and signaling networks. J Clin Invest 2023; 133:e162685. [PMID: 36809258 PMCID: PMC10065080 DOI: 10.1172/jci162685] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Although certain human genetic variants are conspicuously loss of function, decoding the impact of many variants is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) with a germline GATA2 variant that inserts 9 amino acids between the 2 zinc fingers (9aa-Ins). Here, we conducted mechanistic analyses using genomic technologies and a genetic rescue system with Gata2 enhancer-mutant hematopoietic progenitor cells to compare how GATA2 and 9aa-Ins function genome-wide. Despite nuclear localization, 9aa-Ins was severely defective in occupying and remodeling chromatin and regulating transcription. Variation of the inter-zinc finger spacer length revealed that insertions were more deleterious to activation than repression. GATA2 deficiency generated a lineage-diverting gene expression program and a hematopoiesis-disrupting signaling network in progenitors with reduced granulocyte-macrophage colony-stimulating factor (GM-CSF) and elevated IL-6 signaling. As insufficient GM-CSF signaling caused pulmonary alveolar proteinosis and excessive IL-6 signaling promoted bone marrow failure and GATA2 deficiency patient phenotypes, these results provide insight into mechanisms underlying GATA2-linked pathologies.
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Affiliation(s)
- Mabel Minji Jung
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Siqi Shen
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Giovanni A. Botten
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thomas Olender
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Koichi R. Katsumura
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Kirby D. Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Alexandra A. Soukup
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
| | - Peng Liu
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Qingzhou Zhang
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute–General Hospital, Ottawa, Ontario, Canada
| | - Zena D. Jensvold
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Peter W. Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Robert A. Beagrie
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jason K.K. Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lihua Yang
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P. Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Lucy A. Godley
- Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Marjorie Brand
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Jian Xu
- Children’s Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Sunduz Keles
- Department of Biostatistics and Biomedical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, and
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7
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Ikeda M, Kato H, Shima H, Matsumoto M, Furukawa E, Yan Y, Liao R, Xu J, Muto A, Fujiwara T, Harigae H, Bresnick EH, Igarashi K. Heme-dependent induction of mitophagy program during differentiation of murine erythroid cells. Exp Hematol 2023; 118:21-30. [PMID: 36481429 PMCID: PMC10161131 DOI: 10.1016/j.exphem.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022]
Abstract
Although establishment and maintenance of mitochondria are essential for the production of massive amounts of heme in erythroblasts, mitochondria must be degraded upon terminal differentiation to red blood cells (RBCs), thus creating a biphasic regulatory process. Previously, we reported that iron deficiency in mice promotes mitochondrial retention in RBCs, suggesting that a proper amount of iron and/or heme is necessary for the degradation of mitochondria during erythroblast maturation. Because the transcription factor GATA1 regulates autophagy in erythroid cells, which involves mitochondrial clearance (mitophagy), we investigated the relationship between iron or heme and mitophagy by analyzing the expression of genes related to GATA1 and autophagy and the impact of iron or heme restriction on the amount of mitochondria. We found that heme promotes the expression of GATA1-regulated mitophagy-related genes and the induction of mitophagy. GATA1 might induce the expression of the autophagy-related genes Atg4d and Stk11 for mitophagy through a heme-dependent mechanism in murine erythroleukemia (MEL) cells and a genetic rescue system with G1E-ER-GATA1 erythroblast cells derived from Gata1-null murine embryonic stem cells. These results provide evidence for a biphasic mechanism in which mitochondria are essential for heme generation, and the heme generated during differentiation promotes mitophagy and mitochondrial disposal. This mechanism provides a molecular framework for understanding this fundamentally important cell biological process.
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Affiliation(s)
- Masatoshi Ikeda
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Hiroki Kato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan; Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Eijiro Furukawa
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Yan Yan
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Ruiqi Liao
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Akihiko Muto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi, Sendai, Japan.
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8
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Enniatin B and beauvericin affect intestinal cell function and hematological processes in Atlantic salmon (Salmo salar) after acute exposure. Food Chem Toxicol 2023; 172:113557. [PMID: 36526092 DOI: 10.1016/j.fct.2022.113557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/05/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022]
Abstract
Unintentional use of mold-infested plant-based feed ingredients are sources of mycotoxins in fish feeds. The presence of the emerging mycotoxins ENNB and BEA in Norwegian commercial fish feeds and plant-based feed ingredients has raised concerns regarding the health effects on farmed Atlantic salmon (Salmon salar). Atlantic salmon pre-smolts were exposed to non-lethal doses of BEA and ENNB (ctrl, 50 and 500 μg/kg feed for 12 h), after which total RNA sequencing of the intestine and liver was carried out to evaluate gut health and identify possible hepatological changes after acute dietary exposure. ENNB and BEA did not trigger acute toxicity, however ENNB caused the onset of pathways linked to acute intestinal inflammation and BEA exposures caused the onset of hepatic hematological disruption. The prevalence and concentration of ENNB found in today's commercial feed could affect the fish health if consumed over a longer time-period.
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9
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Li C, Yin Z, Xiao R, Huang B, Cui Y, Wang H, Xiang Y, Wang L, Lei L, Ye J, Li T, Zhong Y, Guo F, Xia Y, Fang P, Liang K. G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes. Genome Biol 2022; 23:259. [PMID: 36522639 PMCID: PMC9753424 DOI: 10.1186/s13059-022-02830-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/02/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which have been proposed to physically interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. RESULTS Based on the direct interaction between G4 and natural porphyrins, we establish genome-wide approaches to profile where the iron-liganded porphyrin hemin can bind in the chromatin. Hemin promotes genome-wide G4 formation, impairs transcription initiation, and alters chromatin landscapes, including decreased H3K27ac and H3K4me3 modifications at promoters. Interestingly, G4 status is not involved in the canonical hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, hemin treatment induces specific gene expression profiles in hepatocytes, underscoring the in vivo potential for metabolic control of gene transcription by porphyrins. CONCLUSIONS These studies demonstrate that G4 functions as a sensor for natural porphyrin metabolites in cells, revealing a G4-dependent mechanism for metabolic regulation of gene transcription and chromatin landscapes, which will deepen our knowledge of G4 biology and the contribution of cellular metabolites to gene regulation.
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Affiliation(s)
- Conghui Li
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Zhinang Yin
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Ruijing Xiao
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Beili Huang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Yali Cui
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Honghong Wang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Ying Xiang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Lingrui Wang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Lingyu Lei
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Jiaqin Ye
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Tianyu Li
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Youquan Zhong
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Fangteng Guo
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Yuchen Xia
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071 China
| | - Pingping Fang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
| | - Kaiwei Liang
- grid.49470.3e0000 0001 2331 6153School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071 China ,grid.49470.3e0000 0001 2331 6153Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071 China
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10
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RNA-regulatory exosome complex suppresses an apoptotic program to confer erythroid progenitor cell survival in vivo. Blood Adv 2022; 7:586-601. [PMID: 36161469 PMCID: PMC9984454 DOI: 10.1182/bloodadvances.2022008481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/16/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022] Open
Abstract
The RNA-regulatory exosome complex (EC) posttranscriptionally and cotranscriptionally processes and degrades RNAs in a context-dependent manner. Although the EC functions in diverse cell types, its contributions to stem and progenitor cell development are not well understood. Previously, we demonstrated that the transcriptional regulator of erythrocyte development, GATA1, represses EC subunit genes, and the EC maintains erythroid progenitors in vitro. To determine if this mechanism operates in vivo, we used the hematopoietic-specific Vav1-Cre and "conditional by inversion" mouse system to ablate Exosc3, encoding an EC structural subunit. Although Exosc3C/C Cre+ embryos developed normally until embryonic day 14.5, Exosc3 ablation was embryonic lethal and severely reduced erythromyeloid progenitor activity. RNA sequencing analysis of Exosc3-ablated burst-forming unit-erythroid revealed elevated transcripts encoding multiple proapoptotic factors, and the mutant erythroid progenitors exhibited increased apoptosis. We propose that the EC controls an ensemble of apoptosis-regulatory RNAs, thereby promoting erythroid progenitor survival and developmental erythropoiesis in vivo.
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11
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Gregoricchio S, Polit L, Esposito M, Berthelet J, Delestré L, Evanno E, Diop M, Gallais I, Aleth H, Poplineau M, Zwart W, Rosenbauer F, Rodrigues-Lima F, Duprez E, Boeva V, Guillouf C. HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia. Nucleic Acids Res 2022; 50:7938-7958. [PMID: 35871293 PMCID: PMC9371914 DOI: 10.1093/nar/gkac613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Although originally described as transcriptional activator, SPI1/PU.1, a major player in haematopoiesis whose alterations are associated with haematological malignancies, has the ability to repress transcription. Here, we investigated the mechanisms underlying gene repression in the erythroid lineage, in which SPI1 exerts an oncogenic function by blocking differentiation. We show that SPI1 represses genes by binding active enhancers that are located in intergenic or gene body regions. HDAC1 acts as a cooperative mediator of SPI1-induced transcriptional repression by deacetylating SPI1-bound enhancers in a subset of genes, including those involved in erythroid differentiation. Enhancer deacetylation impacts on promoter acetylation, chromatin accessibility and RNA pol II occupancy. In addition to the activities of HDAC1, polycomb repressive complex 2 (PRC2) reinforces gene repression by depositing H3K27me3 at promoter sequences when SPI1 is located at enhancer sequences. Moreover, our study identified a synergistic relationship between PRC2 and HDAC1 complexes in mediating the transcriptional repression activity of SPI1, ultimately inducing synergistic adverse effects on leukaemic cell survival. Our results highlight the importance of the mechanism underlying transcriptional repression in leukemic cells, involving complex functional connections between SPI1 and the epigenetic regulators PRC2 and HDAC1.
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Affiliation(s)
- Sebastian Gregoricchio
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Lélia Polit
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
| | - Michela Esposito
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Laure Delestré
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Emilie Evanno
- Curie Institute , Inserm U830, F- 75005 Paris, France
| | - M’Boyba Diop
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | | | - Hanna Aleth
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | - Mathilde Poplineau
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute , Amsterdam , The Netherlands
| | - Frank Rosenbauer
- Institute of Molecular Tumor Biology, University of Münster , Münster, Germany
| | | | - Estelle Duprez
- CNRS UMR7258, Inserm U1068, Université Aix Marseille, Paoli-Calmettes Institute , CRCM, F-13009 Marseille , France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
| | - Valentina Boeva
- CNRS UMR8104, Inserm U1016, Université Paris Cité, Cochin Institute , F-75014 Paris , France
- Department of Computer Science and Department of Biology , ETH Zurich, 8092 Zurich , Switzerland
| | - Christel Guillouf
- Inserm U1170, Université Paris-Saclay, Gustave Roussy Cancer Campus , F- 94800 Villejuif, France
- Equipe Labellisée Ligue Nationale Contre le Cancer , France
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12
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The path from stem cells to red blood cells. Int J Hematol 2022; 116:160-162. [PMID: 35841459 DOI: 10.1007/s12185-022-03413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
As oxygen is essential for energy production in mitochondria, a sufficient amount of oxygen should be continuously delivered to the tissues to maintain life. Therefore, the number of red blood cells which carry the oxygen is considerable, at up to 25 trillion in the body, and 2 million new red blood cells are generated per second.
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13
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Hunter GA, Ferreira GC. An Extended C-Terminus, the Possible Culprit for Differential Regulation of 5-Aminolevulinate Synthase Isoforms. Front Mol Biosci 2022; 9:920668. [PMID: 35911972 PMCID: PMC9329541 DOI: 10.3389/fmolb.2022.920668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/30/2022] [Indexed: 12/05/2022] Open
Abstract
5-Aminolevulinate synthase (ALAS; E.C. 2.3.1.37) is a pyridoxal 5′-phosphate (PLP)-dependent enzyme that catalyzes the key regulatory step of porphyrin biosynthesis in metazoa, fungi, and α-proteobacteria. ALAS is evolutionarily related to transaminases and is therefore classified as a fold type I PLP-dependent enzyme. As an enzyme controlling the key committed and rate-determining step of a crucial biochemical pathway ALAS is ideally positioned to be subject to allosteric feedback inhibition. Extensive kinetic and mutational studies demonstrated that the overall enzyme reaction is limited by subtle conformational changes of a hairpin loop gating the active site. These findings, coupled with structural information, facilitated early prediction of allosteric regulation of activity via an extended C-terminal tail unique to eukaryotic forms of the enzyme. This prediction was subsequently supported by the discoveries that mutations in the extended C-terminus of the erythroid ALAS isoform (ALAS2) cause a metabolic disorder known as X-linked protoporphyria not by diminishing activity, but by enhancing it. Furthermore, kinetic, structural, and molecular modeling studies demonstrated that the extended C-terminal tail controls the catalytic rate by modulating conformational flexibility of the active site loop. However, the precise identity of any such molecule remains to be defined. Here we discuss the most plausible allosteric regulators of ALAS activity based on divergences in AlphaFold-predicted ALAS structures and suggest how the mystery of the mechanism whereby the extended C-terminus of mammalian ALASs allosterically controls the rate of porphyrin biosynthesis might be unraveled.
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Affiliation(s)
- Gregory A. Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
| | - Gloria C. Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL, United States
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL, United States
- *Correspondence: Gregory A. Hunter, ; Gloria C. Ferreira,
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14
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Liao R, Bresnick EH. Heme as a differentiation-regulatory transcriptional cofactor. Int J Hematol 2022; 116:174-181. [PMID: 35776402 PMCID: PMC10170499 DOI: 10.1007/s12185-022-03404-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 01/10/2023]
Abstract
The hematopoietic transcription factor GATA1 induces heme accumulation during erythropoiesis by directly activating genes mediating heme biosynthesis. In addition to its canonical functions as a hemoglobin prosthetic group and enzyme cofactor, heme regulates gene expression in erythroid cells both transcriptionally and post-transcriptionally. Heme binding to the transcriptional repressor BACH1 triggers its proteolytic degradation. In heme-deficient cells, BACH1 accumulates and represses transcription of target genes, including α- and β-like globin genes, preventing the accumulation of cytotoxic free globin chains. A recently described BACH1-independent mechanism of heme-dependent transcriptional regulation is associated with a DNA motif termed heme-regulated motif (HERM), which resides at the majority of loci harboring heme-regulated chromatin accessibility sites. Progress on these problems has led to a paradigm in which cell type-specific transcriptional mechanisms determine the expression of enzymes mediating the synthesis of small molecules, which generate feedback loops, converging upon the transcription factor itself and the genome. This marriage between transcription factors and the small molecules that they control is predicted to be a canonical attribute of regulatory networks governing cell state transitions such as differentiation in the hematopoietic system and more broadly.
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Affiliation(s)
- Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI, 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI, 53705, USA.
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15
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Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis. Sci Rep 2022; 12:9024. [PMID: 35637209 PMCID: PMC9151922 DOI: 10.1038/s41598-022-12940-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
X-linked sideroblastic anemia (XLSA), the most common form of congenital sideroblastic anemia, is caused by a germline mutation in the erythroid-specific 5-aminolevulinate synthase (ALAS2) gene. In XLSA, defective heme biosynthesis leads to ring sideroblast formation because of excess mitochondrial iron accumulation. In this study, we introduced ALAS2 missense mutations on human umbilical cord blood-derived erythroblasts; hereafter, we refer to them as XLSA clones. XLSA clones that differentiated into mature erythroblasts showed an increased frequency of ring sideroblast formation with impaired hemoglobin biosynthesis. The expression profiling revealed significant enrichment of genes involved in ferroptosis, which is a form of regulated cell death induced by iron accumulation and lipid peroxidation. Notably, treatment with erastin, a ferroptosis inducer, caused a higher proportion of cell death in XLSA clones. XLSA clones exhibited significantly higher levels of intracellular lipid peroxides and enhanced expression of BACH1, a regulator of iron metabolism and potential accelerator of ferroptosis. In XLSA clones, BACH1 repressed genes involved in iron metabolism and glutathione synthesis. Collectively, defective heme biosynthesis in XLSA clones could confer enhanced BACH1 expression, leading to increased susceptibility to ferroptosis. The results of our study provide important information for the development of novel therapeutic targets for XLSA.
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16
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Taylor JL, Brown BL. Structural basis for dysregulation of aminolevulinic acid synthase in human disease. J Biol Chem 2022; 298:101643. [PMID: 35093382 PMCID: PMC8892079 DOI: 10.1016/j.jbc.2022.101643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/19/2023] Open
Abstract
Heme is a critical biomolecule that is synthesized in vivo by several organisms such as plants, animals, and bacteria. Reflecting the importance of this molecule, defects in heme biosynthesis underlie several blood disorders in humans. Aminolevulinic acid synthase (ALAS) initiates heme biosynthesis in α-proteobacteria and nonplant eukaryotes. Debilitating and painful diseases such as X-linked sideroblastic anemia and X-linked protoporphyria can result from one of more than 91 genetic mutations in the human erythroid-specific enzyme ALAS2. This review will focus on recent structure-based insights into human ALAS2 function in health and how it dysfunctions in disease. We will also discuss how certain genetic mutations potentially result in disease-causing structural perturbations. Furthermore, we use thermodynamic and structural information to hypothesize how the mutations affect the human ALAS2 structure and categorize some of the unique human ALAS2 mutations that do not respond to typical treatments, that have paradoxical in vitro activity, or that are highly intolerable to changes. Finally, we will examine where future structure-based insights into the family of ALA synthases are needed to develop additional enzyme therapeutics.
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Affiliation(s)
- Jessica L Taylor
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Breann L Brown
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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17
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Sidhu I, Barwe SP, Kiick KL, Kolb EA, Gopalakrishnapillai A. A 3-D hydrogel based system for hematopoietic differentiation and its use in modeling down syndrome associated transient myeloproliferative disorder. Biomater Sci 2021; 9:6266-6281. [PMID: 34369483 PMCID: PMC8570143 DOI: 10.1039/d1bm00442e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) provide an extraordinary tool for disease modeling owing to their potential to differentiate into the desired cell type. The differentiation of iPSCs is typically performed on 2-dimensional monolayers of stromal cell or animal tissue derived extracellular matrices. Recent advancements in disease modeling have utilized iPSCs in 3-dimensional (3D) cultures to study diseases such as muscular dystrophy, cardiomyopathy, and pulmonary fibrosis. However, these approaches are yet to be explored in modeling the hematological malignancies. Transient myeloproliferative disorder (TMD) is a preleukemic stage, which is induced in 10-20% of children with trisomy 21 possessing the pathognomonic mutation in the transcription factor GATA1. In this study, we established a synthetic 3D iPSC culture system for modeling TMD via hematopoietic differentiation of customized iPSCs. A chemically cross-linkable PEG hydrogel decorated with integrin binding peptide was found to be permissive of hematopoietic differentiation of iPSCs. It provided a cost-effective system for the generation of hematopoietic stem and progenitor cells (HSPCs) with higher yield of early HSPCs compared to traditional 2D culture on Matrigel coated dishes. Characterization of the HSPCs produced from the iPSC lines cultured in 3D showed that the erythroid population was reduced whereas the megakaryoid and myeloid populations were significantly increased in GATA1 mutant trisomic line compared to disomic or trisomic lines with wild-type GATA1, consistent with TMD characteristics. In conclusion, we have identified a cost-effective tunable 3D hydrogel system to model TMD.
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Affiliation(s)
- Ishnoor Sidhu
- Nemours Centers for Childhood Cancer Research and Cancer & Blood Disorders, A.I. DuPont Hospital for Children, Wilmington, DE 19803, USA.
- University of Delaware, Newark, DE 19711, USA
| | - Sonali P Barwe
- Nemours Centers for Childhood Cancer Research and Cancer & Blood Disorders, A.I. DuPont Hospital for Children, Wilmington, DE 19803, USA.
- University of Delaware, Newark, DE 19711, USA
| | | | - E Anders Kolb
- Nemours Centers for Childhood Cancer Research and Cancer & Blood Disorders, A.I. DuPont Hospital for Children, Wilmington, DE 19803, USA.
| | - Anilkumar Gopalakrishnapillai
- Nemours Centers for Childhood Cancer Research and Cancer & Blood Disorders, A.I. DuPont Hospital for Children, Wilmington, DE 19803, USA.
- University of Delaware, Newark, DE 19711, USA
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18
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Mehta C, Fraga de Andrade I, Matson DR, Dewey CN, Bresnick EH. RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis. Nucleic Acids Res 2021; 49:9007-9025. [PMID: 34059908 PMCID: PMC8450083 DOI: 10.1093/nar/gkab367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Accepted: 05/27/2021] [Indexed: 01/03/2023] Open
Abstract
Cellular differentiation requires vast remodeling of transcriptomes, and therefore machinery mediating remodeling controls differentiation. Relative to transcriptional mechanisms governing differentiation, post-transcriptional processes are less well understood. As an important post-transcriptional determinant of transcriptomes, the RNA exosome complex (EC) mediates processing and/or degradation of select RNAs. During erythropoiesis, the erythroid transcription factor GATA1 represses EC subunit genes. Depleting EC structural subunits prior to GATA1-mediated repression is deleterious to erythroid progenitor cells. To assess the importance of the EC catalytic subunits Dis3 and Exosc10 in this dynamic process, we asked if these subunits function non-redundantly to control erythropoiesis. Dis3 or Exosc10 depletion in primary murine hematopoietic progenitor cells reduced erythroid progenitors and their progeny, while sparing myeloid cells. Dis3 loss severely compromised erythroid progenitor and erythroblast survival, rendered erythroblasts hypersensitive to apoptosis-inducing stimuli and induced γ-H2AX, indicative of DNA double-stranded breaks. Dis3 loss-of-function phenotypes were more severe than those caused by Exosc10 depletion. We innovated a genetic rescue system to compare human Dis3 with multiple myeloma-associated Dis3 mutants S447R and R750K, and only wild type Dis3 was competent to rescue progenitors. Thus, Dis3 establishes a disease mutation-sensitive, cell type-specific survival mechanism to enable a differentiation program.
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Affiliation(s)
- Charu Mehta
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Isabela Fraga de Andrade
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.,Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
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19
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García-Montolio M, Ballaré C, Blanco E, Gutiérrez A, Aranda S, Gómez A, Kok CH, Yeung DT, Hughes TP, Vizán P, Di Croce L. Polycomb Factor PHF19 Controls Cell Growth and Differentiation Toward Erythroid Pathway in Chronic Myeloid Leukemia Cells. Front Cell Dev Biol 2021; 9:655201. [PMID: 33996816 PMCID: PMC8116664 DOI: 10.3389/fcell.2021.655201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Polycomb group (PcG) of proteins are a group of highly conserved epigenetic regulators involved in many biological functions, such as embryonic development, cell proliferation, and adult stem cell determination. PHD finger protein 19 (PHF19) is an associated factor of Polycomb repressor complex 2 (PRC2), often upregulated in human cancers. In particular, myeloid leukemia cell lines show increased levels of PHF19, yet little is known about its function. Here, we have characterized the role of PHF19 in myeloid leukemia cells. We demonstrated that PHF19 depletion decreases cell proliferation and promotes chronic myeloid leukemia (CML) differentiation. Mechanistically, we have shown how PHF19 regulates the proliferation of CML through a direct regulation of the cell cycle inhibitor p21. Furthermore, we observed that MTF2, a PHF19 homolog, partially compensates for PHF19 depletion in a subset of target genes, instructing specific erythroid differentiation. Taken together, our results show that PHF19 is a key transcriptional regulator for cell fate determination and could be a potential therapeutic target for myeloid leukemia treatment.
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Affiliation(s)
- Marc García-Montolio
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cecilia Ballaré
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Blanco
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Arantxa Gutiérrez
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sergi Aranda
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Gómez
- Rheumatology Department, Rheumatology Research Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Chung H Kok
- Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - David T Yeung
- Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Timothy P Hughes
- Precision Medicine Theme, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, Australia.,Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Pedro Vizán
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Epigenetics Events in Cancer Laboratory, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
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20
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Liao R, Zheng Y, Liu X, Zhang Y, Seim G, Tanimura N, Wilson GM, Hematti P, Coon JJ, Fan J, Xu J, Keles S, Bresnick EH. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Rep 2021; 31:107832. [PMID: 32610133 DOI: 10.1016/j.celrep.2020.107832] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/03/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
Abstract
Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A plethora of small molecules orchestrate cellular functions and therefore may link physiological processes with genome biology. The metabolic enzyme and hemoglobin cofactor heme induces proteolysis of a transcriptional repressor, Bach1, and regulates gene expression post-transcriptionally. However, whether heme controls genome function broadly or through prescriptive actions is unclear. Using assay for transposase-accessible chromatin sequencing (ATAC-seq), we establish a heme-dependent chromatin atlas in wild-type and mutant erythroblasts lacking enhancers that confer normal heme synthesis. Amalgamating chromatin landscapes and transcriptomes in cells with sub-physiological heme and post-heme rescue reveals parallel Bach1-dependent and Bach1-independent mechanisms that target heme-sensing chromosomal hotspots. The hotspots harbor a DNA motif demarcating heme-regulated chromatin and genes encoding proteins not known to be heme regulated, including metabolic enzymes. The heme-omics analysis establishes how an essential biochemical cofactor controls genome function and cellular physiology.
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Affiliation(s)
- Ruiqi Liao
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ye Zheng
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gretchen Seim
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Nobuyuki Tanimura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Gary M Wilson
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peiman Hematti
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jing Fan
- Department of Nutritional Sciences, Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sunduz Keles
- Department of Statistics, Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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21
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Bao B, An W, Lu Q, Wang Y, Lu Z, Tu J, Zhang H, Duan Y, Yuan W, Zhu X, Jia H. Sfxn1 is essential for erythrocyte maturation via facilitating hemoglobin production in zebrafish. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166096. [PMID: 33524530 DOI: 10.1016/j.bbadis.2021.166096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/19/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022]
Abstract
Previous reports revealed that mutation of mitochondrial inner-membrane located protein SFXN1 led to pleiotropic hematological and skeletal defects in mice, associated with the presence of hypochromic erythroid cell, iron overload in mitochondrion of erythroblast and the development of sideroblastic anemia (SA). However, the potential role of sfxn1 during erythrocyte differentiation and the development of anemia, especially the pathological molecular mechanism still remains elusive. In this study, the correlation between sfxn1 and erythroid cell development is explored through zebrafish in vivo coupled with human hematopoietic cells assay ex vivo. Both knockdown and knockout of sfxn1 result in hypochromic anemia phenotype in zebrafish. Further analyses demonstrate that the development of anemia attributes to the biosynthetic deficiency of hemoglobin, which is caused by the biosynthetic disorder of heme that associates with one‑carbon (1C) metabolism process of mitochondrial branch in erythrocyte. Sfxn1 is also involved in the differentiation and maturation of erythrocyte in inducible human umbilical cord blood stem cells. In addition, we found that functional disruption of sfxn1 causes hypochromic anemia that is distinct from SA. These findings reveal that sfxn1 is genetically conserved and essential for the maturation of erythrocyte via facilitating the production of hemoglobin, which may provide a possible guidance for the future clinical treatment of sfxn1 mutation associated hematological disorders.
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Affiliation(s)
- Binghao Bao
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Wenbin An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yaqin Wang
- Department of Pediatrics, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zhichao Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Jiayi Tu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Heng Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China
| | - Yongjuan Duan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, ,China.
| | - Haibo Jia
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Center for Human Genome Research, Huazhong University of Science and Technology, Wuhan, China.
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22
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Zwifelhofer NM, Cai X, Liao R, Mao B, Conn DJ, Mehta C, Keles S, Xia Y, Bresnick EH. GATA factor-regulated solute carrier ensemble reveals a nucleoside transporter-dependent differentiation mechanism. PLoS Genet 2020; 16:e1009286. [PMID: 33370779 PMCID: PMC7793295 DOI: 10.1371/journal.pgen.1009286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 01/08/2021] [Accepted: 11/18/2020] [Indexed: 01/19/2023] Open
Abstract
Developmental-regulatory networks often include large gene families encoding mechanistically-related proteins like G-protein-coupled receptors, zinc finger transcription factors and solute carrier (SLC) transporters. In principle, a common mechanism may confer expression of multiple members integral to a developmental process, or diverse mechanisms may be deployed. Using genetic complementation and enhancer-mutant systems, we analyzed the 456 member SLC family that establishes the small molecule constitution of cells. This analysis identified SLC gene cohorts regulated by GATA1 and/or GATA2 during erythroid differentiation. As >50 SLC genes shared GATA factor regulation, a common mechanism established multiple members of this family. These genes included Slc29a1 encoding an equilibrative nucleoside transporter (Slc29a1/ENT1) that utilizes adenosine as a preferred substrate. Slc29a1 promoted erythroblast survival and differentiation ex vivo. Targeted ablation of murine Slc29a1 in erythroblasts attenuated erythropoiesis and erythrocyte regeneration in response to acute anemia. Our results reveal a GATA factor-regulated SLC ensemble, with a nucleoside transporter component that promotes erythropoiesis and prevents anemia, and establish a mechanistic link between GATA factor and adenosine mechanisms. We propose that integration of the GATA factor-adenosine circuit with other components of the GATA factor-regulated SLC ensemble establishes the small molecule repertoire required for progenitor cells to efficiently generate erythrocytes. GATA transcription factors endow blood stem and progenitor cells with activities to produce progeny that transport oxygen to protect cells and tissues, evade pathogens and control physiological processes. GATA factors regulate hundreds of genes, and the actions of these genes mediate important biological functions. While the genes have been documented, many questions remain regarding how the “network” components mediate biological functions. The networks include members of large gene families, and the relationships between the regulation and function of individual family members is not well understood. Analyzing datasets from genetic complementation and enhancer mutant systems revealed that GATA factors regulate an ensemble of membrane transporters termed solute carrier proteins (SLCs), which dictate the small molecule composition of cells. Genetic analyses with Slc29a1, which transports adenosine, revealed its function to promote erythrocyte development, and Slc29a1 attenuated anemia in a mouse model. This study revealed the importance of SLC transporters in GATA factor networks. We propose that the GATA factor-adenosine circuit integrates with other SLCs to establish/maintain the small molecule constitution of progenitor cells as a new mechanism to control blood cell development.
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Affiliation(s)
- Nicole M. Zwifelhofer
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Xiaoli Cai
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas McGovern Medical School at Houston, Houston, Texas, United States of America
| | - Ruiqi Liao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Bin Mao
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Conn
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Yang Xia
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Texas McGovern Medical School at Houston, Houston, Texas, United States of America
- * E-mail: (YX); (EHB)
| | - Emery H. Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail: (YX); (EHB)
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23
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Crispin A, Guo C, Chen C, Campagna DR, Schmidt PJ, Lichtenstein D, Cao C, Sendamarai AK, Hildick-Smith GJ, Huston NC, Boudreaux J, Bottomley SS, Heeney MM, Paw BH, Fleming MD, Ducamp S. Mutations in the iron-sulfur cluster biogenesis protein HSCB cause congenital sideroblastic anemia. J Clin Invest 2020; 130:5245-5256. [PMID: 32634119 PMCID: PMC7524500 DOI: 10.1172/jci135479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/24/2020] [Indexed: 01/15/2023] Open
Abstract
The congenital sideroblastic anemias (CSAs) can be caused by primary defects in mitochondrial iron-sulfur (Fe-S) cluster biogenesis. HSCB (heat shock cognate B), which encodes a mitochondrial cochaperone, also known as HSC20 (heat shock cognate protein 20), is the partner of mitochondrial heat shock protein A9 (HSPA9). Together with glutaredoxin 5 (GLRX5), HSCB and HSPA9 facilitate the transfer of nascent 2-iron, 2-sulfur clusters to recipient mitochondrial proteins. Mutations in both HSPA9 and GLRX5 have previously been associated with CSA. Therefore, we hypothesized that mutations in HSCB could also cause CSA. We screened patients with genetically undefined CSA and identified a frameshift mutation and a rare promoter variant in HSCB in a female patient with non-syndromic CSA. We found that HSCB expression was decreased in patient-derived fibroblasts and K562 erythroleukemia cells engineered to have the patient-specific promoter variant. Furthermore, gene knockdown and deletion experiments performed in K562 cells, zebrafish, and mice demonstrate that loss of HSCB results in impaired Fe-S cluster biogenesis, a defect in RBC hemoglobinization, and the development of siderocytes and more broadly perturbs hematopoiesis in vivo. These results further affirm the involvement of Fe-S cluster biogenesis in erythropoiesis and hematopoiesis and define HSCB as a CSA gene.
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Affiliation(s)
- Andrew Crispin
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Chaoshe Guo
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Caiyong Chen
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Dean R. Campagna
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Paul J. Schmidt
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Daniel Lichtenstein
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Chang Cao
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Anoop K. Sendamarai
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | - Nicholas C. Huston
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jeanne Boudreaux
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Sylvia S. Bottomley
- Department of Medicine, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Matthew M. Heeney
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Barry H. Paw
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mark D. Fleming
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sarah Ducamp
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
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24
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Liu P, Soukup AA, Bresnick EH, Dewey CN, Keleş S. PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Genome Res 2020; 30:1655-1666. [PMID: 32958497 PMCID: PMC7605252 DOI: 10.1101/gr.252445.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/27/2020] [Indexed: 11/25/2022]
Abstract
Publicly available RNA-seq data is routinely used for retrospective analysis to elucidate new biology. Novel transcript discovery enabled by joint analysis of large collections of RNA-seq data sets has emerged as one such analysis. Current methods for transcript discovery rely on a '2-Step' approach where the first step encompasses building transcripts from individual data sets, followed by the second step that merges predicted transcripts across data sets. To increase the power of transcript discovery from large collections of RNA-seq data sets, we developed a novel '1-Step' approach named Pooling RNA-seq and Assembling Models (PRAM) that builds transcript models from pooled RNA-seq data sets. We demonstrate in a computational benchmark that 1-Step outperforms 2-Step approaches in predicting overall transcript structures and individual splice junctions, while performing competitively in detecting exonic nucleotides. Applying PRAM to 30 human ENCODE RNA-seq data sets identified unannotated transcripts with epigenetic and RAMPAGE signatures similar to those of recently annotated transcripts. In a case study, we discovered and experimentally validated new transcripts through the application of PRAM to mouse hematopoietic RNA-seq data sets. We uncovered new transcripts that share a differential expression pattern with a neighboring gene Pik3cg implicated in human hematopoietic phenotypes, and we provided evidence for the conservation of this relationship in human. PRAM is implemented as an R/Bioconductor package.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Alexandra A Soukup
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, Wisconsin Blood Cancer Research Institute, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA.,Department of Computer Sciences, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA.,Department of Statistics, University of Wisconsin, Madison, Wisconsin 53706, USA
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25
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Kim YW, Kang Y, Kang J, Kim A. GATA-1-dependent histone H3K27 acetylation mediates erythroid cell-specific chromatin interaction between CTCF sites. FASEB J 2020; 34:14736-14749. [PMID: 32924169 DOI: 10.1096/fj.202001526r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/31/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022]
Abstract
CCCTC-binding factor (CTCF) sites interact with each other in the chromatin environment, establishing chromatin domains. Our previous study showed that interaction between CTCF sites is cell type-specific around the β-globin locus and is dependent on erythroid-specific activator GATA-1. To find out molecular mechanisms of the cell type-specific interaction, we directly inhibited GATA-1 binding to the β-globin enhancers by deleting its binding motifs and found that histone H3K27 acetylation (H3K27ac) was decreased at CTCF sites surrounding the β-globin locus, even though CTCF binding itself was maintained at the sites. Forced H3K27ac by Trichostatin A treatment or CBP/p300 KD affected the interactions between CTCF sites around the β-globin locus without changes in CTCF binding. Analysis of public ChIA-PET data revealed that H3K27ac is higher at CTCF sites forming short interactions than long interactions. GATA-1 was identified as a representative transcription factor that relates with genes present inside the short interactions in erythroid K562 cells. Depletion of GATA-1-reduced H3K27ac at CTCF sites near erythroid-specific enhancers. These results indicate that H3K27ac at CTCF sites is required for cell type-specific chromatin interactions between them. Tissue-specific activator GATA-1 appears to play a role in H3K27ac at CTCF sites in erythroid cells.
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Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
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26
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Xu D, Huang SK. IL-33: a key player in the development of iron-recycling red pulp macrophages. Cell Mol Immunol 2020; 17:1218-1219. [PMID: 32737432 DOI: 10.1038/s41423-020-0509-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Damo Xu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China. .,Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK.
| | - Shau-Ku Huang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China. .,National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, China. .,Department of Respirology & Allergy, Third Affiliated Hospital of Shenzhen University, Shenzhen, 518020, China. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, USA.
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27
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Interleukin-33 Signaling Controls the Development of Iron-Recycling Macrophages. Immunity 2020; 52:782-793.e5. [PMID: 32272082 PMCID: PMC7237885 DOI: 10.1016/j.immuni.2020.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/31/2020] [Accepted: 03/13/2020] [Indexed: 12/31/2022]
Abstract
Splenic red pulp macrophages (RPMs) contribute to erythrocyte homeostasis and are required for iron recycling. Heme induces the expression of SPIC transcription factor in monocyte-derived macrophages and promotes their differentiation into RPM precursors, pre-RPMs. However, the requirements for differentiation into mature RPMs remain unknown. Here, we have demonstrated that interleukin (IL)-33 associated with erythrocytes and co-cooperated with heme to promote the generation of mature RPMs through activation of the MyD88 adaptor protein and ERK1/2 kinases downstream of the IL-33 receptor, IL1RL1. IL-33- and IL1RL1-deficient mice showed defective iron recycling and increased splenic iron deposition. Gene expression and chromatin accessibility studies revealed a role for GATA transcription factors downstream of IL-33 signaling during the development of pre-RPMs that retained full potential to differentiate into RPMs. Thus, IL-33 instructs the development of RPMs as a response to physiological erythrocyte damage with important implications to iron recycling and iron homeostasis.
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28
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Sanyear C, Butthep P, Eamsaard W, Fucharoen S, Svasti S, Masaratana P. Iron homeostasis in a mouse model of thalassemia intermedia is altered between adolescence and adulthood. PeerJ 2020; 8:e8802. [PMID: 32219031 PMCID: PMC7085893 DOI: 10.7717/peerj.8802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/25/2020] [Indexed: 01/03/2023] Open
Abstract
Background Iron overload is one of common complications of β-thalassemia. Systemic iron homeostasis is regulated by iron-regulatory hormone, hepcidin, which inhibits intestinal iron absorption and iron recycling by reticuloendothelial system. In addition, body iron status and requirement can be altered with age. In adolescence, iron requirement is increased due to blood volume expansion and growth spurt. Heterozygous β-globin knockout mice (Hbbth3/+; BKO) is a mouse model of thalassemia widely used to study iron homeostasis under this pathological condition. However, effects of age on iron homeostasis, particularly the expression of genes involved in hemoglobin metabolism as well as erythroid regulators in the spleen, during adolescence have not been explored in this mouse model. Methods Iron parameters as well as the mRNA expression of hepcidin and genes involved in iron transport and metabolism in wildtype (WT) and BKO mice during adolescence (6–7 weeks old) and adulthood (16–20 weeks old) were analyzed and compared by 2-way ANOVA. Results The transition of adolescence to adulthood was associated with reductions in duodenal iron transporter mRNA expression and serum iron levels of both WT and BKO mice. Erythrocyte parameters in BKO mice remained abnormal in both age groups despite persistent induction of genes involved in hemoglobin metabolism in the spleen and progressively increased extramedullary erythropiesis. In BKO mice, adulthood was associated with increased liver hepcidin and ferroportin mRNA expression along with splenic erythroferrone mRNA suppression compared to adolescence. Conclusion Our results demonstrate that iron homeostasis in a mouse model of thalassemia intermedia is altered between adolescence and adulthood. The present study underscores the importance of the age of thalassemic mice in the study of molecular or pathophysiological changes under thalassemic condition.
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Affiliation(s)
- Chanita Sanyear
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Punnee Butthep
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wiraya Eamsaard
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Patarabutr Masaratana
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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29
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Zhang J, Hamza I. Zebrafish as a model system to delineate the role of heme and iron metabolism during erythropoiesis. Mol Genet Metab 2019; 128:204-212. [PMID: 30626549 PMCID: PMC6591114 DOI: 10.1016/j.ymgme.2018.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 11/17/2022]
Abstract
Coordination of iron acquisition and heme synthesis is required for effective erythropoiesis. The small teleost zebrafish (Danio rerio) is an ideal vertebrate animal model to replicate various aspects of human physiology and provides an efficient and cost-effective way to model human pathophysiology. Importantly, zebrafish erythropoiesis largely resembles mammalian erythropoiesis. Gene discovery by large-scale forward mutagenesis screening has identified key components in heme and iron metabolism. Reverse genetic screens, using morpholino-knockdown and CRISPR/Cas9, coupled with the genetic tractability of the developing embryo have further accelerated functional studies. Ultimately, the ex utero development of zebrafish embryos combined with their transparency and developmental plasticity could provide a deeper understanding of the role of iron and heme metabolism during early vertebrate embryonic development.
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Affiliation(s)
- Jianbing Zhang
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Iqbal Hamza
- Department of Animal & Avian Sciences and Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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30
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Ling T, Crispino JD. GATA1 mutations in red cell disorders. IUBMB Life 2019; 72:106-118. [PMID: 31652397 DOI: 10.1002/iub.2177] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/18/2019] [Indexed: 01/01/2023]
Abstract
GATA1 is an essential regulator of erythroid cell gene expression and maturation. In its absence, erythroid progenitors are arrested in differentiation and undergo apoptosis. Much has been learned about GATA1 function through animal models, which include genetic knockouts as well as ones with decreased levels of expression. However, even greater insights have come from the finding that a number of rare red cell disorders, including Diamond-Blackfan anemia, are associated with GATA1 mutations. These mutations affect the amino-terminal zinc finger (N-ZF) and the amino-terminus of the protein, and in both cases can alter the DNA-binding activity, which is primarily conferred by the third functional domain, the carboxyl-terminal zinc finger (C-ZF). Here we discuss the role of GATA1 in erythropoiesis with an emphasis on the mutations found in human patients with red cell disorders.
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Affiliation(s)
- Te Ling
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
| | - John D Crispino
- Division of Hematology/Oncology, Northwestern University, Chicago, Illinois
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31
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Duvigneau JC, Esterbauer H, Kozlov AV. Role of Heme Oxygenase as a Modulator of Heme-Mediated Pathways. Antioxidants (Basel) 2019; 8:antiox8100475. [PMID: 31614577 PMCID: PMC6827082 DOI: 10.3390/antiox8100475] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
The heme oxygenase (HO) system is essential for heme and iron homeostasis and necessary for adaptation to cell stress. HO degrades heme to biliverdin (BV), carbon monoxide (CO) and ferrous iron. Although mostly beneficial, the HO reaction can also produce deleterious effects, predominantly attributed to excessive product formation. Underrated so far is, however, that HO may exert effects additionally via modulation of the cellular heme levels. Heme, besides being an often-quoted generator of oxidative stress, plays also an important role as a signaling molecule. Heme controls the anti-oxidative defense, circadian rhythms, activity of ion channels, glucose utilization, erythropoiesis, and macrophage function. This broad spectrum of effects depends on its interaction with proteins ranging from transcription factors to enzymes. In degrading heme, HO has the potential to exert effects also via modulation of heme-mediated pathways. In this review, we will discuss the multitude of pathways regulated by heme to enlarge the view on HO and its role in cell physiology. We will further highlight the contribution of HO to pathophysiology, which results from a dysregulated balance between heme and the degradation products formed by HO.
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Affiliation(s)
- J Catharina Duvigneau
- Institute for Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Harald Esterbauer
- Department of Laboratory Medicine, Medical University of Vienna, 1210 Vienna, Austria.
| | - Andrey V Kozlov
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, 1200 Vienna, Austria.
- Laboratory of Navigational Redox Lipidomics, Department of Human Pathology, IM Sechenov Moscow State Medical University, 119992 Moscow, Russia.
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The Formaldehyde Dehydrogenase SsFdh1 Is Regulated by and Functionally Cooperates with the GATA Transcription Factor SsNsd1 in Sclerotinia sclerotiorum. mSystems 2019; 4:4/5/e00397-19. [PMID: 31506263 PMCID: PMC6739101 DOI: 10.1128/msystems.00397-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
S. sclerotiorum is a pathogenic fungus with sclerotium and infection cushion development, making S. sclerotiorum one of the most challenging agricultural pathogens with no effective control method. We identified important sclerotium and compound appressorium formation determinants, SsNsd1 and SsFdh1, and investigated their regulatory mechanism at the molecular level. SsNsd1 and SsFdh1 are zinc finger motif-containing proteins and associate with each other in the nucleus. On other hand, SsNsd1, as a GATA transcription factor, directly binds to GATA-box DNA in the promoter region of Ssfdh1. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Our results provide insights into the role of the GATA transcription factor and its regulation of formaldehyde dehydrogenase in stress resistance, fungal sclerotium and compound appressorium development, and pathogenicity. GATA transcription factors (TFs) are common eukaryotic regulators, and glutathione-dependent formaldehyde dehydrogenases (GD-FDH) are ubiquitous enzymes with formaldehyde detoxification activity. In this study, the formaldehyde dehydrogenase Sclerotinia sclerotiorum Fdh1 (SsFdh1) was first characterized as an interacting partner of a GATA TF, SsNsd1, in S. sclerotiorum. Genetic analysis reveals that SsFdh1 functions in formaldehyde detoxification, nitrogen metabolism, sclerotium development, and pathogenicity. Both SsNsd1 and SsFdh1 harbor typical zinc finger motifs with conserved cysteine residues. SsNsd1 regulates SsFdh1 in two distinct manners. SsNsd1 directly binds to GATA-box DNA in the promoter region of Ssfdh1; SsNsd1 associates with SsFdh1 through disulfide bonds formed by conserved Cys residues. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Site-directed point mutation of these Cys residues influences the SsNsd1-SsFdh1 interaction and SsNsd1 DNA binding capacity. SsFdh1 is regulated by and functions jointly with the SsNsd1 factor, providing new insights into the complex transcriptional regulatory mechanisms of GATA factors. IMPORTANCES. sclerotiorum is a pathogenic fungus with sclerotium and infection cushion development, making S. sclerotiorum one of the most challenging agricultural pathogens with no effective control method. We identified important sclerotium and compound appressorium formation determinants, SsNsd1 and SsFdh1, and investigated their regulatory mechanism at the molecular level. SsNsd1 and SsFdh1 are zinc finger motif-containing proteins and associate with each other in the nucleus. On other hand, SsNsd1, as a GATA transcription factor, directly binds to GATA-box DNA in the promoter region of Ssfdh1. The SsNsd1-SsFdh1 interaction and nuclear translocation were found to prevent efficient binding of SsNsd1 to GATA-box DNA. Our results provide insights into the role of the GATA transcription factor and its regulation of formaldehyde dehydrogenase in stress resistance, fungal sclerotium and compound appressorium development, and pathogenicity.
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Choi H, Song WM, Wang M, Sram RJ, Zhang B. Benzo[a]pyrene is associated with dysregulated myelo-lymphoid hematopoiesis in asthmatic children. ENVIRONMENT INTERNATIONAL 2019; 128:218-232. [PMID: 31059917 DOI: 10.1016/j.envint.2019.04.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The extent to which ambient benzo[a]pyrene (B[a]P) contributes to mechanistically distinct de novo asthma remains unknown. OBJECTIVES To identify molecular signatures and regulatory networks underlying childhood exposure to ambient B[a]P and asthma, using robust and unbiased systems biology approaches. METHODS Clinically confirmed asthmatic (n = 191) vs. control (n = 194) children (aged, 7-15) were enrolled from a polluted urban center and semi-rural region in Czech Republic. Contemporaneous B[a]P concentration, gene expressions, DNA methylation data were analyzed against asthma diagnosis, as well as a modified prognostic index of asthma, using integrative multiscale co-expression network analysis. Sample-wise cell type compositions were inferred by a machine learning approach (i.e. CIBERSORT) with reference gene expressions of purified 38 distinct hematopoietic cell states from umbilical cord (i.e. stem cell/progenitors) or peripheral blood (i.e. lymphocytes). RESULTS The median outdoor B[a]P was increased near the homes of the urban children with 'moderate' or 'severe' prognostic markers of asthma, but not in the urban controls. An elevated B[a]P induced epigenetic suppression of NF-κB inflammation, decreased Natural Killer T (NKT) cells and activated anti-inflammatory IL10-secreting CD8+ T effective memory cells. B[a]P was positively correlated with an increased expression of a heme biosynthesis gene, ALAS2, which in turn, appears to promote concurrent increase of neutrophilic metamyelocyte and mature CD71low erythroid cells. Furthermore, erythroid-specific master transcription regulator gene (GATA1), glutathione transferase genes (GSTM1 and GSTM3) and Eosinophil marker (IL5RA) were simultaneously activated in the urban asthma cases. CONCLUSIONS B[a]P might contribute to concurrent suppression of pro-inflammatory (e.g. NF-κB mediated NKT cells), and activation of anti-inflammatory pathways (e.g. IL10-secreting CD8+ T cells) in the urban asthmatic children. In addition, B[a]P appears to elevate heme biosynthesis, which in turn, promotes neutrophilic metamyelocyte expansion and reduction of CD71+ erythroids.
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Affiliation(s)
- Hyunok Choi
- Departments of Environmental Health Sciences, Epidemiology, and Biostatistics, State University of New York at Albany School of Public Health, Rensselaer, NY, USA.
| | - Won-Min Song
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minghui Wang
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Radim J Sram
- Department of Genetic Toxicology and Nanotoxicology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic; University of Chemistry and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Food Analysis and Nutrition, Technicka 3, 166 28 Prague, Czech Republic
| | - Bin Zhang
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Generation and Molecular Characterization of Human Ring Sideroblasts: a Key Role of Ferrous Iron in Terminal Erythroid Differentiation and Ring Sideroblast Formation. Mol Cell Biol 2019; 39:MCB.00387-18. [PMID: 30670569 DOI: 10.1128/mcb.00387-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
Ring sideroblasts are a hallmark of sideroblastic anemia, although little is known about their characteristics. Here, we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene, a gene responsible for X-linked sideroblastic anemia (XLSA). Although heterozygous female mice showed an anemic phenotype, ring sideroblasts were not observed in their bone marrow. We next established human induced pluripotent stem cell-derived proerythroblast clones harboring the same ALAS2 gene mutation. Through coculture with sodium ferrous citrate, mutant clones differentiated into mature erythroblasts and became ring sideroblasts with upregulation of metal transporters (MFRN1, ZIP8, and DMT1), suggesting a key role for ferrous iron in erythroid differentiation. Interestingly, holo-transferrin (holo-Tf) did not induce erythroid differentiation as well as ring sideroblast formation, and mutant cells underwent apoptosis. Despite massive iron granule content, ring sideroblasts were less apoptotic than holo-Tf-treated undifferentiated cells. Microarray analysis revealed upregulation of antiapoptotic genes in ring sideroblasts, a profile partly shared with erythroblasts from a patient with XLSA. These results suggest that ring sideroblasts exert a reaction to avoid cell death by activating antiapoptotic programs. Our model may become an important tool to clarify the pathophysiology of sideroblastic anemia.
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Fujiwara T, Harigae H. Molecular pathophysiology and genetic mutations in congenital sideroblastic anemia. Free Radic Biol Med 2019; 133:179-185. [PMID: 30098397 DOI: 10.1016/j.freeradbiomed.2018.08.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/19/2023]
Abstract
Sideroblastic anemia is a heterogeneous congenital and acquired disorder characterized by anemia and the presence of ring sideroblasts in the bone marrow. Congenital sideroblastic anemia (CSA) is a rare disease caused by mutations in genes involved in the heme biosynthesis, iron-sulfur [Fe-S] cluster biosynthesis, and mitochondrial protein synthesis. The most prevalent form of CSA is X-linked sideroblastic anemia, caused by mutations in the erythroid-specific δ-aminolevulinate synthase (ALAS2), which is the first enzyme of the heme biosynthesis pathway in erythroid cells. To date, a remarkable number of genetically undefined CSA cases remain, but a recent application of the next-generation sequencing technology has recognized novel causative genes for CSA. However, in most instances, the detailed molecular mechanisms of how defects of each gene result in the abnormal mitochondrial iron accumulation remain unclear. This review aims to cover the current understanding of the molecular pathophysiology of CSA.
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Affiliation(s)
- Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan.
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Rivella S. Iron metabolism under conditions of ineffective erythropoiesis in β-thalassemia. Blood 2019; 133:51-58. [PMID: 30401707 PMCID: PMC6318430 DOI: 10.1182/blood-2018-07-815928] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022] Open
Abstract
β-Thalassemia (BT) is an inherited genetic disorder that is characterized by ineffective erythropoiesis (IE), leading to anemia and abnormal iron metabolism. IE is an abnormal expansion of the number of erythroid progenitor cells with unproductive synthesis of enucleated erythrocytes, leading to anemia and hypoxia. Anemic patients affected by BT suffer from iron overload, even in the absence of chronic blood transfusion, suggesting the presence of ≥1 erythroid factor with the ability to modulate iron metabolism and dietary iron absorption. Recent studies suggest that decreased erythroid cell differentiation and survival also contribute to IE, aggravating the anemia in BT. Furthermore, hypoxia can also affect and increase iron absorption. Understanding the relationship between iron metabolism and IE could provide important insights into the BT condition and help to develop novel treatments. In fact, genetic or pharmacological manipulations of iron metabolism or erythroid cell differentiation and survival have been shown to improve IE, iron overload, and anemia in animal models of BT. Based on those findings, new therapeutic approaches and drugs have been proposed; clinical trials are underway that have the potential to improve erythrocyte production, as well as to reduce the iron overload and organ toxicity in BT and in other disorders characterized by IE.
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Affiliation(s)
- Stefano Rivella
- Division of Hematology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA; and Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA
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Single-cell analyses demonstrate that a heme-GATA1 feedback loop regulates red cell differentiation. Blood 2018; 133:457-469. [PMID: 30530752 DOI: 10.1182/blood-2018-05-850412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/01/2018] [Indexed: 01/07/2023] Open
Abstract
Erythropoiesis is the complex, dynamic, and tightly regulated process that generates all mature red blood cells. To understand this process, we mapped the developmental trajectories of progenitors from wild-type, erythropoietin-treated, and Flvcr1-deleted mice at single-cell resolution. Importantly, we linked the quantity of each cell's surface proteins to its total transcriptome, which is a novel method. Deletion of Flvcr1 results in high levels of intracellular heme, allowing us to identify heme-regulated circuitry. Our studies demonstrate that in early erythroid cells (CD71+Ter119neg-lo), heme increases ribosomal protein transcripts, suggesting that heme, in addition to upregulating globin transcription and translation, guarantees ample ribosomes for globin synthesis. In later erythroid cells (CD71+Ter119lo-hi), heme decreases GATA1, GATA1-target gene, and mitotic spindle gene expression. These changes occur quickly. For example, in confirmatory studies using human marrow erythroid cells, ribosomal protein transcripts and proteins increase, and GATA1 transcript and protein decrease, within 15 to 30 minutes of amplifying endogenous heme synthesis with aminolevulinic acid. Because GATA1 initiates heme synthesis, GATA1 and heme together direct red cell maturation, and heme stops GATA1 synthesis, our observations reveal a GATA1-heme autoregulatory loop and implicate GATA1 and heme as the comaster regulators of the normal erythroid differentiation program. In addition, as excessive heme could amplify ribosomal protein imbalance, prematurely lower GATA1, and impede mitosis, these data may help explain the ineffective (early termination of) erythropoiesis in Diamond Blackfan anemia and del(5q) myelodysplasia, disorders with excessive heme in colony-forming unit-erythroid/proerythroblasts, explain why these anemias are macrocytic, and show why children with GATA1 mutations have DBA-like clinical phenotypes.
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Rego SL, Harvey S, Simpson SR, Hemphill WO, McIver ZA, Grayson JM, Perrino FW. TREX1 D18N mice fail to process erythroblast DNA resulting in inflammation and dysfunctional erythropoiesis. Autoimmunity 2018; 51:333-344. [PMID: 30422000 DOI: 10.1080/08916934.2018.1522305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Anaemia is commonly observed in chronic inflammatory conditions, including systemic lupus erythematosus (SLE), where ∼50% of patients display clinical signs of anaemia. Mutation at the aspartate residue 18 of the three prime repair exonuclease 1 (TREX1) gene causes a monogenic form of cutaneous lupus in humans and the genetically precise TREX1 D18N mice recapitulate a lupus-like disease. TREX1 degrades single- and double-stranded DNA (dsDNA), and the link between failed DNA degradation by nucleases, including nucleoside-diphosphate kinases (NM23H1/H2) and Deoxyribonuclease II (DNase II), and anaemia prompted our studies to investigate whether TREX1 dysfunction contributes to anaemia. Utilizing the TREX1 D18N mice we demonstrate that (1) TREX1 mutant mice develop normocytic normochromic anaemia and (2) TREX1 exonuclease participates in the degradation of DNA originating from erythroblast nuclei during definitive erythropoiesis. Gene expression, hematocrit, hemoglobin, immunohistochemistry (IHC) and flow cytometry were used to quantify dysfunctional erythropoiesis. An altered response to induced anaemia in the TREX1 D18N mice was determined through IHC, flow cytometry, and interferon-stimulated gene (ISG) expression analysis of the liver, spleen and erythroblastic islands (EBIs). IHC, flow cytometry, and ISG expression studies were performed in vitro to determine the role of TREX1 in the degradation of erythroblast DNA within EBIs. The TREX1 D18N mice exhibit altered erythropoiesis including a 20% reduction in hematocrit, 10-20 fold increased erythropoietic gene expression levels in the spleen and phenotypic signs of normocytic normochromic anaemia. Anaemia in TREX1 D18N mice is accompanied by increased erythropoietin (Epo), normal hepcidin levels and the TREX1 D18N mice display an inappropriate response to anaemic challenge. Enhanced ISG expression results from failed processing and subsequent sensing of undegraded erythroblast DNA in EBIs. TREX1 participates in the degradation of erythroblast DNA in the EBI and TREX1 D18N mice exhibit a normocytic normochromic anaemia.
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Affiliation(s)
- Stephen L Rego
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Scott Harvey
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sean R Simpson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Wayne O Hemphill
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Zachariah A McIver
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jason M Grayson
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Fred W Perrino
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
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Liu J, Li Y, Tong J, Gao J, Guo Q, Zhang L, Wang B, Zhao H, Wang H, Jiang E, Kurita R, Nakamura Y, Tanabe O, Engel JD, Bresnick EH, Zhou J, Shi L. Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development. Nat Commun 2018; 9:4386. [PMID: 30349036 PMCID: PMC6197277 DOI: 10.1038/s41467-018-06883-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 10/02/2018] [Indexed: 01/19/2023] Open
Abstract
In addition to serving as a prosthetic group for enzymes and a hemoglobin structural component, heme is a crucial homeostatic regulator of erythroid cell development and function. While lncRNAs modulate diverse physiological and pathological cellular processes, their involvement in heme-dependent mechanisms is largely unexplored. In this study, we elucidated a lncRNA (UCA1)-mediated mechanism that regulates heme metabolism in human erythroid cells. We discovered that UCA1 expression is dynamically regulated during human erythroid maturation, with a maximal expression in proerythroblasts. UCA1 depletion predominantly impairs heme biosynthesis and arrests erythroid differentiation at the proerythroblast stage. Mechanistic analysis revealed that UCA1 physically interacts with the RNA-binding protein PTBP1, and UCA1 functions as an RNA scaffold to recruit PTBP1 to ALAS2 mRNA, which stabilizes ALAS2 mRNA. These results define a lncRNA-mediated posttranscriptional mechanism that provides a new dimension into how the fundamental heme biosynthetic process is regulated as a determinant of erythrocyte development. LncRNAs modulate diverse physiological cellular processes, however, their involvement in heme-dependent processes are not yet clear. Here the authors reveal the role of lncRNA UCA1 in erythroid cell development.
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Affiliation(s)
- Jinhua Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yapu Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jingyuan Tong
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Jie Gao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Qing Guo
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lingling Zhang
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Bingrui Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Zhao
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, 300134, China
| | - Hongtao Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Erlie Jiang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ryo Kurita
- Japanese Red Cross Society, Department of Research and Development, Central Blood Institute, Tokyo, 105-8521, Japan
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Cell Engineering Division, Ibaraki, 305-0074, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics Tohoku Medical Megabank, Tohoku University, Sedai, 980-8573, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Emery H Bresnick
- Wisconsin Institutes for Medical Research, Paul Carbone Cancer Center, Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53562, USA
| | - Jiaxi Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Lihong Shi
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China. .,Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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40
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Bach1: Function, Regulation, and Involvement in Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:1347969. [PMID: 30370001 PMCID: PMC6189649 DOI: 10.1155/2018/1347969] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/12/2018] [Indexed: 12/12/2022]
Abstract
The transcription factor BTB and CNC homology 1 (Bach1) is widely expressed in most mammalian tissues and functions primarily as a transcriptional suppressor by heterodimerizing with small Maf proteins and binding to Maf recognition elements in the promoters of targeted genes. It has a key regulatory role in the production of reactive oxygen species, cell cycle, heme homeostasis, hematopoiesis, and immunity and has been shown to suppress ischemic angiogenesis and promote breast cancer metastasis. This review summarizes how Bach1 controls these and other cellular and physiological and pathological processes. Bach1 expression and function differ between different cell types. Thus, therapies designed to manipulate Bach1 expression will need to be tightly controlled and tailored for each specific disease state or cell type.
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Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keles S, Xu J, Coon JJ, Bresnick EH. GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism. Dev Cell 2018; 46:581-594.e4. [PMID: 30122630 DOI: 10.1016/j.devcel.2018.07.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/01/2018] [Accepted: 07/19/2018] [Indexed: 01/27/2023]
Abstract
By functioning as an enzyme cofactor, hemoglobin component, and gene regulator, heme is vital for life. One mode of heme-regulated transcription involves amplifying the activity of GATA-1, a key determinant of erythrocyte differentiation. To discover biological consequences of the metal cofactor-transcription factor mechanism, we merged GATA-1/heme-regulated sectors of the proteome and transcriptome. This multi-omic analysis revealed a GATA-1/heme circuit involving hemoglobin subunits, ubiquitination components, and proteins not implicated in erythrocyte biology, including the zinc exporter Slc30a1. Though GATA-1 induced expression of Slc30a1 and the zinc importer Slc39a8, Slc39a8 dominantly increased intracellular zinc, which conferred erythroblast survival. Subsequently, a zinc transporter switch, involving decreased importer and sustained exporter expression, reduced intracellular zinc during terminal differentiation. Downregulating Slc30a1 increased intracellular zinc and, strikingly, accelerated differentiation. This analysis established a conserved paradigm in which a GATA-1/heme circuit controls trace metal transport machinery and trace metal levels as a mechanism governing cellular differentiation.
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Affiliation(s)
- Nobuyuki Tanimura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Ruiqi Liao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew R Dent
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Miao Cao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Judith N Burstyn
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peiman Hematti
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Xin Liu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ye Zheng
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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Li C, Chen C, Chen H, Wang S, Chen X, Cui Y. Verification of DNA motifs in Arabidopsis using CRISPR/Cas9-mediated mutagenesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1446-1451. [PMID: 29331085 PMCID: PMC6041440 DOI: 10.1111/pbi.12886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 12/10/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been widely used to discover the potential DNA-binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis. Using a single-guide RNA (sgRNA) targeting the DNA motif bound by REF6, a DNA sequence-specific H3K27 demethylase in plants, we generated stable transgenic plants where the motif was disrupted in a REF6 target gene. We also deleted a cluster of multiple motifs from another REF6 target gene using a pair of sgRNAs, targeting upstream and downstream regions of the cluster, respectively. We demonstrated that endogenous genes with motifs disrupted and/or deleted become inaccessible to REF6. This strategy should be widely applicable for in vivo verification of DNA motifs identified by ChIP-seq in plants.
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Affiliation(s)
- Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
- London Research and Development CenterAgriculture and Agri‐Food CanadaLondonONCanada
| | - Chen Chen
- London Research and Development CenterAgriculture and Agri‐Food CanadaLondonONCanada
- Department of BiologyWestern UniversityLondonONCanada
| | - Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Suikang Wang
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of California RiversideRiversideCAUSA
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of California RiversideRiversideCAUSA
- Howard Hughes Medical InstituteUniversity of California RiversideRiversideCAUSA
| | - Yuhai Cui
- London Research and Development CenterAgriculture and Agri‐Food CanadaLondonONCanada
- Department of BiologyWestern UniversityLondonONCanada
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43
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Liao C, Hardison RC, Kennett MJ, Carlson BA, Paulson RF, Prabhu KS. Selenoproteins regulate stress erythroid progenitors and spleen microenvironment during stress erythropoiesis. Blood 2018; 131:2568-2580. [PMID: 29615406 PMCID: PMC5992864 DOI: 10.1182/blood-2017-08-800607] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 03/15/2018] [Indexed: 12/30/2022] Open
Abstract
Micronutrient selenium (Se) plays a key role in redox regulation through its incorporation into selenoproteins as the 21st amino acid selenocysteine (Sec). Because Se deficiency appears to be a cofactor in the anemia associated with chronic inflammatory diseases, we reasoned that selenoproteins may contribute to erythropoietic recovery from anemia, referred to as stress erythropoiesis. Here, we report that loss of selenoproteins through Se deficiency or by mutation of the Sec tRNA (tRNA[Sec]) gene (Trsp) severely impairs stress erythropoiesis at 2 stages. Early stress erythroid progenitors failed to expand and properly differentiate into burst-forming unit-erythroid cells , whereas late-stage erythroid progenitors exhibited a maturation defect that affected the transition of proerythroblasts to basophilic erythroblasts. These defects were, in part, a result of the loss of selenoprotein W (SelenoW), whose expression was reduced at both transcript and protein levels in Se-deficient erythroblasts. Mutation of SelenoW in the bone marrow cells significantly decreased the expansion of stress burst-forming unit-erythroid cell colonies, which recapitulated the phenotypes induced by Se deficiency or mutation of Trsp Similarly, mutation of SelenoW in murine erythroblast (G1E) cell line led to defects in terminal differentiation. In addition to the erythroid defects, the spleens of Se-deficient mice contained fewer red pulp macrophages and exhibited impaired development of erythroblastic island macrophages, which make up the niche supporting erythroblast development. Taken together, these data reveal a critical role of selenoproteins in the expansion and development of stress erythroid progenitors, as well as the erythroid niche during acute anemia recovery.
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Affiliation(s)
- Chang Liao
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA; and
| | | | - Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Robert F Paulson
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
| | - K Sandeep Prabhu
- Pathobiology Program
- Department of Veterinary and Biomedical Sciences, and
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44
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Mehta C, Johnson KD, Gao X, Ong IM, Katsumura KR, McIver SC, Ranheim EA, Bresnick EH. Integrating Enhancer Mechanisms to Establish a Hierarchical Blood Development Program. Cell Rep 2018; 20:2966-2979. [PMID: 28930689 DOI: 10.1016/j.celrep.2017.08.090] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/30/2017] [Accepted: 08/25/2017] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic development requires the transcription factor GATA-2, and GATA-2 mutations cause diverse pathologies, including leukemia. GATA-2-regulated enhancers increase Gata2 expression in hematopoietic stem/progenitor cells and control hematopoiesis. The +9.5-kb enhancer activates transcription in endothelium and hematopoietic stem cells (HSCs), and its deletion abrogates HSC generation. The -77-kb enhancer activates transcription in myeloid progenitors, and its deletion impairs differentiation. Since +9.5-/- embryos are HSC deficient, it was unclear whether the +9.5 functions in progenitors or if GATA-2 expression in progenitors solely requires -77. We further dissected the mechanisms using -77;+9.5 compound heterozygous (CH) mice. The embryonic lethal CH mutation depleted megakaryocyte-erythrocyte progenitors (MEPs). While the +9.5 suffices for HSC generation, the -77 and +9.5 must reside on one allele to induce MEPs. The -77 generated burst-forming unit-erythroid through the induction of GATA-1 and other GATA-2 targets. The enhancer circuits controlled signaling pathways that orchestrate a GATA factor-dependent blood development program.
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Affiliation(s)
- Charu Mehta
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Kirby D Johnson
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Xin Gao
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Irene M Ong
- UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53705, USA
| | - Koichi R Katsumura
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Skye C McIver
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Erik A Ranheim
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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45
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Khalil S, Delehanty L, Grado S, Holy M, White Z, Freeman K, Kurita R, Nakamura Y, Bullock G, Goldfarb A. Iron modulation of erythropoiesis is associated with Scribble-mediated control of the erythropoietin receptor. J Exp Med 2017; 215:661-679. [PMID: 29282252 PMCID: PMC5789406 DOI: 10.1084/jem.20170396] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/02/2017] [Accepted: 11/17/2017] [Indexed: 12/24/2022] Open
Abstract
Iron deficiency causes resistance in erythroid progenitors against proliferative but not survival signals of erythropoietin. Khalil et al. link this response to the down-regulation of Scribble, an orchestrator of receptor trafficking and signaling. With iron deprivation, transferrin receptor 2 drives Scribble degradation, reconfiguring erythropoietin receptor function. Iron-restricted human anemias are associated with the acquisition of marrow resistance to the hematopoietic cytokine erythropoietin (Epo). Regulation of Epo responsiveness by iron availability serves as the basis for intravenous iron therapy in anemias of chronic disease. Epo engagement of its receptor normally promotes survival, proliferation, and differentiation of erythroid progenitors. However, Epo resistance caused by iron restriction selectively impairs proliferation and differentiation while preserving viability. Our results reveal that iron restriction limits surface display of Epo receptor in primary progenitors and that mice with enforced surface retention of the receptor fail to develop anemia with iron deprivation. A mechanistic pathway is identified in which erythroid iron restriction down-regulates a receptor control element, Scribble, through the mediation of the iron-sensing transferrin receptor 2. Scribble deficiency reduces surface expression of Epo receptor but selectively retains survival signaling via Akt. This mechanism integrates nutrient sensing with receptor function to permit modulation of progenitor expansion without compromising survival.
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Affiliation(s)
- Shadi Khalil
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Lorrie Delehanty
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Stephen Grado
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Maja Holy
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Zollie White
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Katie Freeman
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.,Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.,Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Grant Bullock
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Adam Goldfarb
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA
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46
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Hewitt KJ, Katsumura KR, Matson DR, Devadas P, Tanimura N, Hebert AS, Coon JJ, Kim JS, Dewey CN, Keles S, Hao S, Paulson RF, Bresnick EH. GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia. Dev Cell 2017; 42:213-225.e4. [PMID: 28787589 DOI: 10.1016/j.devcel.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/05/2017] [Accepted: 07/11/2017] [Indexed: 12/31/2022]
Abstract
An enhancer with amalgamated E-box and GATA motifs (+9.5) controls expression of the regulator of hematopoiesis GATA-2. While similar GATA-2-occupied elements are common in the genome, occupancy does not predict function, and GATA-2-dependent genetic networks are incompletely defined. A "+9.5-like" element resides in an intron of Samd14 (Samd14-Enh) encoding a sterile alpha motif (SAM) domain protein. Deletion of Samd14-Enh in mice strongly decreased Samd14 expression in bone marrow and spleen. Although steady-state hematopoiesis was normal, Samd14-Enh-/- mice died in response to severe anemia. Samd14-Enh stimulated stem cell factor/c-Kit signaling, which promotes erythrocyte regeneration. Anemia activated Samd14-Enh by inducing enhancer components and enhancer chromatin accessibility. Thus, a GATA-2/anemia-regulated enhancer controls expression of an SAM domain protein that confers survival in anemia. We propose that Samd14-Enh and an ensemble of anemia-responsive enhancers are essential for erythrocyte regeneration in stress erythropoiesis, a vital process in pathologies, including β-thalassemia, myelodysplastic syndrome, and viral infection.
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Affiliation(s)
- Kyle J Hewitt
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Koichi R Katsumura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Prithvia Devadas
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Nobuyuki Tanimura
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Joshua J Coon
- Department of Chemistry, UW-Madison, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science and Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, South Korea
| | - Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Siyang Hao
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Robert F Paulson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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47
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Seguin A, Takahashi-Makise N, Yien YY, Huston NC, Whitman JC, Musso G, Wallace JA, Bradley T, Bergonia HA, Kafina MD, Matsumoto M, Igarashi K, Phillips JD, Paw BH, Kaplan J, Ward DM. Reductions in the mitochondrial ABC transporter Abcb10 affect the transcriptional profile of heme biosynthesis genes. J Biol Chem 2017; 292:16284-16299. [PMID: 28808058 DOI: 10.1074/jbc.m117.797415] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/09/2017] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette subfamily B member 10 (Abcb10) is a mitochondrial ATP-binding cassette (ABC) transporter that complexes with mitoferrin1 and ferrochelatase to enhance heme biosynthesis in developing red blood cells. Reductions in Abcb10 levels have been shown to reduce mitoferrin1 protein levels and iron import into mitochondria, resulting in reduced heme biosynthesis. As an ABC transporter, Abcb10 binds and hydrolyzes ATP, but its transported substrate is unknown. Here, we determined that decreases in Abcb10 did not result in protoporphyrin IX accumulation in morphant-treated zebrafish embryos or in differentiated Abcb10-specific shRNA murine Friend erythroleukemia (MEL) cells in which Abcb10 was specifically silenced with shRNA. We also found that the ATPase activity of Abcb10 is necessary for hemoglobinization in MEL cells, suggesting that the substrate transported by Abcb10 is important in mediating increased heme biosynthesis during erythroid development. Inhibition of 5-aminolevulinic acid dehydratase (EC 4.2.1.24) with succinylacetone resulted in both 5-aminolevulinic acid (ALA) accumulation in control and Abcb10-specific shRNA MEL cells, demonstrating that reductions in Abcb10 do not affect ALA export from mitochondria and indicating that Abcb10 does not transport ALA. Abcb10 silencing resulted in an alteration in the heme biosynthesis transcriptional profile due to repression by the transcriptional regulator Bach1, which could be partially rescued by overexpression of Alas2 or Gata1, providing a mechanistic explanation for why Abcb10 shRNA MEL cells exhibit reduced hemoglobinization. In conclusion, our findings rule out that Abcb10 transports ALA and indicate that Abcb10's ATP-hydrolysis activity is critical for hemoglobinization and that the substrate transported by Abcb10 provides a signal that optimizes hemoglobinization.
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Affiliation(s)
- Alexandra Seguin
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | | | | | | | | | - Gabriel Musso
- the Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jared A Wallace
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Thomas Bradley
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Hector A Bergonia
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | | | - Mitsuyo Matsumoto
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Kazuhiko Igarashi
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - John D Phillips
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Barry H Paw
- the Division of Hematology and.,the Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, and.,the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jerry Kaplan
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Diane M Ward
- From the Division of Microbiology and Immunology, Department of Pathology, and
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48
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Deletion of transcription factor binding motifs using the CRISPR/spCas9 system in the β-globin LCR. Biosci Rep 2017; 37:BSR20170976. [PMID: 28729249 PMCID: PMC5634328 DOI: 10.1042/bsr20170976] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 11/17/2022] Open
Abstract
Transcription factors play roles in gene transcription through direct binding to their motifs in genome, and inhibiting this binding provides an effective strategy for studying their roles. Here we applied the CRISPR/spCas9 system to mutate the binding motifs of transcription factors. Binding motifs for erythroid specific transcription factors were mutated in the locus control region hypersensitive sites of the human β-globin locus. Guide RNAs targeting binding motifs were cloned into lentiviral CRISPR vector containing the spCas9 gene, and transduced into MEL/ch11 cells carrying a human chromosome 11. DNA mutations in clonal cells were initially screened by quantitative PCR in genomic DNA and then clarified by sequencing. Mutations in binding motifs reduced occupancy by transcription factors in a chromatin environment. Characterization of mutations revealed that the CRISPR/spCas9 system mainly induced deletions in short regions of <20 bp and preferentially deleted nucleotides around the fifth nucleotide upstream of Protospacer adjacent motifs. These results indicate that the CRISPR/Cas9 system is suitable for mutating the binding motifs of transcription factors, and, consequently, would contribute to elucidate the direct roles of transcription factors.
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49
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Perreault AA, Benton ML, Koury MJ, Brandt SJ, Venters BJ. Epo reprograms the epigenome of erythroid cells. Exp Hematol 2017; 51:47-62. [PMID: 28410882 DOI: 10.1016/j.exphem.2017.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/25/2022]
Abstract
The hormone erythropoietin (Epo) is required for erythropoiesis, yet its molecular mechanism of action remains poorly understood, particularly with respect to chromatin dynamics. To investigate how Epo modulates the erythroid epigenome, we performed epigenetic profiling using an ex vivo murine cell system that undergoes synchronous erythroid maturation in response to Epo stimulation. Our findings define the repertoire of Epo-modulated enhancers, illuminating a new facet of Epo signaling. First, a large number of enhancers rapidly responded to Epo stimulation, revealing a cis-regulatory network of Epo-responsive enhancers. In contrast, most of the other identified enhancers remained in an active acetylated state during Epo signaling, suggesting that most erythroid enhancers are established at an earlier precursor stage. Second, we identified several hundred super-enhancers that were linked to key erythroid genes, such as Tal1, Bcl11a, and Mir144/451. Third, experimental and computational validation revealed that many predicted enhancer regions were occupied by TAL1 and enriched with DNA-binding motifs for GATA1, KLF1, TAL1/E-box, and STAT5. Additionally, many of these cis-regulatory regions were conserved evolutionarily and displayed correlated enhancer:promoter acetylation. Together, these findings define a cis-regulatory enhancer network for Epo signaling during erythropoiesis, and provide the framework for future studies involving the interplay of epigenetics and Epo signaling.
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Affiliation(s)
- Andrea A Perreault
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN
| | - Mary Lauren Benton
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Mark J Koury
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Stephen J Brandt
- Department of Cancer Biology, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Chemical and Physical Biology Program, Vanderbilt Genetics Institute, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN.
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50
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Abstract
The discovery of the GATA binding protein (GATA factor) transcription factor family revolutionized hematology. Studies of GATA proteins have yielded vital contributions to our understanding of how hematopoietic stem and progenitor cells develop from precursors, how progenitors generate red blood cells, how hemoglobin synthesis is regulated, and the molecular underpinnings of nonmalignant and malignant hematologic disorders. This thrilling journey began with mechanistic studies on a β-globin enhancer- and promoter-binding factor, GATA-1, the founding member of the GATA family. This work ushered in the cloning of related proteins, GATA-2-6, with distinct and/or overlapping expression patterns. Herein, we discuss how the hematopoietic GATA factors (GATA-1-3) function via a battery of mechanistic permutations, which can be GATA factor subtype, cell type, and locus specific. Understanding this intriguing protein family requires consideration of how the mechanistic permutations are amalgamated into circuits to orchestrate processes of interest to the hematologist and more broadly.
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