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Short JD, Tavakoli S, Nguyen HN, Carrera A, Farnen C, Cox LA, Asmis R. Dyslipidemic Diet-Induced Monocyte "Priming" and Dysfunction in Non-Human Primates Is Triggered by Elevated Plasma Cholesterol and Accompanied by Altered Histone Acetylation. Front Immunol 2017; 8:958. [PMID: 28878765 PMCID: PMC5572238 DOI: 10.3389/fimmu.2017.00958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Monocytes and the recruitment of monocyte-derived macrophages into sites of inflammation play a key role in atherogenesis and other chronic inflammatory diseases linked to cardiometabolic syndrome and obesity. Previous studies from our group have shown that metabolic stress promotes monocyte priming, i.e., enhanced adhesion and accelerated chemotaxis of monocytes in response to chemokines, both in vitro and in dyslipidemic LDLR-/- mice. We also showed that metabolic stress-induced monocyte dysfunction is, at least to a large extent caused by the S-glutathionylation, inactivation, and subsequent degradation of mitogen-activated protein kinase phosphatase 1. Here, we analyzed the effects of a Western-style, dyslipidemic diet (DD), which was composed of high levels of saturated fat, cholesterol, and simple sugars, on monocyte (dys)function in non-human primates (NHPs). We found that similar to mice, a DD enhances monocyte chemotaxis in NHP within 4 weeks, occurring concordantly with the onset of hypercholesterolemia but prior to changes in triglycerides, blood glucose, monocytosis, or changes in monocyte subset composition. In addition, we identified transitory decreases in the acetylation of histone H3 at the lysine residues 18 and 23 in metabolically primed monocytes, and we found that monocyte priming was correlated with the acetylation of histone H3 at lysine 27 after an 8-week DD regimen. Our data show that metabolic stress promotes monocyte priming and hyper-chemotactic responses in NHP. The histone modifications accompanying monocyte priming in primates suggest a reprogramming of the epigenetic landscape, which may lead to dysregulated responses and functionalities in macrophages derived from primed monocytes that are recruited to sites of inflammation.
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Affiliation(s)
- John D Short
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Sina Tavakoli
- Department of Radiology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Huynh Nga Nguyen
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ana Carrera
- Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Chelbee Farnen
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Laura A Cox
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, United States.,Southwest National Primate Research Center, San Antonio, TX, United States
| | - Reto Asmis
- Department of Radiology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States.,Department of Clinical Laboratory Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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52
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Huang KL, Marcora E, Pimenova AA, Di Narzo AF, Kapoor M, Jin SC, Harari O, Bertelsen S, Fairfax BP, Czajkowski J, Chouraki V, Grenier-Boley B, Bellenguez C, Deming Y, McKenzie A, Raj T, Renton AE, Budde J, Smith A, Fitzpatrick A, Bis JC, DeStefano A, Adams HHH, Ikram MA, van der Lee S, Del-Aguila JL, Fernandez MV, Ibañez L, Sims R, Escott-Price V, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Lambert JC, van Duijn C, Launer L, Seshadri S, Williams J, Amouyel P, Schellenberg GD, Zhang B, Borecki I, Kauwe JSK, Cruchaga C, Hao K, Goate AM. A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease. Nat Neurosci 2017; 20:1052-1061. [PMID: 28628103 PMCID: PMC5759334 DOI: 10.1038/nn.4587] [Citation(s) in RCA: 277] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 05/20/2017] [Indexed: 12/12/2022]
Abstract
A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849 controls identified eight previously reported AD risk loci and 14 novel loci associated with age at onset. Linkage disequilibrium score regression of 220 cell types implicated the regulation of myeloid gene expression in AD risk. The minor allele of rs1057233 (G), within the previously reported CELF1 AD risk locus, showed association with delayed AD onset and lower expression of SPI1 in monocytes and macrophages. SPI1 encodes PU.1, a transcription factor critical for myeloid cell development and function. AD heritability was enriched within the PU.1 cistrome, implicating a myeloid PU.1 target gene network in AD. Finally, experimentally altered PU.1 levels affected the expression of mouse orthologs of many AD risk genes and the phagocytic activity of mouse microglial cells. Our results suggest that lower SPI1 expression reduces AD risk by regulating myeloid gene expression and cell function.
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Affiliation(s)
- Kuan-lin Huang
- Department of Medicine, Washington University in St. Louis, Saint
Louis, MO, USA
- Department of McDonnell Genome Institute, Washington University in
St. Louis, Saint Louis, MO, USA
| | - Edoardo Marcora
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Anna A Pimenova
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New
Haven, CT, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Sarah Bertelsen
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, Nuffield Department of
Medicine, University of Oxford, Oxford, United Kingdom
| | - Jake Czajkowski
- Department of Genetics, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Vincent Chouraki
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA
| | - Benjamin Grenier-Boley
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Céline Bellenguez
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Yuetiva Deming
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Andrew McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - Alan E Renton
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
| | - John Budde
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | - Annette Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle,
Washington, USA
| | - Joshua C Bis
- Department of Medicine, University of Washington, Seattle,
Washington, USA
| | - Anita DeStefano
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
| | - Hieab HH Adams
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Sven van der Lee
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Jorge L. Del-Aguila
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | - Laura Ibañez
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | | | | | - Rebecca Sims
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Valentina Escott-Price
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Richard Mayeux
- Taub Institute on Alzheimer’s Disease and the Aging Brain,
Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY,
USA
- Department of Neurology, Columbia University, New York, NY,
USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve
University, Cleveland, OH, USA; Department of Ophthalmology, Boston University
School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Institut Pasteur de Lille, F-59000 Lille, France
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University
School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public
Health, Boston, MA, USA
- The John P. Hussman Institute for Human Genomics, University of
Miami, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of
Miami, Miami, FL, USA
- Macdonald Foundation Department of Human Genetics, University of
Miami, Miami, FL, USA
| | - Jean Charles Lambert
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus University Medical Center,
Rotterdam, The Netherlands
| | - Lenore Launer
- Laboratory of Epidemiology and Population Sciences, National
Institute on Aging, Bethesda, Maryland, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine,
Boston, MA, USA
| | - Julie Williams
- Psychological Medicine and Clinical Neurosciences, Medical Research
Council (MRC) Centre for Neuropsychiatric Genetics and Genomics, Cardiff University,
Cardiff, UK
| | - Philippe Amouyel
- Inserm, U1167, RID-AGE –Risk factors and molecular
determinants of aging-related diseases, F-59000 Lille, France
- Univ. Lille - Excellence laboratory Labex DISTALZ, F-59000 Lille,
France
- Institut Pasteur de Lille, F-59000 Lille, France
- Centre Hospitalier Universitaire de Lille, U1167, F-59000 Lille,
France
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of
Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | | | - John S K Kauwe
- Department of Biology, Brigham Young University, Provo, Utah,
USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis, Saint
Louis, MO, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY, USA
- Department of Ronald M. Loeb Center for Alzheimer’s disease,
Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY,
USA
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53
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Transcriptional mechanisms that control expression of the macrophage colony-stimulating factor receptor locus. Clin Sci (Lond) 2017; 131:2161-2182. [DOI: 10.1042/cs20170238] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/22/2017] [Accepted: 06/11/2017] [Indexed: 12/17/2022]
Abstract
The proliferation, differentiation, and survival of cells of the macrophage lineage depends upon signals from the macrophage colony-stimulating factor (CSF) receptor (CSF1R). CSF1R is expressed by embryonic macrophages and induced early in adult hematopoiesis, upon commitment of multipotent progenitors to the myeloid lineage. Transcriptional activation of CSF1R requires interaction between members of the E26 transformation-specific family of transcription factors (Ets) (notably PU.1), C/EBP, RUNX, AP-1/ATF, interferon regulatory factor (IRF), STAT, KLF, REL, FUS/TLS (fused in sarcoma/ranslocated in liposarcoma) families, and conserved regulatory elements within the mouse and human CSF1R locus. One element, the Fms-intronic regulatory element (FIRE), within intron 2, is conserved functionally across all the amniotes. Lineage commitment in multipotent progenitors also requires down-regulation of specific transcription factors such as MYB, FLI1, basic leucine zipper transcriptional factor ATF-like (BATF3), GATA-1, and PAX5 that contribute to differentiation of alternative lineages and repress CSF1R transcription. Many of these transcription factors regulate each other, interact at the protein level, and are themselves downstream targets of CSF1R signaling. Control of CSF1R transcription involves feed–forward and feedback signaling in which CSF1R is both a target and a participant; and dysregulation of CSF1R expression and/or function is associated with numerous pathological conditions. In this review, we describe the regulatory network behind CSF1R expression during differentiation and development of cells of the mononuclear phagocyte system.
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54
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Abstract
Monocytes and macrophages are professional phagocytes that occupy specific niches in every tissue of the body. Their survival, proliferation, and differentiation are controlled by signals from the macrophage colony-stimulating factor receptor (CSF-1R) and its two ligands, CSF-1 and interleukin-34. In this review, we address the developmental and transcriptional relationships between hematopoietic progenitor cells, blood monocytes, and tissue macrophages as well as the distinctions from dendritic cells. A huge repertoire of receptors allows monocytes, tissue-resident macrophages, or pathology-associated macrophages to adapt to specific microenvironments. These processes create a broad spectrum of macrophages with different functions and individual effector capacities. The production of large transcriptomic data sets in mouse, human, and other species provides new insights into the mechanisms that underlie macrophage functional plasticity.
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55
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Knockdown of miR-128a induces Lin28a expression and reverts myeloid differentiation blockage in acute myeloid leukemia. Cell Death Dis 2017; 8:e2849. [PMID: 28569789 PMCID: PMC5520910 DOI: 10.1038/cddis.2017.253] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/05/2017] [Indexed: 01/15/2023]
Abstract
Lin28A is a highly conserved RNA-binding protein that concurs to control the balance between stemness and differentiation in several tissue lineages. Here, we report the role of miR-128a/Lin28A axis in blocking cell differentiation in acute myeloid leukemia (AML), a genetically heterogeneous disease characterized by abnormally controlled proliferation of myeloid progenitor cells accompanied by partial or total inability to undergo terminal differentiation. First, we found Lin28A underexpressed in blast cells from AML patients and AML cell lines as compared with CD34+ normal precursors. In vitro transfection of Lin28A in NPM1-mutated OCI-AML3 cell line significantly triggered cell-cycle arrest and myeloid differentiation, with increased expression of macrophage associate genes (EGR2, ZFP36 and ANXA1). Furthermore, miR-128a, a negative regulator of Lin28A, was found overexpressed in AML cells compared with normal precursors, especially in acute promyelocytic leukemia (APL) and in ‘AML with maturation’ (according to 2016 WHO classification of myeloid neoplasms and acute leukemia). Its forced overexpression by lentiviral infection in OCI-AML3 downregulated Lin28A with ensuing repression of macrophage-oriented differentiation. Finally, knockdown of miR-128a in OCI-AML3 and in APL/AML leukemic cells (by transfection and lentiviral infection, respectively) induced myeloid cell differentiation and increased expression of Lin28A, EGR2, ZFP36 and ANXA1, reverting myeloid differentiation blockage. In conclusion, our findings revealed a new mechanism for AML differentiation blockage, suggesting new strategies for AML therapy based upon miR-128a inhibition.
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56
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Jia SJ, Gao KQ, Zhao M. Epigenetic regulation in monocyte/macrophage: A key player during atherosclerosis. Cardiovasc Ther 2017; 35. [PMID: 28371472 DOI: 10.1111/1755-5922.12262] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/23/2017] [Accepted: 03/26/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Su-Jie Jia
- Hunan Key Laboratory of Medical Epigenomics; The Second Xiangya Hospital, Central South University; Changsha China
- Department of Pharmaceutics; The Third Xiangya Hospital, Central South University; Changsha China
| | - Ke-Qin Gao
- Department of Pharmaceutics; The Third Xiangya Hospital, Central South University; Changsha China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics; The Second Xiangya Hospital, Central South University; Changsha China
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57
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Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017; 6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
Abstract
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3' inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3' CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.
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58
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Martins AJ, Narayanan M, Prüstel T, Fixsen B, Park K, Gottschalk RA, Lu Y, Andrews-Pfannkoch C, Lau WW, Wendelsdorf KV, Tsang JS. Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network. Cell Syst 2017; 4:379-392.e12. [PMID: 28365150 DOI: 10.1016/j.cels.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/15/2016] [Accepted: 03/01/2017] [Indexed: 01/22/2023]
Abstract
Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cell populations. While gene network "rewiring" is known to accompany cellular adaptation to different environments, how PoV changes between environments and its underlying regulatory mechanisms are less understood. Here, we systematically explored context-dependent PoV among genes in human macrophages, utilizing different cytokines as natural perturbations of multiple molecular parameters that may influence PoV. Our single-cell, epigenomic, computational, and stochastic simulation analyses reveal that environmental adaptation can tune PoV to potentially shape cellular heterogeneity by changing parameters such as the degree of phosphorylation and transcription factor-chromatin interactions. This quantitative tuning of PoV may be a widespread, yet underexplored, property of cellular adaptation to distinct environments.
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Affiliation(s)
- Andrew J Martins
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manikandan Narayanan
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thorsten Prüstel
- Computational Biology Section, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bethany Fixsen
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyemyung Park
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA; Biophysics Program, University of Maryland-NIH Graduate Partnership Program, University of Maryland, College Park, MD 20742, USA
| | - Rachel A Gottschalk
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong Lu
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia Andrews-Pfannkoch
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - William W Lau
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine V Wendelsdorf
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institutes of Health, Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA.
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59
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Abstract
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.
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Affiliation(s)
- Gregory M K Poon
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA.,b Center for Diagnostics and Therapeutics, Georgia State University , Atlanta , GA , USA
| | - Hye Mi Kim
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA
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60
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Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet 2017; 13:e1006641. [PMID: 28263993 PMCID: PMC5358891 DOI: 10.1371/journal.pgen.1006641] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 03/20/2017] [Accepted: 02/17/2017] [Indexed: 12/15/2022] Open
Abstract
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease. Macrophages are immune cells that form the first line of defense against pathogens, but also mediate tissue damage in inflammatory disease. Macrophages initiate inflammation by recognising and responding to components of bacterial cells. Macrophages of the wall of the gut are constantly replenished from the blood. Upon entering the intestine, newly-arrived cells modulate their response to stimuli derived from the bacteria in the wall of the gut. This process fails in chronic inflammatory bowel diseases (IBD). Both the major forms of IBD, Crohn’s disease and ulcerative colitis, run in families. The inheritance is complex, involving more than 200 different regions of the genome. We hypothesised that the genetic risk of IBD is associated specifically with altered regulation of genes that control the development of macrophages. In this study, we used the comprehensive transcriptome dataset produced by the FANTOM5 consortium to identify the sets of promoters and enhancers that are involved in adaptation of macrophages to the gut wall, their response to bacterial stimuli, and how their functions are integrated. A reanalysis of published genome-wide association data based upon regulated genes in monocytes as candidates strongly supports the view that susceptibility to IBD arises from a primary defect in macrophage differentiation.
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61
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Rothenberg EV, Kueh HY, Yui MA, Zhang JA. Hematopoiesis and T-cell specification as a model developmental system. Immunol Rev 2016; 271:72-97. [PMID: 27088908 DOI: 10.1111/imr.12417] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pathway to generate T cells from hematopoietic stem cells guides progenitors through a succession of fate choices while balancing differentiation progression against proliferation, stage to stage. Many elements of the regulatory system that controls this process are known, but the requirement for multiple, functionally distinct transcription factors needs clarification in terms of gene network architecture. Here, we compare the features of the T-cell specification system with the rule sets underlying two other influential types of gene network models: first, the combinatorial, hierarchical regulatory systems that generate the orderly, synchronized increases in complexity in most invertebrate embryos; second, the dueling 'master regulator' systems that are commonly used to explain bistability in microbial systems and in many fate choices in terminal differentiation. The T-cell specification process shares certain features with each of these prevalent models but differs from both of them in central respects. The T-cell system is highly combinatorial but also highly dose-sensitive in its use of crucial regulatory factors. The roles of these factors are not always T-lineage-specific, but they balance and modulate each other's activities long before any mutually exclusive silencing occurs. T-cell specification may provide a new hybrid model for gene networks in vertebrate developmental systems.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hao Yuan Kueh
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Mary A Yui
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jingli A Zhang
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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62
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Chromatin Remodeling in Monocyte and Macrophage Activation. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 106:1-15. [PMID: 28057208 DOI: 10.1016/bs.apcsb.2016.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Increasing evidence collected during the last years supports the idea that monocyte and macrophage activation is not only associated with transcriptional changes but also changes in the chromatin landscape. Moreover, the introduction of a multidimensional model of macrophage activation allows a more precise description of monocytes and macrophages under homeostatic and pathophysiological conditions. Monocytes and macrophages are masters of integrating microenvironmental signals, thereby reshaping their chromatin landscape and as a consequence their transcriptional and functional programs. Albeit these cells share a large number of epigenetic landmarks, their chromatin is significantly shaped by environmental signals. The chromatin landscape of any given tissue macrophage is a rather specific fingerprint of these cells, which is directly linked to tissue-specific functions of these cells. Moreover, chromatin remodeling in response to stress signals also seems to be an important mechanism of these cells to increase their readiness for future stressors. Understanding this sophisticated epigenetic regulatory network in monocytes and macrophages will open up new avenues toward tissue- and disease-specific therapeutic strategies in many of the chronic inflammatory diseases our societies are currently facing.
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63
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Lin J, Hu Y, Nunez S, Foulkes AS, Cieply B, Xue C, Gerelus M, Li W, Zhang H, Rader DJ, Musunuru K, Li M, Reilly MP. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol 2016; 36:1434-47. [PMID: 27230130 PMCID: PMC4919157 DOI: 10.1161/atvbaha.116.307573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Human macrophages can shift phenotype across the inflammatory M1 and reparative M2 spectrum in response to environmental challenges, but the mechanisms promoting inflammatory and cardiometabolic disease-associated M1 phenotypes remain incompletely understood. Alternative splicing (AS) is emerging as an important regulator of cellular function, yet its role in macrophage activation is largely unknown. We investigated the extent to which AS occurs in M1 activation within the cardiometabolic disease context and validated a functional genomic cell model for studying human macrophage-related AS events. APPROACH AND RESULTS From deep RNA-sequencing of resting, M1, and M2 primary human monocyte-derived macrophages, we found 3860 differentially expressed genes in M1 activation and detected 233 M1-induced AS events; the majority of AS events were cell- and M1-specific with enrichment for pathways relevant to macrophage inflammation. Using genetic variant data for 10 cardiometabolic traits, we identified 28 trait-associated variants within the genomic loci of 21 alternatively spliced genes and 15 variants within 7 differentially expressed regulatory splicing factors in M1 activation. Knockdown of 1 such splicing factor, CELF1, in primary human macrophages led to increased inflammatory response to M1 stimulation, demonstrating CELF1's potential modulation of the M1 phenotype. Finally, we demonstrated that an induced pluripotent stem cell-derived macrophage system recapitulates M1-associated AS events and provides a high-fidelity macrophage AS model. CONCLUSIONS AS plays a role in defining macrophage phenotype in a cell- and stimulus-specific fashion. Alternatively spliced genes and splicing factors with trait-associated variants may reveal novel pathways and targets in cardiometabolic diseases.
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Affiliation(s)
- Jennie Lin
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
| | - Yu Hu
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Sara Nunez
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Andrea S Foulkes
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Benjamin Cieply
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Chenyi Xue
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mark Gerelus
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Wenjun Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Hanrui Zhang
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Daniel J Rader
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Kiran Musunuru
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mingyao Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Muredach P Reilly
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
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64
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Human beta-defensin-2 and -3 enhance pro-inflammatory cytokine expression induced by TLR ligands via ATP-release in a P2X7R dependent manner. Immunobiology 2016; 221:1259-65. [PMID: 27377709 DOI: 10.1016/j.imbio.2016.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/03/2016] [Accepted: 06/09/2016] [Indexed: 01/15/2023]
Abstract
Our previous results indicate that HBD2 and HBD3 are chemotactic for a broad spectrum of leukocytes in a CCR6- and CCR2-dependent manner. In this study we report that pre-stimulation of primary human macrophages or THP-1 cells with HBD2 or HBD3 results in a synergistic, enhanced expression of pro-inflammatory cytokines and chemokines induced by TLR ligand re-stimulation. Experiments using specific inhibitors of the ATP-gated channel receptor P2X7 or its functional ligand ATP, suggest that the enhanced expression of pro-inflammatory cytokines and chemokines seems to be mediated by P2X7R. Furthermore, our data provide evidence that beta-defensins do not directly interact with P2X7R but rather induce the release of intracellular ATP. Interference with ATP release abrogated the synergistic effect mediated by HBD2 and HBD3 pre-stimulation in THP-1 cells. However, extracellular ATP alone seems not to be sufficient to elicit the enhanced synergistic effect on cytokine and chemokine expression observed by pre-stimulation of primary human macrophages or THP-1 cells with HBD2 or HBD3. Collectively, our findings provide new insights into the molecular mechanisms how HBD2 and HBD3 interact with cells of myeloid origin and demonstrate their immuno-modulating functions during innate immune responses.
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65
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Stephens DC, Poon GMK. Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains. Nucleic Acids Res 2016; 44:8671-8681. [PMID: 27270080 PMCID: PMC5062964 DOI: 10.1093/nar/gkw528] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/30/2016] [Indexed: 01/25/2023] Open
Abstract
Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-methylated DNA, which occurs following DNA replication and in response to hypomethylating agents, on site recognition by ETS proteins. To address these questions, we measured the affinities of two sequence-divergent ETS homologs, PU.1 and Ets-1, to DNA sites harboring a hemi- and fully methylated CpG dinucleotide. While the two proteins bound unmethylated DNA with indistinguishable affinity, their affinities to methylated DNA are markedly heterogeneous and exhibit major energetic coupling between the two CpG methylcytosines. Analysis of simulated DNA and existing co-crystal structures revealed that hemi-methylation induced non-local backbone and groove geometries that were not conserved in the fully methylated state. Indirect readout of these perturbations was differentially achieved by the two ETS homologs, with the distinctive interfacial hydration in PU.1/DNA binding moderating the inhibitory effects of DNA methylation on binding. This data established a biophysical basis for the pioneering properties associated with PU.1, which robustly bound fully methylated DNA, but not Ets-1, which was substantially inhibited.
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Affiliation(s)
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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66
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Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A. Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment. Sci Rep 2016; 6:24724. [PMID: 27095295 PMCID: PMC4837375 DOI: 10.1038/srep24724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France
| | - Clelia Peano
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | - Luca Petiti
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | | | - Ermanno Rizzi
- Institute of Biomedical Technologies, CNR, Milan, Italy.,Telethon Foundation, Milan, Italy
| | | | - Alessia Cavazza
- Dana Farber Cancer Institute, Harvard Medical School, Boston, US
| | - Claudia Rossi
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy
| | - Pasqualepaolo Pagliaro
- Az. Osp. Policlinico Universitario di Bologna, Policlinico S. Orsola-Malpighi, Unità Operativa di Immunoematologia e Trasfusionale, Bologna, Italy
| | | | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Silvio Bicciato
- Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Genethon, Evry, France
| | - Annarita Miccio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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67
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Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nat Commun 2016; 7:10846. [PMID: 27029405 PMCID: PMC4821877 DOI: 10.1038/ncomms10846] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/26/2016] [Indexed: 02/06/2023] Open
Abstract
A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce transcriptional changes associated with macrophage phenotype, but posttranscriptional control of human macrophage differentiation is less well understood. Here we show that expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes and early human atherosclerotic lesions, but are abundant in macrophages of advanced plaques. Depletion of QKI protein impairs monocyte adhesion, migration, differentiation into macrophages and foam cell formation in vitro and in vivo. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, reveal striking changes in QKI-dependent messenger RNA levels and splicing of RNA transcripts. The biological importance of these transcripts and requirement for QKI during differentiation illustrates a central role for QKI in posttranscriptionally guiding macrophage identity and function. Post-transcriptional control of RNA is important in health and disease. Here, the authors show that the RNA-binding protein Quaking guides pre-mRNA splicing and transcript abundance during monocyte to macrophage differentiation, and that Quaking depletion impairs pro-atherogenic foam cell formation.
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68
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Reddy MA, Das S, Zhuo C, Jin W, Wang M, Lanting L, Natarajan R. Regulation of Vascular Smooth Muscle Cell Dysfunction Under Diabetic Conditions by miR-504. Arterioscler Thromb Vasc Biol 2016; 36:864-73. [PMID: 26941017 DOI: 10.1161/atvbaha.115.306770] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/09/2016] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Diabetes mellitus accelerates proatherogenic and proinflammatory phenotype of vascular smooth muscle cell (VSMC) associated with vascular complications. Evidence shows that microRNAs (miRNAs) play key roles in VSMC functions, but their role under diabetic conditions is unclear. We profiled miRNAs in VSMC from diabetic mice and examined their role in VSMC dysfunction. APPROACH AND RESULTS High throughput small RNA-sequencing identified 135 differentially expressed miRNAs in VSMC from type 2 diabetic db/db mice (db/dbVSMC) versus nondiabetic db/+ mice. Several of these miRNAs were known to regulate VSMC functions. We further focused on miR-504, because it was highly upregulated in db/dbVSMC, and its function in VSMC is unknown. miR-504 and its host gene Fgf13 were significantly increased in db/dbVSMC and in aortas from db/db mice. Bioinformatics analysis predicted that miR-504 targets including signaling adaptor Grb10 and transcription factor Egr2 could regulate growth factor signaling. We experimentally validated Grb10 and Egr2 as novel targets of miR-504. Overexpression of miR-504 in VSMC inhibited contractile genes and enhanced extracellular signal-regulated kinase 1/2 activation, proliferation, and migration. These effects were blocked by miR-504 inhibitors. Grb10 knockdown mimicked miR-504 functions and increased inflammatory genes. Egr2 knockdown-inhibited anti-inflammatory Socs1 and increased proinflammatory genes. Furthermore, high glucose and palmitic acid upregulated miR-504 and inflammatory genes, but downregulated Grb10. CONCLUSIONS Diabetes mellitus misregulates several miRNAs including miR-504 that can promote VSMC dysfunction. Because changes in many of these miRNAs are sustained in diabetic VSMC even after in vitro culture, they may be involved in metabolic memory of vascular complications. Targeting such mechanisms could offer novel therapeutic strategies for diabetic complications.
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Affiliation(s)
- Marpadga A Reddy
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Sadhan Das
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Chen Zhuo
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Wen Jin
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Mei Wang
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Linda Lanting
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA
| | - Rama Natarajan
- From the Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA.
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69
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Schmidt SV, Krebs W, Ulas T, Xue J, Baßler K, Günther P, Hardt AL, Schultze H, Sander J, Klee K, Theis H, Kraut M, Beyer M, Schultze JL. The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin. Cell Res 2016; 26:151-70. [PMID: 26729620 PMCID: PMC4746609 DOI: 10.1038/cr.2016.1] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/31/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022] Open
Abstract
Differentiation of inflammatory macrophages from monocytes is characterized by an orderly integration of epigenetic and transcriptional regulatory mechanisms guided by lineage-determining transcription factors such as PU.1. Further activation of macrophages leads to a stimulus- or microenvironment-specific signal integration with subsequent transcriptional control established by the action of tissue- or signal-associated transcription factors. Here, we assess four histone modifications during human macrophage activation and integrate this information with the gene expression data from 28 different macrophage activation conditions in combination with GM-CSF. Bioinformatically, for inflammatory macrophages we define a unique network of transcriptional and epigenetic regulators (TRs), which was characterized by accessible promoters independent of the activation signal. In contrast to the general accessibility of promoters of TRs, mRNA expression of central TRs belonging to the TR network displayed stimulus-specific expression patterns, indicating a second level of transcriptional regulation beyond epigenetic chromatin changes. In contrast, stringent integration of epigenetic and transcriptional regulation was observed in networks of TRs established from somatic tissues and tissue macrophages. In these networks, clusters of TRs with permissive histone marks were associated with high gene expression whereas clusters with repressive chromatin marks were associated with absent gene expression. Collectively, these results support that macrophage activation during inflammation in contrast to lineage determination is mainly regulated transcriptionally by a pre-defined TR network.
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Affiliation(s)
- Susanne V Schmidt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Wolfgang Krebs
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Jia Xue
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kevin Baßler
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Patrick Günther
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Anna-Lena Hardt
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Hartmut Schultze
- Schultze Know How Beteiligungsgesellschaft mbH, Kirschblütenweg 2, 53639 Königswinter, Germany
| | - Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Kathrin Klee
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Heidi Theis
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Michael Kraut
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Marc Beyer
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany
- German Center for Neurodegenerative Diseases, 53175 Bonn, Germany
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DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia. Nat Genet 2016; 48:253-64. [PMID: 26780610 DOI: 10.1038/ng.3488] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022]
Abstract
Charting differences between tumors and normal tissue is a mainstay of cancer research. However, clonal tumor expansion from complex normal tissue architectures potentially obscures cancer-specific events, including divergent epigenetic patterns. Using whole-genome bisulfite sequencing of normal B cell subsets, we observed broad epigenetic programming of selective transcription factor binding sites coincident with the degree of B cell maturation. By comparing normal B cells to malignant B cells from 268 patients with chronic lymphocytic leukemia (CLL), we showed that tumors derive largely from a continuum of maturation states reflected in normal developmental stages. Epigenetic maturation in CLL was associated with an indolent gene expression pattern and increasingly favorable clinical outcomes. We further uncovered that most previously reported tumor-specific methylation events are normally present in non-malignant B cells. Instead, we identified a potential pathogenic role for transcription factor dysregulation in CLL, where excess programming by EGR and NFAT with reduced EBF and AP-1 programming imbalances the normal B cell epigenetic program.
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71
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Sive JI, Basilico S, Hannah R, Kinston SJ, Calero-Nieto FJ, Göttgens B. Genome-scale definition of the transcriptional programme associated with compromised PU.1 activity in acute myeloid leukaemia. Leukemia 2016; 30:14-23. [PMID: 26126967 PMCID: PMC4705427 DOI: 10.1038/leu.2015.172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 05/15/2015] [Accepted: 06/15/2015] [Indexed: 11/09/2022]
Abstract
Transcriptional dysregulation is associated with haematological malignancy. Although mutations of the key haematopoietic transcription factor PU.1 are rare in human acute myeloid leukaemia (AML), they are common in murine models of radiation-induced AML, and PU.1 downregulation and/or dysfunction has been described in human AML patients carrying the fusion oncogenes RUNX1-ETO and PML-RARA. To study the transcriptional programmes associated with compromised PU.1 activity, we adapted a Pu.1-mutated murine AML cell line with an inducible wild-type PU.1. PU.1 induction caused transition from leukaemia phenotype to monocytic differentiation. Global binding maps for PU.1, CEBPA and the histone mark H3K27Ac with and without PU.1 induction showed that mutant PU.1 retains DNA-binding ability, but the induction of wild-type protein dramatically increases both the number and the height of PU.1-binding peaks. Correlating chromatin immunoprecipitation (ChIP) Seq with gene expression data, we found that PU.1 recruitment coupled with increased histone acetylation induces gene expression and activates a monocyte/macrophage transcriptional programme. PU.1 induction also caused the reorganisation of a subgroup of CEBPA binding peaks. Finally, we show that the PU.1 target gene set defined in our model allows the stratification of primary human AML samples, shedding light on both known and novel AML subtypes that may be driven by PU.1 dysfunction.
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Affiliation(s)
- J I Sive
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - S Basilico
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - R Hannah
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - S J Kinston
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - F J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - B Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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72
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Schultze JL, Schmidt SV. Molecular features of macrophage activation. Semin Immunol 2015; 27:416-23. [DOI: 10.1016/j.smim.2016.03.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
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73
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Doxaki C, Kampranis SC, Eliopoulos AG, Spilianakis C, Tsatsanis C. Coordinated Regulation of miR-155 and miR-146a Genes during Induction of Endotoxin Tolerance in Macrophages. THE JOURNAL OF IMMUNOLOGY 2015; 195:5750-61. [DOI: 10.4049/jimmunol.1500615] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 10/07/2015] [Indexed: 12/12/2022]
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Pacheco MP, John E, Kaoma T, Heinäniemi M, Nicot N, Vallar L, Bueb JL, Sinkkonen L, Sauter T. Integrated metabolic modelling reveals cell-type specific epigenetic control points of the macrophage metabolic network. BMC Genomics 2015; 16:809. [PMID: 26480823 PMCID: PMC4617894 DOI: 10.1186/s12864-015-1984-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 10/06/2015] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The reconstruction of context-specific metabolic models from easily and reliably measurable features such as transcriptomics data will be increasingly important in research and medicine. Current reconstruction methods suffer from high computational effort and arbitrary threshold setting. Moreover, understanding the underlying epigenetic regulation might allow the identification of putative intervention points within metabolic networks. Genes under high regulatory load from multiple enhancers or super-enhancers are known key genes for disease and cell identity. However, their role in regulation of metabolism and their placement within the metabolic networks has not been studied. METHODS Here we present FASTCORMICS, a fast and robust workflow for the creation of high-quality metabolic models from transcriptomics data. FASTCORMICS is devoid of arbitrary parameter settings and due to its low computational demand allows cross-validation assays. Applying FASTCORMICS, we have generated models for 63 primary human cell types from microarray data, revealing significant differences in their metabolic networks. RESULTS To understand the cell type-specific regulation of the alternative metabolic pathways we built multiple models during differentiation of primary human monocytes to macrophages and performed ChIP-Seq experiments for histone H3 K27 acetylation (H3K27ac) to map the active enhancers in macrophages. Focusing on the metabolic genes under high regulatory load from multiple enhancers or super-enhancers, we found these genes to show the most cell type-restricted and abundant expression profiles within their respective pathways. Importantly, the high regulatory load genes are associated to reactions enriched for transport reactions and other pathway entry points, suggesting that they are critical regulatory control points for cell type-specific metabolism. CONCLUSIONS By integrating metabolic modelling and epigenomic analysis we have identified high regulatory load as a common feature of metabolic genes at pathway entry points such as transporters within the macrophage metabolic network. Analysis of these control points through further integration of metabolic and gene regulatory networks in various contexts could be beneficial in multiple fields from identification of disease intervention strategies to cellular reprogramming.
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Affiliation(s)
- Maria Pires Pacheco
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Elisabeth John
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Tony Kaoma
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211, Kuopio, Finland.
| | - Nathalie Nicot
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Laurent Vallar
- Genomics Research Unit, Luxembourg Institute of Health, L-1526, Luxembourg, Luxembourg.
| | - Jean-Luc Bueb
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
| | - Lasse Sinkkonen
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367, Belvaux, Luxembourg.
| | - Thomas Sauter
- Life Sciences Research Unit, University of Luxembourg, 162a, Avenue de la Faïencerie, L-1511, Luxembourg, Luxembourg.
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Shi L, Zhang Z, Song L, Leung YT, Petri MA, Sullivan KE. Monocyte enhancers are highly altered in systemic lupus erythematosus. Epigenomics 2015; 7:921-35. [PMID: 26442457 DOI: 10.2217/epi.15.47] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Histone modifications set transcriptional competency and can perpetuate pathologic expression patterns. We defined systemic lupus erythematosus (SLE)-specific changes in H3K4me3 and K3K27me3, histone marks of gene activation and repression, respectively. METHODS We used ChIP-seq to define histone modifications in monocytes from SLE patients and controls. RESULTS Both promoters and enhancers exhibited significant changes in histone methylation in SLE. Regions with differential H3K4me3 in SLE were significantly enriched in potential interferon-related transcription factor binding sites and pioneer transcription factor sites. CONCLUSION Enhancer activation defines the character of the cell and our data support extensive disease effects in monocytes, a particularly plastic lineage. Type I interferons not only drive altered gene expression but may also alter the character of the cell through chromatin modifications.
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Affiliation(s)
- Lihua Shi
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- The Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 1910, USA
| | - Li Song
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Yiu Tak Leung
- Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kathleen E Sullivan
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
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Zeller T, Haase T, Müller C, Riess H, Lau D, Zeller S, Krause J, Baumert J, Pless O, Dupuis J, Wild PS, Eleftheriadis M, Waldenberger M, Zeilinger S, Ziegler A, Peters A, Tiret L, Proust C, Marzi C, Munzel T, Strauch K, Prokisch H, Lackner KJ, Herder C, Thorand B, Benjamin EJ, Blankenberg S, Koenig W, Schnabel RB. Molecular Characterization of the NLRC4 Expression in Relation to Interleukin-18 Levels. ACTA ACUST UNITED AC 2015; 8:717-26. [PMID: 26362438 DOI: 10.1161/circgenetics.115.001079] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 08/24/2015] [Indexed: 01/27/2023]
Abstract
BACKGROUND Interleukin-18 (IL-18) is a pleiotropic cytokine centrally involved in the cytokine cascade with complex immunomodulatory functions in innate and acquired immunity. Circulating IL-18 concentrations are associated with type 2 diabetes mellitus, cardiovascular events, and diverse inflammatory and autoimmune disorders. METHODS AND RESULTS To identify causal variants affecting circulating IL-18 concentrations, we applied various omics and molecular biology approaches. By genome-wide association study, we confirmed association of IL-18 levels with a single nucleotide polymorphism in the untranslated exon 2 of the inflammasome component NLRC4 (NLR family, caspase recruitment domain-containing 4) gene on chromosome 2 (rs385076; P=2.4 × 10(-45)). Subsequent molecular analyses by gene expression analysis and reporter gene assays indicated an effect of rs385076 on NLRC4 expression and differential isoform usage by modulating binding of the transcription factor PU.1. CONCLUSIONS Our study provides evidence for the functional causality of single nucleotide polymorphism rs385076 within the NLRC4 gene in relation to IL-18 activation.
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Nguyen MLT, Jones SA, Prier JE, Russ BE. Transcriptional Enhancers in the Regulation of T Cell Differentiation. Front Immunol 2015; 6:462. [PMID: 26441967 PMCID: PMC4563239 DOI: 10.3389/fimmu.2015.00462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/24/2015] [Indexed: 12/24/2022] Open
Abstract
The changes in phenotype and function that characterize the differentiation of naïve T cells to effector and memory states are underscored by large-scale, coordinated, and stable changes in gene expression. In turn, these changes are choreographed by the interplay between transcription factors and epigenetic regulators that act to restructure the genome, ultimately ensuring lineage-appropriate gene expression. Here, we focus on the mechanisms that control T cell differentiation, with a particular focus on the role of regulatory elements encoded within the genome, known as transcriptional enhancers (TEs). We discuss the central role of TEs in regulating T cell differentiation, both in health and disease.
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Affiliation(s)
- Michelle L T Nguyen
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
| | - Sarah A Jones
- Monash University Centre for Inflammatory Disease, School of Clinical Sciences at Monash Health , Melbourne, VIC , Australia
| | - Julia E Prier
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
| | - Brendan E Russ
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne , Melbourne, VIC , Australia
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Pundhir S, Poirazi P, Gorodkin J. Emerging applications of read profiles towards the functional annotation of the genome. Front Genet 2015; 6:188. [PMID: 26042150 PMCID: PMC4437211 DOI: 10.3389/fgene.2015.00188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/06/2015] [Indexed: 12/21/2022] Open
Abstract
Functional annotation of the genome is important to understand the phenotypic complexity of various species. The road toward functional annotation involves several challenges ranging from experiments on individual molecules to large-scale analysis of high-throughput sequencing (HTS) data. HTS data is typically a result of the protocol designed to address specific research questions. The sequencing results in reads, which when mapped to a reference genome often leads to the formation of distinct patterns (read profiles). Interpretation of these read profiles is essential for their analysis in relation to the research question addressed. Several strategies have been employed at varying levels of abstraction ranging from a somewhat ad hoc to a more systematic analysis of read profiles. These include methods which can compare read profiles, e.g., from direct (non-sequence based) alignments to classification of patterns into functional groups. In this review, we highlight the emerging applications of read profiles for the annotation of non-coding RNA and cis-regulatory elements (CREs) such as enhancers and promoters. We also discuss the biological rationale behind their formation.
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Affiliation(s)
- Sachin Pundhir
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences (IKVH), University of Copenhagen Frederiksberg C, Denmark
| | - Panayiota Poirazi
- Computational Biology Lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas Heraklion, Greece
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences (IKVH), University of Copenhagen Frederiksberg C, Denmark
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Reschen ME, Gaulton KJ, Lin D, Soilleux EJ, Morris AJ, Smyth SS, O'Callaghan CA. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet 2015; 11:e1005061. [PMID: 25835000 PMCID: PMC4383549 DOI: 10.1371/journal.pgen.1005061] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/09/2015] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influence disease through altered transcriptional regulation in disease-relevant cell types. We explored changes in transcriptional regulation during a key pathophysiological event in CAD, the environmental lipid-induced transformation of macrophages to lipid-laden foam cells. We used a combination of open chromatin mapping with formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and enhancer and transcription factor mapping using chromatin immuno-precipitation (ChIP-seq) in primary human macrophages before and after exposure to atherogenic oxidized low-density lipoprotein (oxLDL), with resultant foam cell formation. OxLDL-induced foam cell formation was associated with changes in a subset of open chromatin and active enhancer sites that strongly correlated with expression changes of nearby genes. OxLDL-regulated enhancers were enriched for several transcription factors including C/EBP-beta, which has no previously documented role in foam cell formation. OxLDL exposure up-regulated C/EBP-beta expression and increased genomic binding events, most prominently around genes involved in inflammatory response pathways. Variants at CAD-associated loci were significantly and specifically enriched in the subset of chromatin sites altered by oxLDL exposure, including rs72664324 in an oxLDL-induced enhancer at the PPAP2B locus. OxLDL increased C/EBP beta binding to this site and C/EBP beta binding and enhancer activity were stronger with the protective A allele of rs72664324. In addition, expression of the PPAP2B protein product LPP3 was present in foam cells in human atherosclerotic plaques and oxLDL exposure up-regulated LPP3 in macrophages resulting in increased degradation of pro-inflammatory mediators. Our results demonstrate a genetic mechanism contributing to CAD risk at the PPAP2B locus and highlight the value of studying epigenetic changes in disease processes involving pathogenic environmental stimuli. Coronary artery disease is a complex disease where over 40 genomic loci contributing to genetic risk have been identified. However, identifying the precise variants, genomic elements and genes that mediate this risk at each locus has proved challenging. We hypothesized that some genetic risk variants may influence a key step in development of coronary artery disease, which occurs when macrophages encounter environmentally-derived lipid. These cells take up lipid and accumulate in atherosclerotic plaques in the walls of blood vessels where they contribute to the inflammatory atherosclerotic disease process. Therefore, we studied the effects of this lipid exposure on the genomic activity of these cells. Environmental lipid exposure triggered changes in transcriptional regulation and gene expression. Variants at coronary artery disease risk loci were enriched for genomic regions altered by lipid exposure. We studied one such risk variant rs72664324 in detail and found that it altered binding of the C/EBP-beta transcription factor and altered expression of the PPAP2B gene. PPAP2B encodes an enzyme that degrades pro-inflammatory substances. Our study demonstrates a hitherto unknown genetic mechanism underlying atherosclerotic heart disease and demonstrates the value of studying changes in transcriptional regulation in key disease processes involving environmental influences.
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Affiliation(s)
- Michael E. Reschen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth J. Soilleux
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford and Department of Cellular Pathology, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
| | - Susan S. Smyth
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
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80
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He G, Tolic A, Bashkin JK, Poon GMK. Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors. Nucleic Acids Res 2015; 43:4322-31. [PMID: 25824951 PMCID: PMC4417174 DOI: 10.1093/nar/gkv267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 01/09/2023] Open
Abstract
The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs’ binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs.
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Affiliation(s)
- Gaofei He
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Ana Tolic
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
| | - James K Bashkin
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Gregory M K Poon
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
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81
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Schönheit J, Leutz A, Rosenbauer F. Chromatin Dynamics during Differentiation of Myeloid Cells. J Mol Biol 2015; 427:670-87. [DOI: 10.1016/j.jmb.2014.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 08/05/2014] [Accepted: 08/20/2014] [Indexed: 12/23/2022]
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Chan CH, Fang C, Yarilina A, Prinjha RK, Qiao Y, Ivashkiv LB. BET bromodomain inhibition suppresses transcriptional responses to cytokine-Jak-STAT signaling in a gene-specific manner in human monocytes. Eur J Immunol 2014; 45:287-297. [PMID: 25345375 DOI: 10.1002/eji.201444862] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/17/2014] [Accepted: 10/21/2014] [Indexed: 11/12/2022]
Abstract
Disruption of the interaction of bromo and extraterminal (BET) proteins with acetylated histones using small molecule inhibitors suppresses Myc-driven cancers and TLR-induced inflammation in mouse models. The predominant mechanism of BET inhibitor action is to suppress BET-mediated recruitment of positive transcription elongation factor b and, thus, transcription elongation. We investigated the effects of BET inhibitor I-BET151 on transcriptional responses to TLR4 and TNF in primary human monocytes and also on responses to cytokines IFN-β, IFN-γ, IL-4, and IL-10, which activate the JAK-STAT signaling pathway and are important for monocyte polarization and inflammatory diseases. I-BET151 suppressed TLR4- and TNF-induced IFN responses by diminishing both autocrine IFN-β expression and transcriptional responses to IFN-β. I-BET151 inhibited cytokine-induced transcription of STAT targets in a gene-specific manner without affecting STAT activation or recruitment. This inhibition was independent of Myc or other upstream activators. IFN-stimulated gene transcription is regulated primarily at the level of transcription initiation. Accordingly, we found that I-BET151 suppressed the recruitment of transcriptional machinery to the CXCL10 promoter and an upstream enhancer. Our findings suggest that BET inhibition reduces inflammation partially through suppressing cytokine activity and expands the understanding of the inhibitory and potentially selective immunosuppressive effects of inhibiting BET proteins.
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Affiliation(s)
- Chun Hin Chan
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Celestia Fang
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Anna Yarilina
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Rab K Prinjha
- GlaxoSmithKline, Epinova DPU, Stevenage, United Kingdom
| | - Yu Qiao
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Center for Genomics Research, Hospital for Special Surgery, New York, New York, USA.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
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Genome-wide identification of hypoxia-inducible factor-1 and -2 binding sites in hypoxic human macrophages alternatively activated by IL-10. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:10-22. [PMID: 25450522 DOI: 10.1016/j.bbagrm.2014.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/21/2014] [Accepted: 10/29/2014] [Indexed: 12/14/2022]
Abstract
Macrophages (MΦ) often accumulate in hypoxic areas, where they significantly influence disease progression. Anti-inflammatory cytokines, such as IL-10, generate alternatively activated macrophages that support tumor growth. To understand how alternative activation affects the transcriptional profile of hypoxic macrophages, we globally mapped binding sites of hypoxia-inducible factor (HIF)-1α and HIF-2α in primary human monocyte-derived macrophages prestimulated with IL-10. 713 HIF-1 and 795 HIF-2 binding sites were identified under hypoxia. Pretreatment with IL-10 altered the binding pattern, with 120 new HIF-1 and 188 new HIF-2 binding sites emerging. HIF-1 binding was most prominent in promoters, while HIF-2 binding was more abundant in enhancer regions. Comparison of ChIP-seq data obtained in other cells revealed a highly cell type specific binding of HIF. In MΦ HIF binding occurred preferentially in already active enhancers or promoters. To assess the roles of HIF on gene expression, primary human macrophages were treated with siRNA against HIF-1α or HIF-2α, followed by genome-wide gene expression analysis. Comparing mRNA expression to the HIF binding profile revealed a significant enrichment of hypoxia-inducible genes previously identified by ChIP-seq. Analysis of gene expression under hypoxia alone and hypoxia/IL-10 showed the enhanced induction of a set of genes including PLOD2 and SLC2A3, while another group including KDM3A and ADM remained unaffected or was reduced by IL-10. Taken together IL-10 influences the DNA binding pattern of HIF and the level of gene induction.
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Lin HS, Gong JN, Su R, Chen MT, Song L, Shen C, Wang F, Ma YN, Zhao HL, Yu J, Li WW, Huang LX, Xu XH, Zhang JW. miR-199a-5p inhibits monocyte/macrophage differentiation by targeting the activin A type 1B receptor gene and finally reducing C/EBPα expression. J Leukoc Biol 2014; 96:1023-35. [PMID: 25258381 DOI: 10.1189/jlb.1a0514-240r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
miRNAs are short, noncoding RNAs that regulate expression of target genes at post-transcriptional levels and function in many important cellular processes, including differentiation, proliferation, etc. In this study, we observed down-regulation of miR-199a-5p during monocyte/macrophage differentiation of HL-60 and THP-1 cells, as well as human CD34(+) HSPCs. This down-regulation of miR-199a-5p resulted from the up-regulation of PU.1 that was demonstrated to regulate transcription of the miR-199a-2 gene negatively. Overexpression of miR-199a-5p by miR-199a-5p mimic transfection or lentivirus-mediated gene transfer significantly inhibited monocyte/macrophage differentiation of the cell lines or HSPCs. The mRNA encoding an ACVR1B was identified as a direct target of miR-199a-5p. Gradually increased ACVR1B expression level was detected during monocyte/macrophage differentiation of the leukemic cell lines and HSPCs, and knockdown of ACVR1B resulted in inhibition of monocyte/macrophage differentiation of HL-60 and THP-1 cells, which suggested that ACVR1B functions as a positive regulator of monocyte/macrophage differentiation. We demonstrated that miR-199a-5p overexpression or ACVR1B knockdown promoted proliferation of THP-1 cells through increasing phosphorylation of Rb. We also demonstrated that the down-regulation of ACVR1B reduced p-Smad2/3, which resulted in decreased expression of C/EBPα, a key regulator of monocyte/macrophage differentiation, and finally, inhibited monocyte/macrophage differentiation.
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Affiliation(s)
- Hai-Shuang Lin
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia-Nan Gong
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Su
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ming-Tai Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Song
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Shen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fang Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan-Ni Ma
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua-Lu Zhao
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei-Wei Li
- Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China
| | - Li-Xia Huang
- First Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, China; and
| | - Xin-Hua Xu
- Taizhou Cancer Hospital, Zhejiang Province, China
| | - Jun-Wu Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China;
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85
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Carpenter S, Fitzgerald KA. Transcription of inflammatory genes: long noncoding RNA and beyond. J Interferon Cytokine Res 2014; 35:79-88. [PMID: 25250698 DOI: 10.1089/jir.2014.0120] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The innate immune system must coordinate elaborate signaling pathways to turn on expression of hundreds of genes to provide protection against pathogens and resolve acute inflammation. Multiple genes within distinct functional categories are coordinately and temporally regulated by transcriptional on and off switches in response to distinct external stimuli. Three classes of transcription factors act together with transcriptional coregulators and chromatin-modifying complexes to control these programs. In addition, newer studies implicate long noncoding RNA (lncRNA) as additional regulators of these responses. LncRNAs promote, fine-tune, and restrain the inflammatory program. In this study, we provide an overview of gene regulation and the emerging importance of lncRNAs in the immune system.
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Affiliation(s)
- Susan Carpenter
- 1 Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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86
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Huang E, Wells CA. The ground state of innate immune responsiveness is determined at the interface of genetic, epigenetic, and environmental influences. THE JOURNAL OF IMMUNOLOGY 2014; 193:13-9. [PMID: 24951823 DOI: 10.4049/jimmunol.1303410] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Monocytes and macrophages form the major cellular component of the innate immune system, with roles in tissue development, homeostasis, and host defense against infection. Environmental factors were shown to play a significant part in determining innate immune responsiveness, and this included systemic conditions, such as circulating glucose levels, gut microflora, time of year, and even diurnal rhythm, which had a direct impact on innate immune receptor expression. Although the underlying molecular processes are just beginning to emerge, it is clear that environmental factors may alter epigenetic states of peripheral blood monocytes and resident tissue macrophages. We conclude that some measure of cellular ground state must become an essential part of the analysis of myeloid responsiveness or infectious susceptibility.
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Affiliation(s)
- Edward Huang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia; and
| | - Christine Anne Wells
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia; and Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
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87
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Tamura I, Ohkawa Y, Sato T, Suyama M, Jozaki K, Okada M, Lee L, Maekawa R, Asada H, Sato S, Yamagata Y, Tamura H, Sugino N. Genome-wide analysis of histone modifications in human endometrial stromal cells. Mol Endocrinol 2014; 28:1656-69. [PMID: 25073104 DOI: 10.1210/me.2014-1117] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dramatic changes of gene expressions occur in human endometrial stromal cells (ESCs) during decidualization. The changes in gene expression are associated with changes of chromatin structure, which are regulated by histone modifications. Here we investigated genome-wide changes in histone modifications associated with decidualization in human ESCs using chromatin immunoprecipitation combined with next-generation sequencing. ESCs were incubated with estradiol and medroxyprogesterone acetate for 14 days to induce decidualization. The chromatin immunoprecipitation-sequence data showed that induction of decidualization increased H3K27ac and H3K4me3 signals in many genomic regions but decreased in only a few regions. Most of the H3K27ac-increased regions (80%) and half of the H3K4me3-increased regions were located in the distal promoter regions (more than 3 kb upstream or downstream of the transcription start site). RNA sequence showed that induction of decidualization up-regulated 881 genes, 223 of which had H3K27ac- or H3K4me3-increased regions in the proximal and distal promoter regions. Induction of decidualization increased the mRNA levels of these genes more than it increased the mRNA levels of genes without H3K27ac- or H3K4me3-increased regions. Pathway analysis revealed that up-regulated genes with the H3K27ac- or H3K4me3-increased regions were associated with the insulin signaling, which may be involved in glucose uptake that is necessary for ESCs to undergo decidualization. These results show that histone modification statuses on a genome-wide basis change in human ESCs during decidualization. The main changes of histone modifications are increases of H3K27ac and H3K4me3 in both the proximal and distal promoter regions, which are involved in the up-regulation of gene expression that occurs during decidualization.
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Affiliation(s)
- Isao Tamura
- Department of Obstetrics and Gynecology (I.T., K.J., M.O., L.L., R.M., H.A., S.S., Y.Y., H.T., N.S.), Yamaguchi University Graduate School of Medicine, Ube 755-8505, Japan; Department of Advanced Initiative Medicine (Y.O.), Faculty of Medicine, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan; and Division of Bioinformatics (T.S., M.S.), Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
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88
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Wang S, Linde MH, Munde M, Carvalho VD, Wilson WD, Poon GMK. Mechanistic heterogeneity in site recognition by the structurally homologous DNA-binding domains of the ETS family transcription factors Ets-1 and PU.1. J Biol Chem 2014; 289:21605-16. [PMID: 24952944 DOI: 10.1074/jbc.m114.575340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a "dry" mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1 · DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
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Affiliation(s)
- Shuo Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Miles H Linde
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - Manoj Munde
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Victor D Carvalho
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - W David Wilson
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Gregory M K Poon
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
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89
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Damm F, Mylonas E, Cosson A, Yoshida K, Della Valle V, Mouly E, Diop M, Scourzic L, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Kikushige Y, Davi F, Lambert J, Gautheret D, Merle-Béral H, Sutton L, Dessen P, Solary E, Akashi K, Vainchenker W, Mercher T, Droin N, Ogawa S, Nguyen-Khac F, Bernard OA. Acquired Initiating Mutations in Early Hematopoietic Cells of CLL Patients. Cancer Discov 2014; 4:1088-101. [DOI: 10.1158/2159-8290.cd-14-0104] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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90
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Abstract
Key Points
In-depth regulome analysis of human monocyte subsets, including transcription and enhancer profiling. Description of metabolomic differences in human monocyte subsets.
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91
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Karpurapu M, Ranjan R, Deng J, Chung S, Lee YG, Xiao L, Nirujogi TS, Jacobson JR, Park GY, Christman JW. Krüppel like factor 4 promoter undergoes active demethylation during monocyte/macrophage differentiation. PLoS One 2014; 9:e93362. [PMID: 24695324 PMCID: PMC3973678 DOI: 10.1371/journal.pone.0093362] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 03/05/2014] [Indexed: 11/25/2022] Open
Abstract
The role of different lineage specific transcription factors in directing hematopoietic cell fate towards myeloid lineage is well established but the status of epigenetic modifications has not been defined during this important developmental process. We used non proliferating, PU.1 inducible myeloid progenitor cells and differentiating bone marrow derived macrophages to study the PU.1 dependent KLF4 transcriptional regulation and its promoter demethylation during monocyte/macrophage differentiation. Expression of KLF4 was regulated by active demethylation of its promoter and PU.1 specifically bound to KLF4 promoter oligo harboring the PU.1 consensus sequence. Methylation specific quantitative PCR and Bisulfite sequencing indicated demethylation of CpG residues most proximal to the transcription start site of KLF4 promoter. Cloned KLF4 promoter in pGL3 Luciferase and CpG free pcpgf-bas vectors showed accentuated reporter activity when co-transfected with the PU.1 expression vector. In vitro methylation of both KLF4 promoter oligo and cloned KLF4 promoter vectors showed attenuated in vitro DNA binding activity and Luciferase/mouse Alkaline phosphotase reporter activity indicating the negative influence of KLF4 promoter methylation on PU.1 binding. The Cytosine deaminase, Activation Induced Cytidine Deaminase (AICDA) was found to be critical for KLF4 promoter demethylation. More importantly, knock down of AICDA resulted in blockade of KLF4 promoter demethylation, decreased F4/80 expression and other phenotypic characters of macrophage differentiation. Our data proves that AICDA mediated active demethylation of the KLF4 promoter is necessary for transcriptional regulation of KLF4 by PU.1 during monocyte/macrophage differentiation.
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Affiliation(s)
- Manjula Karpurapu
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
| | - Ravi Ranjan
- Section of Pulmonary, Critical Care, Sleep and Allergy, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Jing Deng
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
| | - Sangwoon Chung
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
| | - Yong Gyu Lee
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
| | - Lei Xiao
- Section of Pulmonary, Critical Care, Sleep and Allergy, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Teja Srinivas Nirujogi
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
| | - Jeffrey R. Jacobson
- Institute for Personalized Respiratory Medicine, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Gye Young Park
- Section of Pulmonary, Critical Care, Sleep and Allergy, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - John W Christman
- Section of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University Wexner Medical Center, Davis Heart and Lung Research Institute, Columbus, Ohio, United States of America
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92
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Affiliation(s)
- Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK.
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
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93
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Mokry M, Middendorp S, Wiegerinck CL, Witte M, Teunissen H, Meddens CA, Cuppen E, Clevers H, Nieuwenhuis EES. Many inflammatory bowel disease risk loci include regions that regulate gene expression in immune cells and the intestinal epithelium. Gastroenterology 2014; 146:1040-7. [PMID: 24333384 DOI: 10.1053/j.gastro.2013.12.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 11/30/2013] [Accepted: 12/03/2013] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The contribution of genetic factors to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin, targeted-sequencing, and genome-wide association studies. These studies identified many risk loci, and research is underway to identify causal variants. These studies have focused mainly on protein-coding genes. We investigated other functional elements in the human genome, such as regulatory regions. METHODS Using acetylated histone 3 lysine 27 chromatin immunoprecipitation and sequencing, we identified tens of thousands of potential regulatory regions that are active in intestinal epithelium (primary intestinal crypts and cultured organoids) isolated from resected material and from biopsies collected during ileo-colonoscopies and immune cells (monocytes, macrophages, CD34(+), CD4(+), and CD8(+)). We correlated these regions with susceptibility loci for IBD. RESULTS We have generated acetylated histone 3 lysine 27 profiles from primary intestinal epithelium and cultured organoids, which we have made publically available. We found that 45 of 163 single nucleotide polymorphisms (SNPs) associated with IBD overlap specifically with active regulatory elements. In addition, by taking strong linkage disequilibrium into account, another 47 IBD-associated SNPs colocalized with active regulatory elements through other SNPs in their vicinity. Altogether, 92 of 163 IBD-associated SNPs correlated with distinct active regulatory elements-a frequency 2.5- to 3.5-fold greater than that expected from random sampling. The variations in these SNPs often create or disrupt known binding motifs; they might affect the binding of transcriptional regulators to alter expression of regulated genes. CONCLUSIONS In addition to variants in protein coding genes, variants in noncoding DNA regulatory regions that are active in intestinal epithelium and immune cells are potentially involved in the pathogenesis of IBD.
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Affiliation(s)
- Michal Mokry
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine Middendorp
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline L Wiegerinck
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Merlijn Witte
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Hans Teunissen
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Claartje A Meddens
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands; Department of Medical Genetics, Medical Center Utrecht, Utrecht, The Netherlands
| | - Hans Clevers
- Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands
| | - Edward E S Nieuwenhuis
- Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
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94
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Abstract
Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.
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95
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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014; 507:455-461. [PMID: 24670763 PMCID: PMC5215096 DOI: 10.1038/nature12787] [Citation(s) in RCA: 1731] [Impact Index Per Article: 173.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 10/16/2013] [Indexed: 02/07/2023]
Abstract
Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.
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Affiliation(s)
- Robin Andersson
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Irene Miguel-Escalada
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ilka Hoof
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Jette Bornholdt
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Xiaobei Zhao
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Christian Schmidl
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Takahiro Suzuki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Evgenia Ntini
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Erik Arner
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Eivind Valen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- Department of Molecular and Cellular Biology, Harvard University, USA
| | - Kang Li
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Lucia Schwarzfischer
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Berit Lilje
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Nicolas Rapin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet and Danish Stem Cell Centre (DanStem), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Denmark
| | - Frederik Otzen Bagger
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet and Danish Stem Cell Centre (DanStem), University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
| | - Peter Refsing Andersen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Nicolas Bertin
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Owen Rackham
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - A. Maxwell Burroughs
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - J. Kenneth Baillie
- Roslin Institute, Edinburgh University, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Yuri Ishizu
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuri Shimizu
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shiori Maeda
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yutaka Negishi
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Christopher J. Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 64-121, Berkeley, CA 94720, USA
| | - Terrence F. Meehan
- EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD
| | - Timo Lassmann
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hideya Kawaji
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Naoto Kondo
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Jun Kawai
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Carsten O. Daub
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Stockholm, Sweden
| | - Peter Heutink
- Department of Clinical Genetics, VU University Medical Center, van der Boechorststraat 7, 1081 BT Amsterdam, Netherlands
| | - David A. Hume
- Roslin Institute, Edinburgh University, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, C.F. Møllers Alle 3, Bldg. 1130, DK-8000 Aarhus, Denmark
| | - Harukazu Suzuki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Ferenc Müller
- School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alistair R.R. Forrest
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Piero Carninci
- RIKEN OMICS Science Centre, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
- RIKEN Center for Life Science Technologies (Division of Genomic Technologies), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93042 Regensburg, Germany
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen, Denmark
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96
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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014. [DOI: 10.10.1038/nature12787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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97
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The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood 2014; 123:e68-78. [PMID: 24671953 DOI: 10.1182/blood-2013-02-486944] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
CD4(+)CD25(+)FOXP3(+) human regulatory T cells (Tregs) are essential for self-tolerance and immune homeostasis. Here, we describe the promoterome of CD4(+)CD25(high)CD45RA(+) naïve and CD4(+)CD25(high)CD45RA(-) memory Tregs and their CD25(-) conventional T-cell (Tconv) counterparts both before and after in vitro expansion by cap analysis of gene expression (CAGE) adapted to single-molecule sequencing (HeliScopeCAGE). We performed comprehensive comparative digital gene expression analyses and revealed novel transcription start sites, of which several were validated as alternative promoters of known genes. For all in vitro expanded subsets, we additionally generated global maps of poised and active enhancer elements marked by histone H3 lysine 4 monomethylation and histone H3 lysine 27 acetylation, describe their cell type-specific motif signatures, and evaluate the role of candidate transcription factors STAT5, FOXP3, RUNX1, and ETS1 in both Treg- and Tconv-specific enhancer architectures. Network analyses of gene expression data revealed additional candidate transcription factors contributing to cell type specificity and a transcription factor network in Tregs that is dominated by FOXP3 interaction partners and targets. In summary, we provide a comprehensive and easily accessible resource of gene expression and gene regulation in human Treg and Tconv subpopulations.
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98
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Shi L, Song L, Fitzgerald M, Maurer K, Bagashev A, Sullivan KE. Noncoding RNAs and LRRFIP1 regulate TNF expression. THE JOURNAL OF IMMUNOLOGY 2014; 192:3057-67. [PMID: 24567534 DOI: 10.4049/jimmunol.1302063] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Noncoding RNAs have been implicated in the regulation of expression of numerous genes; however, the mechanism is not fully understood. We identified bidirectional, long noncoding RNAs upstream of the TNF gene using five different methods. They arose in a region where the repressors LRRFIP1, EZH2, and SUZ12 were demonstrated to bind, suggesting a role in repression. The noncoding RNAs were polyadenylated, capped, and chromatin associated. Knockdown of the noncoding RNAs was associated with derepression of TNF mRNA and diminished binding of LRRFIP1 to both RNA targets and chromatin. Overexpression of the noncoding RNAs led to diminished expression of TNF and recruitment of repressor proteins to the locus. One repressor protein, LRRFIP1, bound directly to the noncoding RNAs. These data place the noncoding RNAs upstream of TNF gene as central to the transcriptional regulation. They appear to serve as a platform for the assembly of a repressive complex.
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Affiliation(s)
- Lihua Shi
- Division of Allergy Immunology, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
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99
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Esterhuyse MM, Kaufmann SH. Diagnostic biomarkers are hidden in the infected host's epigenome. Expert Rev Mol Diagn 2013; 13:625-37. [PMID: 23895131 DOI: 10.1586/14737159.2013.811897] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The success of our immune system depends on its ability to react efficiently, which in turn is supported by a large degree of plasticity as well as memory. Some aspects of this plasticity and memory are now known to be under epigenetic control - determined both by default, during differentiation, and by responses to environmental factors, including infectious agents. Thus, epigenetic marks in the immune system can occur as predetermined or as responsive marks and as such can potentially serve as diagnostic markers for disease susceptibility and disease progression or treatment response. Here, the authors review some examples of epigenetic control and epigenetic marks during the differentiation process of the immune system and memory formation, followed by some examples of epigenetic marks in the immune system subsequent to infection. These are used to illustrate the potential use of epigenetic marks as diagnostic markers in adverse immune system conditions and treatment thereof.
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Affiliation(s)
- Maria M Esterhuyse
- Max Planck Institute for Infection Biology, Department of Immunology, Berlin, Germany
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100
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Kittan NA, Allen RM, Dhaliwal A, Cavassani KA, Schaller M, Gallagher KA, Carson WF, Mukherjee S, Grembecka J, Cierpicki T, Jarai G, Westwick J, Kunkel SL, Hogaboam CM. Cytokine induced phenotypic and epigenetic signatures are key to establishing specific macrophage phenotypes. PLoS One 2013; 8:e78045. [PMID: 24205083 PMCID: PMC3804553 DOI: 10.1371/journal.pone.0078045] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/08/2013] [Indexed: 11/18/2022] Open
Abstract
Macrophages (MΦ) play an essential role in innate immune responses and can either display a pro-inflammatory, classically activated phenotype (M1) or undergo an alternative activation program (M2) promoting immune regulation. M-CSF is used to differentiate monocytes into MΦ and IFN-γ or IL-4+IL-13 to further polarize these cells towards M1 or M2, respectively. Recently, differentiation using only GM-CSF or M-CSF has been described to induce a M1- or M2-like phenotype, respectively. In this study, we combined both approaches by differentiating human MΦ in GM-CSF or M-CSF followed by polarization with either IFN-γ or IL-4+IL-13. We describe the phenotypic differences between CD14(hi) CD163(hi) CD206(int) FOLR2-expressing M-CSF MΦ and CD14(lo) CD163(lo) CD206(hi) GM-CSF MΦ but show that both macrophage populations reacted similarly to further polarization with IFN-γ or IL-4+IL-13 with up- and down-regulation of common M1 and M2 marker genes. We also show that high expression of the mannose receptor (CD206), a marker of alternative activation, is a distinct feature of GM-CSF MΦ. Changes of the chromatin structure carried out by chromatin modification enzymes (CME) have been shown to regulate myeloid differentiation. We analyzed the expression patterns of CME during MΦ polarization and show that M1 up-regulate the histone methyltransferase MLL and demethylase KDM6B, while resting and M2 MΦ were characterized by DNA methyltransferases and histone deacetylases. We demonstrate that MLL regulates CXCL10 expression and that this effect could be abrogated using a MLL-Menin inhibitor. Taken together we describe the distinct phenotypic differences of GM-CSF or M-CSF MΦ and demonstrate that MΦ polarization is regulated by specific epigenetic mechanisms. In addition, we describe a novel role for MLL as marker for classical activation. Our findings provide new insights into MΦ polarization that could be helpful to distinguish MΦ activation states.
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Affiliation(s)
- Nicolai A. Kittan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ronald M. Allen
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Abhay Dhaliwal
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Karen A. Cavassani
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Matthew Schaller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katherine A. Gallagher
- Division of Vascular Surgery, University of Michigan Hospital, Ann Arbor, Michigan, United States of America
| | - William F. Carson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Sumanta Mukherjee
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Gabor Jarai
- Novartis Institutes of Biomedical Research, Respiratory Disease Area, Horsham, West Sussex, United Kingdom
| | - John Westwick
- Novartis Institutes of Biomedical Research, Respiratory Disease Area, Horsham, West Sussex, United Kingdom
| | - Steven L. Kunkel
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Cory M. Hogaboam
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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