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Nehme Z, Pasquereau S, Herbein G. Control of viral infections by epigenetic-targeted therapy. Clin Epigenetics 2019; 11:55. [PMID: 30917875 PMCID: PMC6437953 DOI: 10.1186/s13148-019-0654-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/13/2019] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is defined as the science that studies the modifications of gene expression that are not owed to mutations or changes in the genetic sequence. Recently, strong evidences are pinpointing toward a solid interplay between such epigenetic alterations and the outcome of human cytomegalovirus (HCMV) infection. Guided by the previous possibly promising experimental trials of human immunodeficiency virus (HIV) epigenetic reprogramming, the latter is paving the road toward two major approaches to control viral gene expression or latency. Reactivating HCMV from the latent phase ("shock and kill" paradigm) or alternatively repressing the virus lytic and reactivation phases ("block and lock" paradigm) by epigenetic-targeted therapy represent encouraging options to overcome latency and viral shedding or otherwise replication and infectivity, which could lead eventually to control the infection and its complications. Not limited to HIV and HCMV, this concept is similarly studied in the context of hepatitis B and C virus, herpes simplex virus, and Epstein-Barr virus. Therefore, epigenetic manipulations stand as a pioneering research area in modern biology and could constitute a curative methodology by potentially consenting the development of broad-spectrum antivirals to control viral infections in vivo.
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Affiliation(s)
- Zeina Nehme
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
- Université Libanaise, Beirut, Lebanon
| | - Sébastien Pasquereau
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Georges Herbein
- Department Pathogens & Inflammation-EPILAB, UPRES EA4266, University of Franche-Comté, University of Bourgogne Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
- Department of Virology, CHRU Besancon, F-25030 Besançon, France
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52
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The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection. Cell Mol Immunol 2019; 17:247-260. [PMID: 30842630 PMCID: PMC7052164 DOI: 10.1038/s41423-019-0219-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 02/17/2019] [Accepted: 02/17/2019] [Indexed: 12/12/2022] Open
Abstract
Epigenetic modifications to histones dictate the differentiation of naïve CD4+ T cells into different subsets of effector T helper (TH) cells. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the mechanism regulating the differentiation of TH1, TH2 and regulatory T (Treg) cells. However, whether and how EZH2 regulates follicular helper T (TFH) cell differentiation remain unknown. Using a mouse model of acute lymphocytic choriomeningitis virus (LCMV) infection, we observed abundant EZH2 expression and associated H3K27me3 modifications preferentially in the early committed virus-specific TFH cells compared to those in TH1 cells. Ablation of EZH2 in LCMV-specific CD4+ T cells leads to a selective impairment of early TFH cell fate commitment, but not late TFH differentiation or memory TFH maintenance. Mechanistically, EZH2 specifically stabilizes the chromatin accessibility of a cluster of genes that are important for TFH fate commitment, particularly B cell lymphoma 6 (Bcl6), and thus directs TFH cell commitment. Therefore, we identified the chromatin-modifying enzyme EZH2 as a novel regulator of early TFH differentiation during acute viral infection.
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53
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
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54
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Abstract
In this review, Boothby et al. summarize some salient advances toward elucidation of the molecular programming of the fate choices and function of B cells in the periphery. They also note unanswered questions that pertain to differences among subsets of B lymphocytes and plasma cells. Mature B lymphocytes are crucial components of adaptive immunity, a system essential for the evolutionary fitness of mammals. Adaptive lymphocyte function requires an initially naïve cell to proliferate extensively and its progeny to have the capacity to assume a variety of fates. These include either terminal differentiation (the long-lived plasma cell) or metastable transcriptional reprogramming (germinal center and memory B cells). In this review, we focus principally on the regulation of differentiation and functional diversification of the “B2” subset. An overview is combined with an account of more recent advances, including initial work on mechanisms that eliminate DNA methylation and potential links between intracellular metabolites and chromatin editing.
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55
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Daniel S, Nylander V, Ingerslev LR, Zhong L, Fabre O, Clifford B, Johnston K, Cohn RJ, Barres R, Simar D. T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors. Clin Epigenetics 2018; 10:138. [PMID: 30400990 PMCID: PMC6219017 DOI: 10.1186/s13148-018-0561-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 10/07/2018] [Indexed: 01/08/2023] Open
Abstract
Background Cancer treatments have substantially improved childhood cancer survival but are accompanied by long-term complications, notably chronic inflammatory diseases. We hypothesize that cancer treatments could lead to long-term epigenetic changes in immune cells, resulting in increased prevalence of inflammatory diseases in cancer survivors. Results To test this hypothesis, we established the epigenetic and transcriptomic profiles of immune cells from 44 childhood cancer survivors (CCS, > 16 years old) on full remission (> 5 years) who had received chemotherapy alone or in combination with total body irradiation (TBI) and hematopoietic stem cell transplant (HSCT). We found that more than 10 years post-treatment, CCS treated with TBI/HSCT showed an altered DNA methylation signature in T cell, particularly at genes controlling immune and inflammatory processes and oxidative stress. DNA methylation remodeling in T cell was partially associated with chronic expression changes of nearby genes, increased frequency of type 1 cytokine-producing T cell, elevated systemic levels of these cytokines, and over-activation of related signaling pathways. Survivors exposed to TBI/HSCT were further characterized by an Epigenetic-Aging-Signature of T cell consistent with accelerated epigenetic aging. To investigate the potential contribution of irradiation to these changes, we established two cell culture models. We identified that radiation partially recapitulated the immune changes observed in survivors through a bystander effect that could be mediated by circulating factors. Conclusion Cancer treatments, in particular TBI/HSCT, are associated with long-term immune disturbances. We propose that epigenetic remodeling of immune cells following cancer therapy augments inflammatory- and age-related diseases, including metabolic complications, in childhood cancer survivors. Electronic supplementary material The online version of this article (10.1186/s13148-018-0561-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Daniel
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Vibe Nylander
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, Australia
| | - Odile Fabre
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Briana Clifford
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Karen Johnston
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Richard J Cohn
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Romain Barres
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
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56
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Morales-Nebreda L, Alakija O, Ferguson KT, Singer BD. Systemic lupus erythematosus-associated diffuse alveolar hemorrhage: A case report and review of the literature. CLINICAL PULMONARY MEDICINE 2018; 25:166-169. [PMID: 30220838 PMCID: PMC6136257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Systemic lupus erythematosus is associated with numerous pleuropulmonary complications. Although uncommon, diffuse alveolar hemorrhage represents a life-threatening cause of acute respiratory failure among patients with lupus. Here, we present a 24-year-old woman with a history of lupus who developed hemoptysis and respiratory failure associated with diffuse radiographic infiltrates and anemia. Bronchoscopy confirmed diffuse alveolar hemorrhage. She was managed with supportive care, plasmapheresis, and immunosuppressive pharmacotherapy leading to sustained resolution of her pulmonary hemorrhage and respiratory failure. We then review the available literature on the pathophysiology and management of lupus-associated diffuse alveolar hemorrhage, which centers on supportive care, reversal of coagulopathy, and immunosuppressive measures.
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Affiliation(s)
- Luisa Morales-Nebreda
- Northwestern University Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, 60611, USA
| | - Omolola Alakija
- Northwestern University Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, 60611, USA
| | - Keith T. Ferguson
- Northwestern University Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, 60611, USA
| | - Benjamin D. Singer
- Northwestern University Feinberg School of Medicine, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Chicago, IL, 60611, USA
- Northwestern University Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, IL, 60611, USA
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57
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Arama C, Quin JE, Kouriba B, Östlund Farrants AK, Troye-Blomberg M, Doumbo OK. Epigenetics and Malaria Susceptibility/Protection: A Missing Piece of the Puzzle. Front Immunol 2018; 9:1733. [PMID: 30158923 PMCID: PMC6104485 DOI: 10.3389/fimmu.2018.01733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022] Open
Abstract
A better understanding of stable changes in regulation of gene expression that result from epigenetic events is of great relevance in the development of strategies to prevent and treat infectious diseases. Histone modification and DNA methylation are key epigenetic mechanisms that can be regarded as marks, which ensure an accurate transmission of the chromatin states and gene expression profiles over generations of cells. There is an increasing list of these modifications, and the complexity of their action is just beginning to be understood. It is clear that the epigenetic landscape plays a fundamental role in most biological processes that involve the manipulation and expression of DNA. Although the molecular mechanism of gene regulation is relatively well understood, the hierarchical order of events and dependencies that lead to protection against infection remain largely unknown. In this review, we propose that host epigenetics is an essential, though relatively under studied, factor in the protection or susceptibility to malaria.
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Affiliation(s)
- Charles Arama
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jaclyn E Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bourèma Kouriba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | | | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
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58
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Bugide S, Janostiak R, Wajapeyee N. Epigenetic Mechanisms Dictating Eradication of Cancer by Natural Killer Cells. Trends Cancer 2018; 4:553-566. [PMID: 30064663 PMCID: PMC6085095 DOI: 10.1016/j.trecan.2018.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 12/27/2022]
Abstract
Natural killer (NK) cells of the innate immune system are the first line of defense against infectious agents and cancer cells. However, only a few mechanisms that regulate eradication of tumors by NK cells have been identified. In this review, we present an account of epigenetic mechanisms that modulate the ability of NK cells to eradicate cancer cells. To date, several drugs that target epigenetic modifiers have shown clinical efficacy in cancer. Therefore, once a given epigenetic modifier is validated as a regulator of NK cell function, it can be targeted for NK cell-based cancer immunotherapies.
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Affiliation(s)
- Suresh Bugide
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Narendra Wajapeyee
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06510, USA.
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59
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Casimir GJ, Lefèvre N, Corazza F, Duchateau J, Chamekh M. The Acid-Base Balance and Gender in Inflammation: A Mini-Review. Front Immunol 2018; 9:475. [PMID: 29593728 PMCID: PMC5854649 DOI: 10.3389/fimmu.2018.00475] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/22/2018] [Indexed: 12/31/2022] Open
Abstract
In humans, acid–base balance is crucial to cell homeostasis. Acidosis is observed in numerous inflammatory processes, primarily acute conditions such as sepsis, trauma, or acute respiratory distress where females tend to exhibit better prognosis compared with males. The mechanisms underlying these gender-dependent differences are multiple, probably involving hormonal and genetic factors, particularly the X chromosome. Although pH influences multiple immunological functions, gender differences in acid–base balance have been poorly investigated. In this review, we provide an update on gender differences in human susceptibility to inflammatory diseases. We additionally discuss the potential impact of acid–base balance on the gender bias of the inflammatory response in view of our recent observation that girls present higher neutrophilic inflammation and lower pH with a trend toward better prognosis in severe sepsis. We also highlight the potent role played by endothelial cells in gender differences of inflammation through activation of proton-sensing G protein-coupled receptors.
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Affiliation(s)
- Georges Jacques Casimir
- Laboratoire académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Lefèvre
- Laboratoire académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium.,Laboratoire de Médecine translationnelle, Centre Hospitalier Universitaire Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Francis Corazza
- Laboratoire de Médecine translationnelle, Centre Hospitalier Universitaire Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean Duchateau
- Laboratoire académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Mustapha Chamekh
- Laboratoire académique de Pédiatrie, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
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60
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Jasiulionis MG. Abnormal Epigenetic Regulation of Immune System during Aging. Front Immunol 2018; 9:197. [PMID: 29483913 PMCID: PMC5816044 DOI: 10.3389/fimmu.2018.00197] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/23/2018] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to the study of mechanisms controlling the chromatin structure, which has fundamental role in the regulation of gene expression and genome stability. Epigenetic marks, such as DNA methylation and histone modifications, are established during embryonic development and epigenetic profiles are stably inherited during mitosis, ensuring cell differentiation and fate. Under the effect of intrinsic and extrinsic factors, such as metabolic profile, hormones, nutrition, drugs, smoke, and stress, epigenetic marks are actively modulated. In this sense, the lifestyle may affect significantly the epigenome, and as a result, the gene expression profile and cell function. Epigenetic alterations are a hallmark of aging and diseases, such as cancer. Among biological systems compromised with aging is the decline of immune response. Different regulators of immune response have their promoters and enhancers susceptible to the modulation by epigenetic marks, which is fundamental to the differentiation and function of immune cells. Consistent evidence has showed the regulation of innate immune cells, and T and B lymphocytes by epigenetic mechanisms. Therefore, age-dependent alterations in epigenetic marks may result in the decline of immune function and this might contribute to the increased incidence of diseases in old people. In order to maintain health, we need to better understand how to avoid epigenetic alterations related to immune aging. In this review, the contribution of epigenetic mechanisms to the loss of immune function during aging will be discussed, and the promise of new means of disease prevention and management will be pointed.
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Affiliation(s)
- Miriam G Jasiulionis
- Laboratory of Ontogeny and Epigenetics, Pharmacology Department, Universidade Federal de São Paulo, São Paulo, Brazil
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61
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The Secrets of T Cell Polarization. Oncoimmunology 2018. [DOI: 10.1007/978-3-319-62431-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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62
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Ecker S, Pancaldi V, Valencia A, Beck S, Paul DS. Epigenetic and Transcriptional Variability Shape Phenotypic Plasticity. Bioessays 2017; 40. [PMID: 29251357 DOI: 10.1002/bies.201700148] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/31/2017] [Indexed: 12/15/2022]
Abstract
Epigenetic and transcriptional variability contribute to the vast diversity of cellular and organismal phenotypes and are key in human health and disease. In this review, we describe different types, sources, and determinants of epigenetic and transcriptional variability, enabling cells and organisms to adapt and evolve to a changing environment. We highlight the latest research and hypotheses on how chromatin structure and the epigenome influence gene expression variability. Further, we provide an overview of challenges in the analysis of biological variability. An improved understanding of the molecular mechanisms underlying epigenetic and transcriptional variability, at both the intra- and inter-individual level, provides great opportunity for disease prevention, better therapeutic approaches, and personalized medicine.
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Affiliation(s)
- Simone Ecker
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Vera Pancaldi
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 39-31, 08034, Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), C/ Jordi Girona 39-31, 08034, Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,Department of Human Genetics Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
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63
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Statistical and integrative system-level analysis of DNA methylation data. Nat Rev Genet 2017; 19:129-147. [PMID: 29129922 DOI: 10.1038/nrg.2017.86] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information.
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64
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Metallothioneins: Emerging Modulators in Immunity and Infection. Int J Mol Sci 2017; 18:ijms18102197. [PMID: 29065550 PMCID: PMC5666878 DOI: 10.3390/ijms18102197] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Metallothioneins (MTs) are a family of metal-binding proteins virtually expressed in all organisms including prokaryotes, lower eukaryotes, invertebrates and mammals. These proteins regulate homeostasis of zinc (Zn) and copper (Cu), mitigate heavy metal poisoning, and alleviate superoxide stress. In recent years, MTs have emerged as an important, yet largely underappreciated, component of the immune system. Innate and adaptive immune cells regulate MTs in response to stress stimuli, cytokine signals and microbial challenge. Modulation of MTs in these cells in turn regulates metal ion release, transport and distribution, cellular redox status, enzyme function and cell signaling. While it is well established that the host strictly regulates availability of metal ions during microbial pathogenesis, we are only recently beginning to unravel the interplay between metal-regulatory pathways and immunological defenses. In this perspective, investigation of mechanisms that leverage the potential of MTs to orchestrate inflammatory responses and antimicrobial defenses has gained momentum. The purpose of this review, therefore, is to illumine the role of MTs in immune regulation. We discuss the mechanisms of MT induction and signaling in immune cells and explore the therapeutic potential of the MT-Zn axis in bolstering immune defenses against pathogens.
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65
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Ecker S, Beck S. Epigenetic variation taking center stage in immunological research. Epigenomics 2017; 9:375-378. [DOI: 10.2217/epi-2017-0006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Simone Ecker
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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66
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Abstract
Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus–host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype. Epigenetic modifications, such as histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, function as important regulators that remodel host chromatin, altering host expression patterns and networks in a highly flexible manner. For most of the past two and a half decades, research has focused on the molecular mechanisms by which RNA viruses antagonize the signaling and sensing components that regulate induction of the host innate immune and antiviral defense programs upon infection. More recently, a growing body of evidence supports the hypothesis that viruses, even lytic RNA viruses that replicate in the cytoplasm, have developed intricate, highly evolved, and well-coordinated processes that are designed to regulate the host epigenome, and control host innate immune antiviral defense processes, thereby promoting robust virus replication and pathogenesis. In this article, we discuss the strategies that are used to evaluate the mechanisms by which viruses regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus infections as a model. By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host’s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection.
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67
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Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biol 2017; 18:18. [PMID: 28126036 PMCID: PMC5270224 DOI: 10.1186/s13059-017-1156-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/17/2017] [Indexed: 12/11/2022] Open
Abstract
Background A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16− monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naïve T cells from the same 125 healthy individuals. We discover substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression are found to be implicated in key immune pathways and are associated with cellular properties and environmental exposure. We also observe increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. Conclusions Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1156-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain. .,UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Lu Chen
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Frederik O Bagger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - José María Fernández
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Enrique Carrillo de Santa Pau
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - David Juan
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Alice L Mann
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Stephen Watt
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Nikos Sidiropoulos
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Angelika Merkel
- National Center for Genomic Analysis (CNAG), Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer Baldiri i Reixac 4, 08028, Barcelona, Spain
| | | | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, 6525GA, The Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK.,British Heart Foundation Centre of Excellence, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.,National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, CB2 0PT, UK
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield, Montreal, H3A 0G1, Canada
| | - Taco W Kuijpers
- Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam, 1066CX, The Netherlands.,Emma Children's Hospital, Academic Medical Center (AMC), University of Amsterdam, Location H7-230, Meibergdreef 9, Amsterdam, 1105AX, The Netherlands
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1HH, UK. .,Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge, Hinxton, UK.
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK. .,Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge, CB1 8RN, UK.
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68
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Lomvardas S, Maniatis T. Histone and DNA Modifications as Regulators of Neuronal Development and Function. Cold Spring Harb Perspect Biol 2016; 8:8/7/a024208. [PMID: 27371659 DOI: 10.1101/cshperspect.a024208] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA and histone modifications, together with constraints imposed by nuclear architecture, contribute to the transcriptional regulatory landscape of the nervous system. Here, we provide select examples showing how these regulatory layers, often referred to as epigenetic, contribute to neuronal differentiation and function. We describe the interplay between DNA methylation and Polycomb-mediated repression during neuronal differentiation, the role of DNA methylation and long-range enhancer-promoter interactions in Protocadherin promoter choice, and the contribution of heterochromatic silencing and nuclear organization in singular olfactory receptor expression. Finally, we explain how the activity-dependent expression of a histone variant determines the longevity of olfactory sensory neurons.
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Affiliation(s)
- Stavros Lomvardas
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032
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69
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Abstract
Over the past 20 years, breakthrough discoveries of chromatin-modifying enzymes and associated mechanisms that alter chromatin in response to physiological or pathological signals have transformed our knowledge of epigenetics from a collection of curious biological phenomena to a functionally dissected research field. Here, we provide a personal perspective on the development of epigenetics, from its historical origins to what we define as 'the modern era of epigenetic research'. We primarily highlight key molecular mechanisms of and conceptual advances in epigenetic control that have changed our understanding of normal and perturbed development.
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Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York 10065, New York, USA
| | - Thomas Jenuwein
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg D-79108, Germany
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70
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Almouzni G, Cedar H. Maintenance of Epigenetic Information. Cold Spring Harb Perspect Biol 2016; 8:8/5/a019372. [PMID: 27141050 DOI: 10.1101/cshperspect.a019372] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genome is subject to a diverse array of epigenetic modifications from DNA methylation to histone posttranslational changes. Many of these marks are somatically stable through cell division. This article focuses on our knowledge of the mechanisms governing the inheritance of epigenetic marks, particularly, repressive ones, when the DNA and chromatin template are duplicated in S phase. This involves the action of histone chaperones, nucleosome-remodeling enzymes, histone and DNA methylation binding proteins, and chromatin-modifying enzymes. Last, the timing of DNA replication is discussed, including the question of whether this constitutes an epigenetic mark that facilitates the propagation of epigenetic marks.
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Affiliation(s)
- Geneviève Almouzni
- Department of Nuclear Dynamics and Genome Plasticity, Institut Curie, Section de recherche, 75231 Paris Cedex 05, France
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel 91120
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71
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Abstract
Histone posttranslational modifications represent a versatile set of epigenetic marks involved not only in dynamic cellular processes, such as transcription and DNA repair, but also in the stable maintenance of repressive chromatin. In this article, we review many of the key and newly identified histone modifications known to be deregulated in cancer and how this impacts function. The latter part of the article addresses the challenges and current status of the epigenetic drug development process as it applies to cancer therapeutics.
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Affiliation(s)
- James E Audia
- Constellation Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Robert M Campbell
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285
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72
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Patel DJ. A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks. Cold Spring Harb Perspect Biol 2016; 8:a018754. [PMID: 26931326 DOI: 10.1101/cshperspect.a018754] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This article outlines the protein modules that target methylated lysine histone marks and 5mC DNA marks, and the molecular principles underlying recognition. The article focuses on the structural basis underlying readout of isolated marks by single reader molecules, as well as multivalent readout of multiple marks by linked reader cassettes at the histone tail and nucleosome level. Additional topics addressed include the role of histone mimics, cross talk between histone marks, technological developments at the genome-wide level, advances using chemical biology approaches, the linkage between histone and DNA methylation, the role for regulatory lncRNAs, and the promise of chromatin-based therapeutic modalities.
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Affiliation(s)
- Dinshaw J Patel
- Structural Biology Department, Memorial Sloan-Kettering Cancer Center, New York, New York 10065
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73
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Harnessing the plasticity of CD4(+) T cells to treat immune-mediated disease. Nat Rev Immunol 2016; 16:149-63. [PMID: 26875830 DOI: 10.1038/nri.2015.18] [Citation(s) in RCA: 353] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CD4(+) T cells differentiate and acquire distinct functions to combat specific pathogens but can also adapt their functions in response to changing circumstances. Although this phenotypic plasticity can be potentially deleterious, driving immune pathology, it also provides important benefits that have led to its evolutionary preservation. Here, we review CD4(+) T cell plasticity by examining the molecular mechanisms that regulate it - from the extracellular cues that initiate and drive cells towards varying phenotypes, to the cytosolic signalling cascades that decipher these cues and transmit them into the cell and to the nucleus, where these signals imprint specific gene expression programmes. By understanding how this functional flexibility is achieved, we may open doors to new therapeutic approaches that harness this property of T cells.
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74
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Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y, Uno N, Oshimura M, Elowitz MB. Dynamics of epigenetic regulation at the single-cell level. Science 2016; 351:720-4. [PMID: 26912859 PMCID: PMC5108652 DOI: 10.1126/science.aab2956] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chromatin regulators play a major role in establishing and maintaining gene expression states. Yet how they control gene expression in single cells, quantitatively and over time, remains unclear. We used time-lapse microscopy to analyze the dynamic effects of four silencers associated with diverse modifications: DNA methylation, histone deacetylation, and histone methylation. For all regulators, silencing and reactivation occurred in all-or-none events, enabling the regulators to modulate the fraction of cells silenced rather than the amount of gene expression. These dynamics could be described by a three-state model involving stochastic transitions between active, reversibly silent, and irreversibly silent states. Through their individual transition rates, these regulators operate over different time scales and generate distinct types of epigenetic memory. Our results provide a framework for understanding and engineering mammalian chromatin regulation and epigenetic memory.
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Affiliation(s)
- Lacramioara Bintu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John Yong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yaron E Antebi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kayla McCue
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center, Tottori University, 86 Nishicho, Yonago, Japan
| | - Narumi Uno
- Chromosome Engineering Research Center, Tottori University, 86 Nishicho, Yonago, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center, Tottori University, 86 Nishicho, Yonago, Japan
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Howard Hughes Medical Institute (HHMI) and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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75
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Abstract
Epigenetic mechanisms play an essential role in the germline and imprinting cycle. Germ cells show extensive epigenetic programming in preparation for the generation of the totipotent state, which in turn leads to the establishment of pluripotent cells in blastocysts. The latter are the cells from which pluripotent embryonic stem cells are derived and maintained in culture. Following blastocyst implantation, postimplantation epiblast cells develop, which give rise to all somatic cells as well as primordial germ cells, the precursors of sperm and eggs. Pluripotent stem cells in culture can be induced to undergo differentiation into somatic cells and germ cells in culture. Understanding the natural cycles of epigenetic reprogramming that occur in the germline will allow the generation of better and more versatile stem cells for both therapeutic and research purposes.
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Affiliation(s)
- Wolf Reik
- The Babraham Institute, Babraham Research Campus, Cambridge CB2 3EG, United Kingdom Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - M Azim Surani
- Wellcome Trust Cancer Research UK Gurdon Institute & Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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76
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Abstract
To accommodate genomes in the limited space of the cell nucleus and ensure the correct execution of gene expression programs, genomes are packaged in complex fashion in the three-dimensional cell nucleus. As a consequence of the extensive higher-order organization of chromosomes, distantly located genomic regions on the same or distinct chromosomes undergo long-range interactions. This article discusses the nature of long interactions, mechanisms of their formation, and their emerging functional roles in gene regulation and genome maintenance.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
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77
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Provençal N, Booij L, Tremblay RE. The developmental origins of chronic physical aggression: biological pathways triggered by early life adversity. ACTA ACUST UNITED AC 2015; 218:123-33. [PMID: 25568459 DOI: 10.1242/jeb.111401] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Longitudinal epidemiological studies with birth cohorts have shown that physical aggression in humans does not appear suddenly in adolescence as commonly thought. In fact, physically aggressive behaviour is observed as early as 12 months after birth, its frequency peaks around 2-4 years of age and decreases in frequency until early adulthood. However, a minority of children (3-7%) maintain a high frequency of physical aggression from childhood to adolescence and develop serious social adjustment problems during adulthood. Genetic factors and early social experiences, as well as their interaction, have been shown to play an important role in the development of chronic aggressive behaviour. However, the biological mechanisms underlying these associations are just beginning to be uncovered. Recent evidence suggests that epigenetic mechanisms are responsive to adverse environments and could be involved in the development of chronic aggression. Using both gene candidate and genomic approaches, recent studies have identified epigenetic marks, such as DNA methylation alterations in genes involved in the stress response and the serotonin and immune systems to be partly responsible for the long-lasting effects of early adversity. Further longitudinal studies with biological, environmental and behavioural assessments from birth onwards are needed to elucidate the sequence of events that leads to these long-lasting epigenetic marks associated with early adversity and aggression.
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Affiliation(s)
- Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Linda Booij
- Ste-Justine Hospital Research Center, Montreal, QC H3T 1C5, Canada Department of Psychology and Psychiatry, Queen's University, Kingston, ON K7L 3N6, Canada Department of Psychiatry, University of Montreal, Montreal, QC H3T 1J4, Canada Department of Psychiatry, McGill University, Montreal, QC H3A 1A1, Canada
| | - Richard E Tremblay
- Ste-Justine Hospital Research Center, Montreal, QC H3T 1C5, Canada Department of Psychology and Pediatrics, University of Montreal, Montreal, QC H2V 2S9, Canada School of Public Health, Physiotherapy and Population Sciences, University College Dublin, Dublin 4, Ireland Institute of Genetic, Neurobiological, and Social Foundations of Child Development, Tomsk State University, Tomsk 634050, Russian Federation
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78
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Rocha-Perugini V, González-Granado JM. Nuclear envelope lamin-A as a coordinator of T cell activation. Nucleus 2015; 5:396-401. [PMID: 25482193 PMCID: PMC4164483 DOI: 10.4161/nucl.36361] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nuclear lamins A/C control several critical cellular functions, e.g., chromatin organization, gene transcription, DNA replication, DNA damage responses, cell cycle progression, cell differentiation, and cell polarization during migration. However, few studies have addressed the role of lamins A/C in the control of the functions of immune cells. Recently, we have demonstrated that lamins A/C are induced in T cells upon antigen recognition. Lamins A/C enhance T cell responses by coupling the plasma membrane to the nucleus via the linker of nucleoskeleton and cytoskeleton (LINC) complex and the actin cytoskeleton. Here, we discuss the possible physiological relevance and functional context of lamin A/C in T cell activation and propose a model in which lamins A/C are key modulators of immune cell functions.
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Affiliation(s)
- Vera Rocha-Perugini
- a Servicio de Inmunología; Hospital Universitario de la Princesa; Instituto de Investigación Sanitaria de la Princesa; Madrid, Spain
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79
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Marmorstein R, Zhou MM. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol 2014; 6:a018762. [PMID: 24984779 DOI: 10.1101/cshperspect.a018762] [Citation(s) in RCA: 378] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone acetylation marks are written by histone acetyltransferases (HATs) and read by bromodomains (BrDs), and less commonly by other protein modules. These proteins regulate many transcription-mediated biological processes, and their aberrant activities are correlated with several human diseases. Consequently, small molecule HAT and BrD inhibitors with therapeutic potential have been developed. Structural and biochemical studies of HATs and BrDs have revealed that HATs fall into distinct subfamilies containing a structurally related core for cofactor binding, but divergent flanking regions for substrate-specific binding, catalysis, and autoregulation. BrDs adopt a conserved left-handed four-helix bundle to recognize acetyllysine; divergent loop residues contribute to substrate-specific acetyllysine recognition.
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Affiliation(s)
- Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10065
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80
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Schaefer U. Pharmacological inhibition of bromodomain-containing proteins in inflammation. Cold Spring Harb Perspect Biol 2014; 6:6/6/a018671. [PMID: 24890512 DOI: 10.1101/cshperspect.a018671] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inflammation is associated with the activation of genes that contribute to immune defense and tissue repair. The bromodomain-containing proteins of the BET family, which recognize histone lysine acetylation, play a key role in the transcriptional control of inflammatory genes. Inhibition of BET proteins by the small-molecule inhibitor I-BET affects the expression of a particular subset of inflammatory genes-namely, ones that follow an "analog-like," but not "digital-like" activation pattern. This ability of I-BET to target genes based on the dynamic pattern of their activation may facilitate the further development of anti-inflammatory treatment protocols that are tuned to the individual or to disease-specific patterns of gene expression.
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Affiliation(s)
- Uwe Schaefer
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York 10065
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81
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Seto E, Yoshida M. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol 2014; 6:a018713. [PMID: 24691964 DOI: 10.1101/cshperspect.a018713] [Citation(s) in RCA: 1250] [Impact Index Per Article: 125.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl functional groups from the lysine residues of both histone and nonhistone proteins. In humans, there are 18 HDAC enzymes that use either zinc- or NAD(+)-dependent mechanisms to deacetylate acetyl lysine substrates. Although removal of histone acetyl epigenetic modification by HDACs regulates chromatin structure and transcription, deacetylation of nonhistones controls diverse cellular processes. HDAC inhibitors are already known potential anticancer agents and show promise for the treatment of many diseases.
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Affiliation(s)
- Edward Seto
- Department of Molecular Oncology, Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
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82
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Abstract
Research using ciliates revealed early examples of epigenetic phenomena and continues to provide novel findings. These protozoans maintain separate germline and somatic nuclei that carry transcriptionally silent and active genomes, respectively. Examining the differences in chromatin within distinct nuclei of Tetrahymena identified histone variants and established that transcriptional regulators act by modifying histones. Formation of somatic nuclei requires both transcriptional activation of silent chromatin and large-scale DNA elimination. This somatic genome remodeling is directed by homologous RNAs, acting with an RNA interference (RNAi)-related machinery. Furthermore, the content of the parental somatic genome provides a homologous template to guide this genome restructuring. The mechanisms regulating ciliate DNA rearrangements reveal the surprising power of homologous RNAs to remodel the genome and transmit information transgenerationally.
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Affiliation(s)
- Douglas L Chalker
- Department of Biology, Washington University, St. Louis, Missouri 63130
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83
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Blackledge NP, Thomson JP, Skene PJ. CpG island chromatin is shaped by recruitment of ZF-CxxC proteins. Cold Spring Harb Perspect Biol 2013; 5:a018648. [PMID: 24186071 DOI: 10.1101/cshperspect.a018648] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Most mammalian gene promoters are embedded within genomic regions called CpG islands, characterized by elevated levels of nonmethylated CpG dinucleotides. Here, we describe recent work demonstrating that CpG islands act as specific nucleation sites for the zinc finger CxxC domain-containing proteins CFP1 and KDM2A. Importantly, both CFP1 and KDM2A are associated with enzymatic activities that modulate specific histone lysine methylation marks. The action of these zinc finger CxxC domain proteins therefore imposes a defined chromatin architecture on CpG islands that distinguishes these important regulatory elements from the surrounding genome. The functional consequence of this CpG island-directed chromatin environment is discussed.
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Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
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