51
|
Vitamin C and immune cell function in inflammation and cancer. Biochem Soc Trans 2018; 46:1147-1159. [PMID: 30301842 PMCID: PMC6195639 DOI: 10.1042/bst20180169] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/16/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022]
Abstract
Vitamin C (ascorbate) is maintained at high levels in most immune cells and can affect many aspects of the immune response. Intracellular levels generally respond to variations in plasma ascorbate availability, and a combination of inadequate intake and increased turnover during severe stress can result in low plasma ascorbate status. Intracellular ascorbate supports essential functions and, in particular, acts as an enzyme cofactor for Fe- or Cu-containing oxygenases. Newly discovered enzymes in this family regulate cell metabolism and epigenetics, and dysregulation of their activity can affect cell phenotype, growth and survival pathways, and stem cell phenotype. This brief overview details some of the recent advances in our understanding of how ascorbate availability can affect the hydroxylases controlling the hypoxic response and the DNA and histone demethylases. These processes play important roles in the regulation of the immune system, altering cell survival pathways, metabolism and functions.
Collapse
|
52
|
Salhab A, Nordström K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Müller F, Polansky JK, Cadenas C, G Hengstler J, Lengauer T, Manke T, Walter J. A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains. Genome Biol 2018; 19:150. [PMID: 30266094 PMCID: PMC6161375 DOI: 10.1186/s13059-018-1510-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them. Results Partially methylated domains are present in up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Each cell type has a distinct set of partially methylated domains, and genes expressed in such domains show a strong cell type effect. The methylation level varies between cell types with a more pronounced effect in differentiating and replicating cells. The lowest level of methylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA methylation within partially methylated domains tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expression. Characteristic combinations of heterochromatic signatures in partially methylated domains are linked to domains of early and middle S-phase and late S-G2 phases of DNA replication. Conclusions Partially methylated domains are prominent signatures of long-range epigenomic organization. Integrative analysis identifies them as important general, lineage- and cell type-specific topological features. Changes in partially methylated domains are hallmarks of cell differentiation, with decreased methylation levels and increased heterochromatic marks being linked to enhanced cell proliferation. In combination with broad histone marks, partially methylated domains demarcate distinct domains of late DNA replication. Electronic supplementary material The online version of this article (10.1186/s13059-018-1510-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Abdulrahman Salhab
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Karl Nordström
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Fidel Ramirez
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Julia K Polansky
- Berlin-Brandenburg Center for Regenerative Therapies at the Charité, Berlin, Germany.,University Medicine Berlin and German Rheumatism Research Centre, Berlin, Germany
| | - Cristina Cadenas
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Jan G Hengstler
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | | | - Jörn Walter
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany.
| |
Collapse
|
53
|
Russell‐Hallinan A, Watson CJ, Baugh JA. Epigenetics of Aberrant Cardiac Wound Healing. Compr Physiol 2018; 8:451-491. [DOI: 10.1002/cphy.c170029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
54
|
de Groot AE, Pienta KJ. Epigenetic control of macrophage polarization: implications for targeting tumor-associated macrophages. Oncotarget 2018; 9:20908-20927. [PMID: 29755698 PMCID: PMC5945509 DOI: 10.18632/oncotarget.24556] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/08/2017] [Indexed: 12/23/2022] Open
Abstract
The progression of cancer is a result of not only the growth of the malignant cells but also the behavior of other components of the tumor microenvironment (TME). Tumor-associated macrophages (TAMs) are key components of the TME that influence tumor growth and disease progression. TAMs can either inhibit or support tumor growth depending on their polarization to classically-activated macrophages (M1s) or alternatively-activated macrophages (M2s), respectively. Epigenetic regulation plays a significant role in determining this polarization and manipulating the epigenetic regulation in macrophages would provide a means for selectively targeting M2s thereby eliminating tumor-supporting TAMs while sparing tumor-inhibiting M1 TAMs. Many pharmacologic modulators of epigenetic enzymes are currently used clinically and could be repurposed for treating tumors with high TAM infiltrate. While much research involving epigenetic enzymes and their modulators has been performed in M1s, significantly less is known about the epigenetic regulation of M2s. This review highlights the field’s current knowledge of key epigenetic enzymes and their pharmacologic modulators known to influence macrophage polarization.
Collapse
Affiliation(s)
- Amber E de Groot
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| |
Collapse
|
55
|
|
56
|
Giuranna J, Diebels I, Hinney A. Polygene Varianten und Epigenetik bei Adipositas. MED GENET-BERLIN 2017. [DOI: 10.1007/s11825-017-0156-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zusammenfassung
Hintergrund
Durch molekulargenetische Analysen wurde eine kleine Anzahl von Hauptgenen identifiziert, die Übergewicht (Body Mass Index, BMI ≥ 25 kg/m2) und Adipositas (BMI ≥ 30 kg/m2) bei Menschen mit bedingen können. Die zugrunde liegenden Mutationen sind selten. Die genetische Prädisposition zur Entwicklung einer Adipositas ist meist polygener Natur.
Ziel der Arbeit
Darstellung der polygenen Formen der Adipositas und epigenetischer Befunde.
Material und Methoden
Literaturübersicht.
Ergebnisse und Diskussion
Metaanalysen genomweiter Assoziationsstudien (GWAMA) haben bisher mehr als 100 Polygene oder polygene Loci identifiziert, die genomweit mit dem BMI assoziiert sind. Jedes einzelne Polygen leistet nur einen kleinen Beitrag zur Entwicklung einer Adipositas. Effektstärken liegen im Bereich von ca. 100 g bis 1,5 kg. Eine Reihe solcher prädisponierenden Genvarianten (Allele) findet sich bei adipösen Probanden. Allerdings tragen auch normalgewichtige und schlanke Individuen diese Allele, wenn auch in geringerer Frequenz. Diese Allele können durch statistische Analysen als Adipositas-Risikoallele identifiziert und validiert werden. Vor Kurzem haben sogenannte Cross-Disorder- und Cross-Phänotyp-Analysen zur Identifizierung von Genen geführt, die nicht allein durch Analysen der einzelnen Erkrankungen/Phänotypen nachgewiesen werden konnten. Funktionelle in-vitro- und in-vivo-Studien der GWAS-abgeleiteten Polygene könnten zu einem besseren Verständnis der molekulargenetischen Mechanismen der Körpergewichtsregulation führen. Erste genomweite Methylierungsmusteranalysen und Studien zu metastabilen Epiallelen tragen zudem zu einem besseren Verständnis der Pathomechanismen der Adipositas bei.
Collapse
Affiliation(s)
- Johanna Giuranna
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
| | - Inga Diebels
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
| | - Anke Hinney
- Aff1 0000 0001 2187 5445 grid.5718.b Klinik für Psychiatrie, Psychosomatik und Psychotherapie des Kindes- und Jugendalters, Universitätsklinikum Essen (AöR) Universität Duisburg-Essen Virchowstr. 171 45147 Essen Deutschland
| |
Collapse
|
57
|
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.
Collapse
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
| |
Collapse
|
58
|
Schröder C, Leitão E, Wallner S, Schmitz G, Klein-Hitpass L, Sinha A, Jöckel KH, Heilmann-Heimbach S, Hoffmann P, Nöthen MM, Steffens M, Ebert P, Rahmann S, Horsthemke B. Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function. Epigenetics Chromatin 2017; 10:37. [PMID: 28747224 PMCID: PMC5530492 DOI: 10.1186/s13072-017-0144-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/20/2017] [Indexed: 01/23/2023] Open
Abstract
Background There is increasing evidence for inter-individual methylation differences at CpG dinucleotides in the human genome, but the regional extent and function of these differences have not yet been studied in detail. For identifying regions of common methylation differences, we used whole genome bisulfite sequencing data of monocytes from five donors and a novel bioinformatic strategy. Results We identified 157 differentially methylated regions (DMRs) with four or more CpGs, almost none of which has been described before. The DMRs fall into different chromatin states, where methylation is inversely correlated with active, but not repressive histone marks. However, methylation is not correlated with the expression of associated genes. High-resolution single nucleotide polymorphism (SNP) genotyping of the five donors revealed evidence for a role of cis-acting genetic variation in establishing methylation patterns. To validate this finding in a larger cohort, we performed genome-wide association studies (GWAS) using SNP genotypes and 450k array methylation data from blood samples of 1128 individuals. Only 30/157 (19%) DMRs include at least one 450k CpG, which shows that these arrays miss a large proportion of DNA methylation variation. In most cases, the GWAS peak overlapped the CpG position, and these regions are enriched for CREB group, NF-1, Sp100 and CTCF binding motifs. In two cases, there was tentative evidence for a trans-effect by KRAB zinc finger proteins. Conclusions Allele-specific DNA methylation occurs in discrete chromosomal regions and is driven by genetic variation in cis and trans, but in general has little effect on gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0144-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Christopher Schröder
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Elsa Leitão
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Stefan Wallner
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Kiel University, University Hospital, Kiel, Germany
| | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.,Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine, University Hospital of Bonn, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Peter Ebert
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, Saarland Informatics Campus, Saarbrücken, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University of Duisburg-Essen, University Hospital Essen, Hufelandstraße 55, 45147, Essen, Germany.
| |
Collapse
|
59
|
Ancey PB, Ecsedi S, Lambert MP, Talukdar FR, Cros MP, Glaise D, Narvaez DM, Chauvet V, Herceg Z, Corlu A, Hernandez-Vargas H. TET-Catalyzed 5-Hydroxymethylation Precedes HNF4A Promoter Choice during Differentiation of Bipotent Liver Progenitors. Stem Cell Reports 2017; 9:264-278. [PMID: 28648900 PMCID: PMC5511103 DOI: 10.1016/j.stemcr.2017.05.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 12/17/2022] Open
Abstract
Understanding the processes that govern liver progenitor cell differentiation has important implications for the design of strategies targeting chronic liver diseases, whereby regeneration of liver tissue is critical. Although DNA methylation (5mC) and hydroxymethylation (5hmC) are highly dynamic during early embryonic development, less is known about their roles at later stages of differentiation. Using an in vitro model of hepatocyte differentiation, we show here that 5hmC precedes the expression of promoter 1 (P1)-dependent isoforms of HNF4A, a master transcription factor of hepatocyte identity. 5hmC and HNF4A expression from P1 are dependent on ten-eleven translocation (TET) dioxygenases. In turn, the liver pioneer factor FOXA2 is necessary for TET1 binding to the P1 locus. Both FOXA2 and TETs are required for the 5hmC-related switch in HNF4A expression. The epigenetic event identified here may be a key step for the establishment of the hepatocyte program by HNF4A.
Collapse
Affiliation(s)
- Pierre-Benoit Ancey
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Szilvia Ecsedi
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; MTA-DE Public Health Research Group, University of Debrecen, 4028 Debrecen, Hungary
| | - Marie-Pierre Lambert
- Epissage alternatif et progression tumorale, Centre de Recherche en Cancérologie de Lyon (CRCL), 28 rue Laennec, 69008 Lyon, France
| | - Fazlur Rahman Talukdar
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Marie-Pierre Cros
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Denise Glaise
- Inserm, Inra, UBL, Nutrition Metabolism and Cancer (NuMeCan), 35033 Rennes Cedex 9, France
| | - Diana Maria Narvaez
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France; Human Genetics Laboratory, Department of Biological Sciences, Universidad de Los Andes, Cr. 1 No. 18A-10 Building M1-2 Floor, Bogotá 110321, Colombia
| | - Veronique Chauvet
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France
| | - Anne Corlu
- Inserm, Inra, UBL, Nutrition Metabolism and Cancer (NuMeCan), 35033 Rennes Cedex 9, France
| | - Hector Hernandez-Vargas
- Epigenetics Group, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008 Lyon, France.
| |
Collapse
|
60
|
Teif VB, Mallm JP, Sharma T, Mark Welch DB, Rippe K, Eils R, Langowski J, Olins AL, Olins DE. Nucleosome repositioning during differentiation of a human myeloid leukemia cell line. Nucleus 2017; 8:188-204. [PMID: 28406749 PMCID: PMC5403151 DOI: 10.1080/19491034.2017.1295201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope). Nucleosome positions changed genome-wide, exhibiting a specific class of alterations involving nucleosome loss in extended (∼1kb) regions, pronounced in enhancers and promoters. Genes that lost nucleosomes at their promoters showed a tendency to be upregulated. On the other hand, nucleosome gain did not show simple effects on transcript levels. The average genome-wide nucleosome repeat length (NRL) did not change significantly with differentiation. However, we detected an approximate 10 bp NRL decrease around the haematopoietic transcription factor (TF) PU.1 and the architectural protein CTCF, suggesting an effect on NRL proximal to TF binding sites. Nucleosome occupancy changed in regions associated with active promoters in differentiated cells, compared with untreated HL-60/S4 cells. Epichromatin regions revealed an increased GC content and high nucleosome density compared with surrounding chromatin. Epichromatin showed depletion of major histone modifications and revealed enrichment with PML body-associated genes. In general, chromatin changes during HL-60/S4 differentiation appeared to be more localized to regulatory regions, compared with genome-wide changes among diverse cell types studied elsewhere.
Collapse
Affiliation(s)
- Vladimir B Teif
- a School of Biological Sciences , University of Essex, Wivenhoe Park , Colchester , UK
| | | | - Tanvi Sharma
- a School of Biological Sciences , University of Essex, Wivenhoe Park , Colchester , UK
| | - David B Mark Welch
- c Josephine Bay Paul Center for Comparative Molecular Biology and Evolution , Marine Biological Laboratory , Woods Hole , MA , USA
| | - Karsten Rippe
- b German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Roland Eils
- b German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Langowski
- b German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Ada L Olins
- d Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
| | - Donald E Olins
- d Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
| |
Collapse
|
61
|
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell 2017; 167:1145-1149. [PMID: 27863232 DOI: 10.1016/j.cell.2016.11.007] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal at http://www.cell.com/consortium/IHEC) highlight the coordinated achievements of IHEC teams to gather and interpret comprehensive epigenomic datasets to gain insights in the epigenetic control of cell states relevant for human health and disease. PAPERCLIP.
Collapse
|
62
|
Wu H, Fu S, Zhao M, Lu L, Lu Q. Dysregulation of Cell Death and Its Epigenetic Mechanisms in Systemic Lupus Erythematosus. Molecules 2016; 22:E30. [PMID: 28035990 PMCID: PMC6155917 DOI: 10.3390/molecules22010030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a systemic autoimmune disease involving multiple organs and tissues, which is characterized by the presence of excessive anti-nuclear autoantibodies. The pathogenesis of SLE has been intensively studied but remains far from clear. Increasing evidence has shown that the genetic susceptibilities and environmental factors-induced abnormalities in immune cells, dysregulation of apoptosis, and defects in the clearance of apoptotic materials contribute to the development of SLE. As the main source of auto-antigens, aberrant cell death may play a critical role in the pathogenesis of SLE. In this review, we summarize up-to-date research progress on different levels of cell death-including increasing rate of apoptosis, necrosis, autophagy and defects in clearance of dying cells-and discuss the possible underlying mechanisms, especially epigenetic modifications, which may provide new insight in the potential development of therapeutic strategies for SLE.
Collapse
Affiliation(s)
- Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha 410011, China.
| | - Siqi Fu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha 410011, China.
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha 410011, China.
| | - Liwei Lu
- Department of Pathology and Center for Infection and Immunology, the University of Hong Kong, Hong Kong, China.
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha 410011, China.
| |
Collapse
|
63
|
Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad A, Ardakani F, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch C, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter A, Sieverling L, Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz M, Schultze J, Radbruch A, Walter J, Hamann A, Polansky J. Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity 2016; 45:1148-1161. [DOI: 10.1016/j.immuni.2016.10.022] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 06/22/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
|