51
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Atlante S, Mongelli A, Barbi V, Martelli F, Farsetti A, Gaetano C. The epigenetic implication in coronavirus infection and therapy. Clin Epigenetics 2020; 12:156. [PMID: 33087172 PMCID: PMC7576975 DOI: 10.1186/s13148-020-00946-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
Epigenetics is a relatively new field of science that studies the genetic and non-genetic aspects related to heritable phenotypic changes, frequently caused by environmental and metabolic factors. In the host, the epigenetic machinery can regulate gene expression through a series of reversible epigenetic modifications, such as histone methylation and acetylation, DNA/RNA methylation, chromatin remodeling, and non-coding RNAs. The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which emerged in Wuhan, China, and spread worldwide, causes it. COVID-19 severity and consequences largely depend on patient age and health status. In this review, we will summarize and comparatively analyze how viruses regulate the host epigenome. Mainly, we will be focusing on highly pathogenic respiratory RNA virus infections such as coronaviruses. In this context, epigenetic alterations might play an essential role in the onset of coronavirus disease complications. Although many therapeutic approaches are under study, more research is urgently needed to identify effective vaccine or safer chemotherapeutic drugs, including epigenetic drugs, to cope with this viral outbreak and to develop pre- and post-exposure prophylaxis against COVID-19.
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Affiliation(s)
- Sandra Atlante
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Alessia Mongelli
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Veronica Barbi
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
| | - Fabio Martelli
- Laboratorio di Cardiologia Molecolare, Policlinico San Donato IRCCS, Milan, Italy
| | - Antonella Farsetti
- Institute for Systems Analysis and Computer Science “A. Ruberti” (IASI), National Research Council (CNR), Rome, Italy
| | - Carlo Gaetano
- Laboratorio di Epigenetica, Istituti Clinici Scientifici Maugeri IRCCS, Via Maugeri 4, 27100 Pavia, Italy
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52
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Rapid Enhancer Remodeling and Transcription Factor Repurposing Enable High Magnitude Gene Induction upon Acute Activation of NK Cells. Immunity 2020; 53:745-758.e4. [PMID: 33010223 DOI: 10.1016/j.immuni.2020.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 05/08/2020] [Accepted: 09/11/2020] [Indexed: 12/24/2022]
Abstract
Innate immune responses rely on rapid and precise gene regulation mediated by accessibility of regulatory regions to transcription factors (TFs). In natural killer (NK) cells and other innate lymphoid cells, competent enhancers are primed during lineage acquisition, and formation of de novo enhancers characterizes the acquisition of innate memory in activated NK cells and macrophages. Here, we investigated how primed and de novo enhancers coordinate to facilitate high-magnitude gene induction during acute activation. Epigenomic and transcriptomic analyses of regions near highly induced genes (HIGs) in NK cells both in vitro and in a model of Toxoplasma gondii infection revealed de novo chromatin accessibility and enhancer remodeling controlled by signal-regulated TFs STATs. Acute NK cell activation redeployed the lineage-determining TF T-bet to de novo enhancers, independent of DNA-sequence-specific motif recognition. Thus, acute stimulation reshapes enhancer function through the combinatorial usage and repurposing of both lineage-determining and signal-regulated TFs to ensure an effective response.
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53
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New disease old vaccine: Is recombinant BCG vaccine an answer for COVID-19? Cell Immunol 2020; 356:104187. [PMID: 32745670 PMCID: PMC7386780 DOI: 10.1016/j.cellimm.2020.104187] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 12/25/2022]
Abstract
Mycobacterium bovis BCG, a live attenuated tuberculosis vaccine offers protection against disseminated TB in children. BCG exhibits heterologous protective effects against unrelated infections and reduces infant mortality due to non-mycobacterial infections. Recent reports have suggested that BCG vaccination might have protective effects against COVID-19, however it is highly unlikely that BCG vaccine in its current form can offer complete protection against SARS-CoV-2 infection due to the lack of specific immunity. Nonetheless, recombinant BCG strains expressing antigens of SARS-CoV-2 may offer protection against COVID-19 due to the activation of innate as well as specific adaptive immune response. Further proven safety records of BCG in humans, its adjuvant activity and low cost manufacturing makes it a frontrunner in the vaccine development to stop this pandemic. In this review we discuss about the heterologous effects of BCG, induction of trained immunity and its implication in development of a potential vaccine against COVID-19 pandemic.
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54
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Beacon TH, Su RC, Lakowski TM, Delcuve GP, Davie JR. SARS-CoV-2 multifaceted interaction with the human host. Part II: Innate immunity response, immunopathology, and epigenetics. IUBMB Life 2020; 72:2331-2354. [PMID: 32936531 DOI: 10.1002/iub.2379] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 makes its way into the cell via the ACE2 receptor and the proteolytic action of TMPRSS2. In response to the SARS-CoV-2 infection, the innate immune response is the first line of defense, triggering multiple signaling pathways to produce interferons, pro-inflammatory cytokines and chemokines, and initiating the adaptive immune response against the virus. Unsurprisingly, the virus has developed strategies to evade detection, which can result in delayed, excessive activation of the innate immune system. The response elicited by the host depends on multiple factors, including health status, age, and sex. An overactive innate immune response can lead to a cytokine storm, inflammation, and vascular disruption, leading to the vast array of symptoms exhibited by COVID-19 patients. What is known about the expression and epigenetic regulation of the ACE2 gene and the various players in the host response are explored in this review.
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Affiliation(s)
- Tasnim H Beacon
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ruey-Chyi Su
- National HIV and Retrovirology Laboratory, JC Wilt Infectious Disease Research Centre, Winnipeg, Manitoba, Canada
| | - Ted M Lakowski
- College of Pharmacy, Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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55
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Histone deacetylase 3 promotes innate antiviral immunity through deacetylation of TBK1. Protein Cell 2020; 12:261-278. [PMID: 32772249 PMCID: PMC8018997 DOI: 10.1007/s13238-020-00751-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
TANK-binding kinase 1 (TBK1), a core kinase of antiviral pathways, activates the production of interferons (IFNs). It has been reported that deacetylation activates TBK1; however, the precise mechanism still remains to be uncovered. We show here that during the early stage of viral infection, the acetylation of TBK1 was increased, and the acetylation of TBK1 at Lys241 enhanced the recruitment of IRF3 to TBK1. HDAC3 directly deacetylated TBK1 at Lys241 and Lys692, which resulted in the activation of TBK1. Deacetylation at Lys241 and Lys692 was critical for the kinase activity and dimerization of TBK1 respectively. Using knockout cell lines and transgenic mice, we confirmed that a HDAC3 null mutant exhibited enhanced susceptibility to viral challenge via impaired production of type I IFNs. Furthermore, activated TBK1 phosphorylated HDAC3, which promoted the deacetylation activity of HDAC3 and formed a feedback loop. In this study, we illustrated the roles the acetylated and deacetylated forms of TBK1 play in antiviral innate responses and clarified the post-translational modulations involved in the interaction between TBK1 and HDAC3.
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56
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Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature 2020; 583:852-857. [PMID: 32699416 PMCID: PMC7517595 DOI: 10.1038/s41586-020-2533-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/05/2020] [Indexed: 01/07/2023]
Abstract
Complex organisms can rapidly induce select genes in response to diverse environmental cues. This regulation occurs in the context of large genomes condensed by histone proteins into chromatin. The sensing of pathogens by macrophages engages conserved signalling pathways and transcription factors to coordinate the induction of inflammatory genes1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a general feature of dynamically regulated chromatin and transcription4-7. However, how chromatin is regulated at induced genes, and what features of H3.3 might enable rapid and high-level transcription, are unknown. The amino terminus of H3.3 contains a unique serine residue (Ser31) that is absent in 'canonical' H3.1 and H3.2. Here we show that this residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along rapidly induced genes in mouse macrophages. This selective mark of stimulation-responsive genes directly engages the histone methyltransferase SETD2, a component of the active transcription machinery, and 'ejects' the elongation corepressor ZMYND118,9. We propose that features of H3.3 at stimulation-induced genes, including H3.3S31ph, provide preferential access to the transcription apparatus. Our results indicate dedicated mechanisms that enable rapid transcription involving the histone variant H3.3, its phosphorylation, and both the recruitment and the ejection of chromatin regulators.
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Affiliation(s)
- Anja Armache
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Alexia Martínez de Paz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lexi E Robbins
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ceyda Durmaz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jin Q Cheong
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W Daman
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dughan J Ahimovic
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thaís Klevorn
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Yue
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tanja Arslan
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Shu Lin
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Tanya Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Samuel Thudium
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Erica Korb
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sandra B Hake
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
- Institute for Genetics, Justus-Liebig-University, Giessen, Germany
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Steven Z Josefowicz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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57
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Ordovas-Montanes J, Beyaz S, Rakoff-Nahoum S, Shalek AK. Distribution and storage of inflammatory memory in barrier tissues. Nat Rev Immunol 2020; 20:308-320. [PMID: 32015472 PMCID: PMC7547402 DOI: 10.1038/s41577-019-0263-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2019] [Indexed: 12/17/2022]
Abstract
Memories of previous immune events enable barrier tissues to rapidly recall distinct environmental exposures. To effectively inform future responses, these past experiences can be stored in cell types that are long-term residents or essential constituents of tissues. There is an emerging understanding that, in addition to antigen-specific immune cells, diverse haematopoietic, stromal, parenchymal and neuronal cell types can store inflammatory memory. Here, we explore the impact of previous immune activity on various cell lineages with the goal of presenting a unified view of inflammatory memory to environmental exposures (such as allergens, antigens, noxious agents and microorganisms) at barrier tissues. We propose that inflammatory memory is distributed across diverse cell types and stored through shifts in cell states, and we provide a framework to guide future experiments. This distribution and storage may promote adaptation or maladaptation in homeostatic, maintenance and disease settings - especially if the distribution of memory favours cellular cooperation during storage or recall.
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Affiliation(s)
- Jose Ordovas-Montanes
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA.
- Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA.
- Department of Chemistry, MIT, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Seth Rakoff-Nahoum
- Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Alex K Shalek
- Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, USA
- Department of Chemistry, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA, USA
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58
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Orozco-Solis R, Aguilar-Arnal L. Circadian Regulation of Immunity Through Epigenetic Mechanisms. Front Cell Infect Microbiol 2020; 10:96. [PMID: 32232012 PMCID: PMC7082642 DOI: 10.3389/fcimb.2020.00096] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
The circadian clock orchestrates daily rhythms in many physiological, behavioral and molecular processes, providing means to anticipate, and adapt to environmental changes. A specific role of the circadian clock is to coordinate functions of the immune system both at steady-state and in response to infectious threats. Hence, time-of-day dependent variables are found in the physiology of immune cells, host-parasite interactions, inflammatory processes, or adaptive immune responses. Interestingly, the molecular clock coordinates transcriptional-translational feedback loops which orchestrate daily oscillations in expression of many genes involved in cellular functions. This clock function is assisted by tightly controlled transitions in the chromatin fiber involving epigenetic mechanisms which determine how a when transcriptional oscillations occur. Immune cells are no exception, as they also present a functional clock dictating transcriptional rhythms. Hereby, the molecular clock and the chromatin regulators controlling rhythmicity represent a unique scaffold mediating the crosstalk between the circadian and the immune systems. Certain epigenetic regulators are shared between both systems and uncovering them and characterizing their dynamics can provide clues to design effective chronotherapeutic strategies for modulation of the immune system.
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Affiliation(s)
- Ricardo Orozco-Solis
- Laboratorio de Cronobiología y Metabolismo, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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59
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Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, Fuchs E, Joosten LAB, van der Meer JWM, Mhlanga MM, Mulder WJM, Riksen NP, Schlitzer A, Schultze JL, Stabell Benn C, Sun JC, Xavier RJ, Latz E. Defining trained immunity and its role in health and disease. Nat Rev Immunol 2020; 20:375-388. [PMID: 32132681 PMCID: PMC7186935 DOI: 10.1038/s41577-020-0285-6] [Citation(s) in RCA: 1275] [Impact Index Per Article: 318.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2020] [Indexed: 12/14/2022]
Abstract
Immune memory is a defining feature of the acquired immune system, but activation of the innate immune system can also result in enhanced responsiveness to subsequent triggers. This process has been termed ‘trained immunity’, a de facto innate immune memory. Research in the past decade has pointed to the broad benefits of trained immunity for host defence but has also suggested potentially detrimental outcomes in immune-mediated and chronic inflammatory diseases. Here we define ‘trained immunity’ as a biological process and discuss the innate stimuli and the epigenetic and metabolic reprogramming events that shape the induction of trained immunity. Here a group of leaders in the field define our current understanding of ‘trained immunity’, which refers to the memory-type responses that occur in the innate immune system. The authors discuss our current understanding of the key epigenetic and metabolic processes involved in trained immunity and consider its relevance in immune-mediated diseases and cancer.
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Affiliation(s)
- Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands. .,Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada.,Genetics Section, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.,Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jos W M van der Meer
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Musa M Mhlanga
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Willem J M Mulder
- Translational and Molecular Imaging Institute, Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Andreas Schlitzer
- Myeloid Cell Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Christine Stabell Benn
- Bandim Health Project, OPEN, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital, University of Bonn, Bonn, Germany. .,Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA. .,German Center for Neurodegenerative Diseases, Bonn, Germany.
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60
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Abstract
Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and organisms. The coordination of individual immune cells is essential for the generation of effective immune responses to pathogens while immune tolerance is maintained to protect the host. In rheumatic diseases, when immune responses are dysregulated, pathologically important cells might represent only a small fraction of the immune system. Interrogation of the contributions of individual immune cells to pathogenesis and disease progression should therefore reveal important insights into the complicated aetiology of rheumatic diseases. Technological advances are enabling the high-dimensional dissection of single cells at multiple omics levels, which could facilitate the identification of dysregulated molecular mechanisms in patients with rheumatic diseases and the discovery of new therapeutic targets and biomarkers. The single-cell technologies that have been developed over the past decade and the experimental platforms that enable multi-omics integrative analyses have already made inroads into immunology-related fields of study and have potential for use in rheumatology. Layers of omics data derived from single cells are likely to fundamentally change our understanding of the molecular pathways that underpin the pathogenesis of rheumatic diseases.
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61
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Frankiw L, Mann M, Li G, Joglekar A, Baltimore D. Alternative splicing coupled with transcript degradation modulates OAS1g antiviral activity. RNA (NEW YORK, N.Y.) 2020; 26:126-136. [PMID: 31740586 PMCID: PMC6961538 DOI: 10.1261/rna.073825.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/13/2019] [Indexed: 05/17/2023]
Abstract
At the heart of an innate immune response lies a tightly regulated gene expression program. This precise regulation is crucial because small changes can shift the balance from protective to destructive immunity. Here we identify a frequently used alternative splice site in the gene oligoadenylate synthetase 1g (Oas1g), a key component of the 2-5A antiviral system. Usage of this splice site leads to the generation of a transcript subject to decay, and removal of the site leads to increased expression of Oas1g and an improved antiviral response. However, removal of the splice site also leads to an increase in apoptotic cell death, suggesting this splicing event exists as a compromise between the pathogen protective benefits and collateral damage associated with OAS1g activity. Across the innate immune response, we show that a multitude of alternative splicing events predicted to lead to decay exist, and thus have the potential to play a significant role in the regulation of gene expression in innate immunity.
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Affiliation(s)
- Luke Frankiw
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Mati Mann
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Guideng Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Center of Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Alok Joglekar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
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62
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Csumita M, Csermely A, Horvath A, Nagy G, Monori F, Göczi L, Orbea HA, Reith W, Széles L. Specific enhancer selection by IRF3, IRF5 and IRF9 is determined by ISRE half-sites, 5' and 3' flanking bases, collaborating transcription factors and the chromatin environment in a combinatorial fashion. Nucleic Acids Res 2020; 48:589-604. [PMID: 31799619 PMCID: PMC6954429 DOI: 10.1093/nar/gkz1112] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 12/28/2022] Open
Abstract
IRF3, IRF5 and IRF9 are transcription factors, which play distinct roles in the regulation of antiviral and inflammatory responses. The determinants that mediate IRF-specific enhancer selection are not fully understood. To uncover regions occupied predominantly by IRF3, IRF5 or IRF9, we performed ChIP-seq experiments in activated murine dendritic cells. The identified regions were analysed with respect to the enrichment of DNA motifs, the interferon-stimulated response element (ISRE) and ISRE half-site variants, and chromatin accessibility. Using a machine learning method, we investigated the predictability of IRF-dominance. We found that IRF5-dominant regions differed fundamentally from the IRF3- and IRF9-dominant regions: ISREs were rare, while the NFKB motif and special ISRE half-sites, such as 5'-GAGA-3' and 5'-GACA-3', were enriched. IRF3- and IRF9-dominant regions were characterized by the enriched ISRE motif and lower frequency of accessible chromatin. Enrichment analysis and the machine learning method uncovered the features that favour IRF3 or IRF9 dominancy (e.g. a tripartite form of ISRE and motifs for NF-κB for IRF3, and the GAS motif and certain ISRE variants for IRF9). This study contributes to our understanding of how IRF members, which bind overlapping sets of DNA sequences, can initiate signal-dependent responses without activating superfluous or harmful programmes.
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Affiliation(s)
- Mária Csumita
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Attila Csermely
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Gergely Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Fanny Monori
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Loránd Göczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
| | - Hans-Acha Orbea
- Department of Biochemistry, University of Lausanne, CH-1066 Epalinges, Switzerland
| | - Walter Reith
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Centre Médical Universitaire (CMU), CH-1211 Geneva, Switzerland
| | - Lajos Széles
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen H-4032, Hungary
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63
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Locati M, Curtale G, Mantovani A. Diversity, Mechanisms, and Significance of Macrophage Plasticity. ANNUAL REVIEW OF PATHOLOGY 2020; 15:123-147. [PMID: 31530089 PMCID: PMC7176483 DOI: 10.1146/annurev-pathmechdis-012418-012718] [Citation(s) in RCA: 1027] [Impact Index Per Article: 256.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Macrophages are a diverse set of cells present in all body compartments. This diversity is imprinted by their ontogenetic origin (embryonal versus adult bone marrow-derived cells); the organ context; by their activation or deactivation by various signals in the contexts of microbial invasion, tissue damage, and metabolic derangement; and by polarization of adaptive T cell responses. Classic adaptive responses of macrophages include tolerance, priming, and a wide spectrum of activation states, including M1, M2, or M2-like. Moreover, macrophages can retain long-term imprinting of microbial encounters (trained innate immunity). Single-cell analysis of mononuclear phagocytes in health and disease has added a new dimension to our understanding of the diversity of macrophage differentiation and activation. Epigenetic landscapes, transcription factors, and microRNA networks underlie the adaptability of macrophages to different environmental cues. Macrophage plasticity, an essential component of chronic inflammation, and its involvement in diverse human diseases, most notably cancer, is discussed here as a paradigm.
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Affiliation(s)
- Massimo Locati
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, 20089 Milan, Italy
- Humanitas Clinical and Research Center, 20089 Milan, Italy;
| | - Graziella Curtale
- Department of Medical Biotechnologies and Translational Medicine, Università degli Studi di Milano, 20089 Milan, Italy
- Humanitas Clinical and Research Center, 20089 Milan, Italy;
| | - Alberto Mantovani
- Humanitas Clinical and Research Center, 20089 Milan, Italy;
- Humanitas University, 20090 Milan, Italy
- The William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
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64
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Weiterer S, Meier‐Soelch J, Georgomanolis T, Mizi A, Beyerlein A, Weiser H, Brant L, Mayr‐Buro C, Jurida L, Beuerlein K, Müller H, Weber A, Tenekeci U, Dittrich‐Breiholz O, Bartkuhn M, Nist A, Stiewe T, van IJcken WFJ, Riedlinger T, Schmitz ML, Papantonis A, Kracht M. Distinct IL-1α-responsive enhancers promote acute and coordinated changes in chromatin topology in a hierarchical manner. EMBO J 2020; 39:e101533. [PMID: 31701553 PMCID: PMC6939198 DOI: 10.15252/embj.2019101533] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
How cytokine-driven changes in chromatin topology are converted into gene regulatory circuits during inflammation still remains unclear. Here, we show that interleukin (IL)-1α induces acute and widespread changes in chromatin accessibility via the TAK1 kinase and NF-κB at regions that are highly enriched for inflammatory disease-relevant SNPs. Two enhancers in the extended chemokine locus on human chromosome 4 regulate the IL-1α-inducible IL8 and CXCL1-3 genes. Both enhancers engage in dynamic spatial interactions with gene promoters in an IL-1α/TAK1-inducible manner. Microdeletions of p65-binding sites in either of the two enhancers impair NF-κB recruitment, suppress activation and biallelic transcription of the IL8/CXCL2 genes, and reshuffle higher-order chromatin interactions as judged by i4C interactome profiles. Notably, these findings support a dominant role of the IL8 "master" enhancer in the regulation of sustained IL-1α signaling, as well as for IL-8 and IL-6 secretion. CRISPR-guided transactivation of the IL8 locus or cross-TAD regulation by TNFα-responsive enhancers in a different model locus supports the existence of complex enhancer hierarchies in response to cytokine stimulation that prime and orchestrate proinflammatory chromatin responses downstream of NF-κB.
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Affiliation(s)
- Sinah‐Sophia Weiterer
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Johanna Meier‐Soelch
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | | | - Athanasia Mizi
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Anna Beyerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Hendrik Weiser
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Lilija Brant
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Christin Mayr‐Buro
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Liane Jurida
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Knut Beuerlein
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Helmut Müller
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Axel Weber
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Ulas Tenekeci
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
| | - Oliver Dittrich‐Breiholz
- Research Core Unit GenomicsInstitute of Physiological ChemistryMedical School HannoverHannoverGermany
| | - Marek Bartkuhn
- Institute for GeneticsJustus Liebig University GiessenGiessenGermany
| | - Andrea Nist
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
| | - Thorsten Stiewe
- Genomics Core Facility and Institute of Molecular OncologyPhilipps University MarburgMarburgGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
| | | | - Tabea Riedlinger
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - M Lienhard Schmitz
- Member of the German Center for Lung Research (DZL)GiessenGermany
- Institute of BiochemistryJustus Liebig University GiessenGiessenGermany
| | - Argyris Papantonis
- Center for Molecular Medicine CologneUniversity of CologneCologneGermany
- Department of PathologyUniversity Medical Center GöttingenGöttingenGermany
| | - Michael Kracht
- Rudolf Buchheim Institute of PharmacologyJustus Liebig University GiessenGiessenGermany
- Member of the German Center for Lung Research (DZL)GiessenGermany
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65
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Bellanti F, Pannone G, Tartaglia N, Serviddio G. Redox Control of the Immune Response in the Hepatic Progenitor Cell Niche. Front Cell Dev Biol 2020; 8:295. [PMID: 32435643 PMCID: PMC7218163 DOI: 10.3389/fcell.2020.00295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/06/2020] [Indexed: 02/05/2023] Open
Abstract
The liver commonly self-regenerates by a proliferation of mature cell types. Nevertheless, in case of severe or protracted damage, the organ renewal is mediated by the hepatic progenitor cells (HPCs), adult progenitors capable of differentiating toward the biliary and the hepatocyte lineages. This regeneration process is determined by the formation of a stereotypical niche surrounding the emerging progenitors. The organization of the HPC niche microenvironment is crucial to drive biliary or hepatocyte regeneration. Furthermore, this is the site of a complex immunological activity mediated by several immune and non-immune cells. Indeed, several cytokines produced by monocytes, macrophages and T-lymphocytes may promote the activation of HPCs in the niche. On the other side, HPCs may produce pro-inflammatory cytokines induced by liver inflammation. The inflamed liver is characterized by high generation of reactive oxygen and nitrogen species, which in turn lead to the oxidation of macromolecules and the alteration of signaling pathways. Reactive species and redox signaling are involved in both the immunological and the adult stem cell regeneration processes. It is then conceivable that redox balance may finely regulate the immune response in the HPC niche, modulating the regeneration process and the immune activity of HPCs. In this perspective article, we summarize the current knowledge on the role of reactive species in the regulation of hepatic immunity, suggesting future research directions for the study of redox signaling on the immunomodulatory properties of HPCs.
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Affiliation(s)
- Francesco Bellanti
- Center for Experimental and Regenerative Medicine, Institute of Internal Medicine, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
- *Correspondence: Francesco Bellanti,
| | - Giuseppe Pannone
- Institute of Anatomical Pathology, Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Nicola Tartaglia
- Institute of General Surgery, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Gaetano Serviddio
- Center for Experimental and Regenerative Medicine, Institute of Internal Medicine, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
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66
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Barrat FJ, Crow MK, Ivashkiv LB. Interferon target-gene expression and epigenomic signatures in health and disease. Nat Immunol 2019; 20:1574-1583. [PMID: 31745335 PMCID: PMC7024546 DOI: 10.1038/s41590-019-0466-2] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 07/10/2019] [Indexed: 02/06/2023]
Abstract
Multiple type I interferons and interferon-γ (IFN-γ) are expressed under physiological conditions and are increased by stress and infections, and in autoinflammatory and autoimmune diseases. Interferons activate the Jak-STAT signaling pathway and induce overlapping patterns of expression, called 'interferon signatures', of canonical interferon-stimulated genes (ISGs) encoding molecules important for antiviral responses, antigen presentation, autoimmunity and inflammation. It has now become clear that interferons also induce an 'interferon epigenomic signature' by activating latent enhancers and 'bookmarking' chromatin, thus reprogramming cell responses to environmental cues. The interferon epigenomic signature affects ISGs and other gene sets, including canonical targets of the transcription factor NF-κB that encode inflammatory molecules, and is involved in the priming of immune cells, tolerance and the training of innate immune memory. Here we review the mechanisms through which interferon signatures and interferon epigenomic signatures are generated, as well as the expression and functional consequences of these signatures in homeostasis and autoimmune diseases, including systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis.
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Affiliation(s)
- Franck J Barrat
- Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, USA
| | - Mary K Crow
- Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lionel B Ivashkiv
- Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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67
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Ramirez-Prado JS, Latrasse D, Rodriguez-Granados NY, Huang Y, Manza-Mianza D, Brik-Chaouche R, Jaouannet M, Citerne S, Bendahmane A, Hirt H, Raynaud C, Benhamed M. The Polycomb protein LHP1 regulates Arabidopsis thaliana stress responses through the repression of the MYC2-dependent branch of immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1118-1131. [PMID: 31437321 DOI: 10.1111/tpj.14502] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/26/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.
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Affiliation(s)
- Juan Sebastian Ramirez-Prado
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Natalia Yaneth Rodriguez-Granados
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Ying Huang
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Deborah Manza-Mianza
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Rim Brik-Chaouche
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Maelle Jaouannet
- CNRS, INRA, Université Nice Sophia Antipolis, UMR 1355-7254, Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Heribert Hirt
- Desert Agriculture Initiative, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Kingdom of Saudi Arabia
| | - Cecile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405, Orsay, France
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68
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Negi S, Das DK, Pahari S, Nadeem S, Agrewala JN. Potential Role of Gut Microbiota in Induction and Regulation of Innate Immune Memory. Front Immunol 2019; 10:2441. [PMID: 31749793 PMCID: PMC6842962 DOI: 10.3389/fimmu.2019.02441] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
The gut microbiota significantly regulates the development and function of the innate and adaptive immune system. The attribute of immunological memory has long been linked only with adaptive immunity. Recent evidence indicates that memory is also present in the innate immune cells such as monocytes/macrophages and natural killer cells. These cells exhibit pattern recognition receptors (PRRs) that recognize microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs) expressed by the microbes. Interaction between PRRs and MAMPs is quite crucial since it triggers the sequence of signaling events and epigenetic rewiring that not only play a cardinal role in modulating the activation and function of the innate cells but also impart a sense of memory response. We discuss here how gut microbiota can influence the generation of innate memory and functional reprogramming of bone marrow progenitors that helps in protection against infections. This article will broaden our current perspective of association between the gut microbiome and innate memory. In the future, this knowledge may pave avenues for development and designing of novel immunotherapies and vaccination strategies.
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Affiliation(s)
- Shikha Negi
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Gastroenterology Division, Washington University in St. Louis, St. Louis, MO, United States
| | - Deepjyoti Kumar Das
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Susanta Pahari
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Immunology Division, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Sajid Nadeem
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Microbiology, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Center for Biomedical Engineering, Indian Institute of Technology-Ropar, Rupnagar, India
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69
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Glycerol phosphate shuttle enzyme GPD2 regulates macrophage inflammatory responses. Nat Immunol 2019; 20:1186-1195. [PMID: 31384058 PMCID: PMC6707851 DOI: 10.1038/s41590-019-0453-7] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 06/26/2019] [Indexed: 01/25/2023]
Abstract
Macrophages are activated during microbial infection to coordinate inflammatory responses and host defense. Here we find that in macrophages activated by bacterial lipopolysaccharide (LPS), mitochondrial glycerol 3-phosphate dehydrogenase (GPD2) regulates glucose oxidation to drive inflammatory responses. GPD2, a component of the glycerol phosphate shuttle, boosts glucose oxidation to fuel the production of acetyl coenzyme A, acetylation of histones and induction of genes encoding inflammatory mediators. While acute exposure to LPS drives macrophage activation, prolonged exposure to LPS triggers tolerance to LPS, where macrophages induce immunosuppression to limit the detrimental effects of sustained inflammation. The shift in the inflammatory response is modulated by GPD2, which coordinates a shutdown of oxidative metabolism; this limits the availability of acetyl coenzyme A for histone acetylation at genes encoding inflammatory mediators and thus contributes to the suppression of inflammatory responses. Therefore, GPD2 and the glycerol phosphate shuttle integrate the extent of microbial stimulation with glucose oxidation to balance the beneficial and detrimental effects of the inflammatory response.
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70
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Ivashkiv LB. IFNγ: signalling, epigenetics and roles in immunity, metabolism, disease and cancer immunotherapy. Nat Rev Immunol 2019; 18:545-558. [PMID: 29921905 DOI: 10.1038/s41577-018-0029-z] [Citation(s) in RCA: 689] [Impact Index Per Article: 137.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
IFNγ is a cytokine with important roles in tissue homeostasis, immune and inflammatory responses and tumour immunosurveillance. Signalling by the IFNγ receptor activates the Janus kinase (JAK)-signal transducer and activator of transcription 1 (STAT1) pathway to induce the expression of classical interferon-stimulated genes that have key immune effector functions. This Review focuses on recent advances in our understanding of the transcriptional, chromatin-based and metabolic mechanisms that underlie IFNγ-mediated polarization of macrophages to an 'M1-like' state, which is characterized by increased pro-inflammatory activity and macrophage resistance to tolerogenic and anti-inflammatory factors. In addition, I describe the newly discovered effects of IFNγ on other leukocytes, vascular cells, adipose tissue cells, neurons and tumour cells that have important implications for autoimmunity, metabolic diseases, atherosclerosis, neurological diseases and immune checkpoint blockade cancer therapy.
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Affiliation(s)
- Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program, David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY, USA.
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71
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Natoli G, Ostuni R. Adaptation and memory in immune responses. Nat Immunol 2019; 20:783-792. [PMID: 31213714 DOI: 10.1038/s41590-019-0399-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/12/2019] [Indexed: 02/07/2023]
Abstract
Adaptation is the ability of cells, tissues and organisms to rapidly and reversibly modify their properties to maximize fitness in a changing environment. The activity of immune-system components unfolds in the remarkably heterogeneous milieus to which they are exposed in different tissues, during homeostasis or during various acute or chronic pathological states. Therefore, adaptation is essential for immune cells to tune their responses to a large variety of contexts and conditions. The adaptation of immune cells reflects the integration of multiple inputs acting simultaneously or in a temporal sequence, which eventually leads to transcriptional reprogramming and to various functional consequences, some of which extend beyond the duration of the stimulus. A range of adaptive responses have been observed in both adaptive immune cells and innate immune cells; these are referred to with terms such as 'plasticity', 'priming', 'training', 'exhaustion' and 'tolerance', among others, all of which can be useful for defining a certain immunological process or outcome but whose underlying molecular frameworks are often incompletely understood. Here we review and analyze mechanisms of adaptation and memory in immunity with the aim of providing basic concepts that rationalize the properties and molecular bases of these essential processes.
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Affiliation(s)
- Gioacchino Natoli
- Humanitas University, Pieve Emanuele, Milan, Italy. .,IRCCS Humanitas, Rozzano, Milan, Italy.
| | - Renato Ostuni
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy. .,Vita-Salute San Raffaele University, Milan, Italy.
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72
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Roy AL. Transcriptional Regulation in the Immune System: One Cell at a Time. Front Immunol 2019; 10:1355. [PMID: 31258532 PMCID: PMC6587892 DOI: 10.3389/fimmu.2019.01355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
Transcriptional regulation of cells in the immune system must be strictly controlled at multiple levels to ensure that a proper immune response is elicited only when required. Analysis in bulk, or ensemble of cells, provides a wealth of important information leading to a better understanding of the various molecular steps and mechanisms involved in regulating gene expression in immune cells. However, given the substantial heterogeneity of these cells, it is imperative now to decipher these mechanisms at a single cell level. Here I bring together several recent examples to review our understanding of transcriptional regulation of the immune system via single cell analysis and to further illustrate the immense power of such analyses to interrogate immune cell heterogeneity.
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Affiliation(s)
- Ananda L Roy
- National Institutes of Health, Laboratory of Molecular Biology and Immunology, Biomedical Research Center, National Institute on Aging (NIH), Baltimore, MD, United States
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73
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Boukhaled GM, Corrado M, Guak H, Krawczyk CM. Chromatin Architecture as an Essential Determinant of Dendritic Cell Function. Front Immunol 2019; 10:1119. [PMID: 31214161 PMCID: PMC6557980 DOI: 10.3389/fimmu.2019.01119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/02/2019] [Indexed: 12/18/2022] Open
Abstract
Epigenetics has widespread implications in a variety of cellular processes ranging from cell identity and specification, to cellular adaptation to environmental stimuli. While typically associated with heritable changes in gene expression, epigenetic mechanisms are now appreciated to regulate dynamic changes in gene expression—even in post-mitotic cells. Cells of the innate immune system, including dendritic cells (DC), rapidly integrate signals from their microenvironment and respond accordingly, undergoing massive changes in transcriptional programming. This dynamic transcriptional reprogramming relies on epigenetic changes mediated by numerous enzymes and their substrates. This review highlights our current understanding of epigenetic regulation of DC function. Epigenetic mechanisms contribute to the maintenance of the steady state and are important for precise responses to proinflammatory stimuli. Interdependence between epigenetic modifications and the delicate balance of metabolites present another layer of complexity. In addition, dynamic regulation of the expression of proteins that modify chromatin architecture in DCs significantly impacts DC function. Environmental factors, including inflammation, aging, chemicals, nutrients, and lipid mediators, are increasingly appreciated to affect the epigenome in DCs, and, in doing so, regulate host immunity. Our understanding of how epigenetic mechanisms regulate DC function is in its infancy, and it must be expanded in order to discern the mechanisms underlying the balance between health and disease states.
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Affiliation(s)
- Giselle M Boukhaled
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Mario Corrado
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Hannah Guak
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada
| | - Connie M Krawczyk
- Department of Physiology, Goodman Cancer Research Center, McGill University, Montreal, QC, Canada.,Center for Cancer and Cell Biology, Program in Metabolic and Nutritional Programming, Van Andel Institute, Grand Rapids, MI, United States
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Donlin LT, Park SH, Giannopoulou E, Ivovic A, Park-Min KH, Siegel RM, Ivashkiv LB. Insights into rheumatic diseases from next-generation sequencing. Nat Rev Rheumatol 2019; 15:327-339. [PMID: 31000790 PMCID: PMC6673602 DOI: 10.1038/s41584-019-0217-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rheumatic diseases have complex aetiologies that are not fully understood, which makes the study of pathogenic mechanisms in these diseases a challenge for researchers. Next-generation sequencing (NGS) and related omics technologies, such as transcriptomics, epigenomics and genomics, provide an unprecedented genome-wide view of gene expression, environmentally responsive epigenetic changes and genetic variation. The integrated application of NGS technologies to samples from carefully phenotyped clinical cohorts of patients has the potential to solve remaining mysteries in the pathogenesis of several rheumatic diseases, to identify new therapeutic targets and to underpin a precision medicine approach to the diagnosis and treatment of rheumatic diseases. This Review provides an overview of the NGS technologies available, showcases important advances in rheumatic disease research already powered by these technologies and highlights NGS approaches that hold particular promise for generating new insights and advancing the field.
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Affiliation(s)
- Laura T Donlin
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sung-Ho Park
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Eugenia Giannopoulou
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, USA
| | - Aleksandra Ivovic
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Richard M Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA.
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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76
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Emerging Principles of Gene Expression Programs and Their Regulation. Mol Cell 2019; 71:389-397. [PMID: 30075140 DOI: 10.1016/j.molcel.2018.07.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022]
Abstract
Many mechanisms contribute to regulation of gene expression to ensure coordinated cellular behaviors and fate decisions. Transcriptional responses to external signals can consist of many hundreds of genes that can be parsed into different categories based on kinetics of induction, cell-type and signal specificity, and duration of the response. Here we discuss the structure of transcription programs and suggest a basic framework to categorize gene expression programs based on characteristics related to their control mechanisms. We also discuss possible evolutionary implications of this framework.
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77
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Gene activation precedes DNA demethylation in response to infection in human dendritic cells. Proc Natl Acad Sci U S A 2019; 116:6938-6943. [PMID: 30886108 PMCID: PMC6452747 DOI: 10.1073/pnas.1814700116] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Immune response to infection is accompanied by active demethylation of thousands of CpG sites. Yet, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we investigated the role of DNA methylation in the regulation of innate immune responses to bacterial infections. We found that virtually all changes in gene expression in response to infection occur prior to detectable alterations in the methylome. We also found that the binding of most infection-induced transcription factors precedes loss of methylation. Collectively, our results show that changes in methylation are a downstream consequence of transcription factor binding, and not essential for the establishment of the core regulatory program engaged upon infection. DNA methylation is considered to be a relatively stable epigenetic mark. However, a growing body of evidence indicates that DNA methylation levels can change rapidly; for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells with Mycobacterium tuberculosis. We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements. However, virtually all changes in gene expression in response to infection occur before detectable changes in DNA methylation, indicating that the observed losses in methylation are a downstream consequence of transcriptional activation. Footprinting analysis revealed that immune-related transcription factors (TFs), such as NF-κB/Rel, are recruited to enhancer elements before the observed losses in methylation, suggesting that DNA demethylation is mediated by TF binding to cis-acting elements. Collectively, our results show that DNA demethylation plays a limited role to the establishment of the core regulatory program engaged upon infection.
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Ramón-Vázquez A, de la Rosa JV, Tabraue C, Lopez F, Díaz-Chico BN, Bosca L, Tontonoz P, Alemany S, Castrillo A. Common and Differential Transcriptional Actions of Nuclear Receptors Liver X Receptors α and β in Macrophages. Mol Cell Biol 2019; 39:e00376-18. [PMID: 30602495 PMCID: PMC6379585 DOI: 10.1128/mcb.00376-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/07/2023] Open
Abstract
The liver X receptors α and β (LXRα and LXRβ) are oxysterol-activated transcription factors that coordinately regulate gene expression that is important for cholesterol and fatty acid metabolism. In addition to their roles in lipid metabolism, LXRs participate in the transcriptional regulation of macrophage activation and are considered potent regulators of inflammation. LXRs are highly similar, and despite notable exceptions, most of their reported functions are substantially overlapping. However, their individual genomic distribution and transcriptional capacities have not been characterized. Here, we report a macrophage cellular model expressing equivalent levels of tagged LXRs. Analysis of data from chromatin immunoprecipitation coupled with deep sequencing revealed that LXRα and LXRβ occupy both overlapping and exclusive genomic regulatory sites of target genes and also control the transcription of a receptor-exclusive set of genes. Analysis of genomic H3K27 acetylation and mRNA transcriptional changes in response to synthetic agonist or antagonist treatments revealed a putative mode of pharmacologically independent regulation of transcription. Integration of microarray and sequencing data enabled the description of three possible mechanisms of LXR transcriptional activation. Together, these results contribute to our understanding of the common and differential genomic actions of LXRs and their impact on biological processes in macrophages.
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Affiliation(s)
- Ana Ramón-Vázquez
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Juan Vladimir de la Rosa
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Carlos Tabraue
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Felix Lopez
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Bonifacio Nicolas Díaz-Chico
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Lisardo Bosca
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Peter Tontonoz
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Susana Alemany
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Antonio Castrillo
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, Madrid, Spain
- Unidad de Biomedicina (Unidad Asociada al CSIC), Instituto Universitario de Investigaciones Biomédicas y Sanitarias, Grupo de Investigación Medio Ambiente y Salud, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
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79
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Epigenetics of autoimmune liver diseases: current progress and future directions. JOURNAL OF BIO-X RESEARCH 2019. [DOI: 10.1097/jbr.0000000000000030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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80
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Churpek JE, Bresnick EH. Transcription factor mutations as a cause of familial myeloid neoplasms. J Clin Invest 2019; 129:476-488. [PMID: 30707109 DOI: 10.1172/jci120854] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The initiation and evolution of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are driven by genomic events that disrupt multiple genes controlling hematopoiesis. Human genetic studies have discovered germline mutations in single genes that instigate familial MDS/AML. The best understood of these genes encode transcription factors, such as GATA-2, RUNX1, ETV6, and C/EBPα, which establish and maintain genetic networks governing the genesis and function of blood stem and progenitor cells. Many questions remain unanswered regarding how genes and circuits within these networks function in physiology and disease and whether network integrity is exquisitely sensitive to or efficiently buffered from perturbations. In familial MDS/AML, mutations change the coding sequence of a gene to generate a mutant protein with altered activity or introduce frameshifts or stop codons or disrupt regulatory elements to alter protein expression. Each mutation has the potential to exert quantitatively and qualitatively distinct influences on networks. Consistent with this mechanistic diversity, disease onset is unpredictable and phenotypic variability can be considerable. Efforts to elucidate mechanisms and forge prognostic and therapeutic strategies must therefore contend with a spectrum of patient-specific leukemogenic scenarios. Here we illustrate mechanistic advances in our understanding of familial MDS/AML syndromes caused by germline mutations of hematopoietic transcription factors.
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Affiliation(s)
- Jane E Churpek
- Section of Hematology/Oncology and Center for Clinical Cancer Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Emery H Bresnick
- UW-Madison Blood Research Program, Department of Cell and Regenerative Biology, Wisconsin Institutes for Medical Research, UW Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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81
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Borst K, Schwabenland M, Prinz M. Microglia metabolism in health and disease. Neurochem Int 2018; 130:104331. [PMID: 30423423 DOI: 10.1016/j.neuint.2018.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/24/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022]
Abstract
In the last decade tremendous progress has been made in understanding how the immune system reacts to insults. During this progress it became obvious that those immune responses are tightly regulated and cross-linked with distinct metabolic changes in immune cells. Extensive research has been conducted mainly on subtypes of T cells, which use different metabolic pathways during differentiation processes and activation states. In addition, it has also been established later, that the innate immune cell lineage of myeloid cells includes a variety of different subsets of bone marrow-derived as well as tissue-specific macrophages, which elicit much more functions than simply killing bacteria. To execute this high variety of functions, also macrophages use different metabolic pathways and are tightly regulated by key metabolic regulators, such as the mechanistic target of rapamycin (mTOR). Upon activation, metabolic changes within the cell occur to meet the requirements of the phenotypic switch. In addition, metabolic changes correlate with the ability of innate immune cells to show hallmarks of adaptive immune responses. Little is known about specific metabolic changes of myeloid cells and specifically microglia in vivo. Microglia are key players in neurodegenerative and neuroinflammatory diseases and have become a major target of medical research. Here, we review the existing data on microglia metabolism and the connection of microglia phenotypes with neuroinflammatory and neurodegenerative diseases. Lastly, we will discuss how our knowledge about the cellular metabolism might be used to develop new treatment options for neurological diseases.
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Affiliation(s)
- Katharina Borst
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Germany
| | - Marius Schwabenland
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Germany.
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Tamassia N, Bianchetto-Aguilera F, Arruda-Silva F, Gardiman E, Gasperini S, Calzetti F, Cassatella MA. Cytokine production by human neutrophils: Revisiting the "dark side of the moon". Eur J Clin Invest 2018; 48 Suppl 2:e12952. [PMID: 29772063 DOI: 10.1111/eci.12952] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/10/2018] [Indexed: 12/17/2022]
Abstract
Polymorphonuclear neutrophils are the most numerous leucocytes present in human blood, and function as crucial players in innate immune responses. Neutrophils are indispensable for the defence towards microbes, as they effectively counter them by releasing toxic enzymes, by synthetizing reactive oxygen species and by producing inflammatory mediators. Interestingly, recent findings have highlighted an important role of neutrophils also as promoters of the resolution of inflammation process, indicating that their biological functions go well beyond simple pathogen killing. Consistently, data from the last decades have highlighted that neutrophils may even contribute to the development of adaptive immunity by performing previously unanticipated functions, including the capacity to extend their survival, directly interact with other leucocytes or cell types, and produce and release a variety of cytokines. In this article, we will summarize the main features of, as well as emphasize some important concepts on, the production of cytokines by human neutrophils.
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Affiliation(s)
- Nicola Tamassia
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | | | - Fabio Arruda-Silva
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy.,CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil
| | - Elisa Gardiman
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Sara Gasperini
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Federica Calzetti
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
| | - Marco A Cassatella
- Department of Medicine, Section of General Pathology, University of Verona, Verona, Italy
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Vandenbon A, Kumagai Y, Lin M, Suzuki Y, Nakai K. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol 2018; 19:138. [PMID: 30231913 PMCID: PMC6146659 DOI: 10.1186/s13059-018-1524-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. RESULTS Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data reveals potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 are associated with binding by STAT1/2 and were severely impaired in Stat1-/- cells. CONCLUSIONS While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs and their interactions with chromatin modifiers.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
- Institute for Liberal Arts and Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, Immunology Frontier Research Center (IFReC), Osaka University, Suita, 565-0871, Japan
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8565, Japan
| | - Mengjie Lin
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kenta Nakai
- Laboratory of Functional Analysis in silico, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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Interferon stimulation creates chromatin marks and establishes transcriptional memory. Proc Natl Acad Sci U S A 2018; 115:E9162-E9171. [PMID: 30201712 DOI: 10.1073/pnas.1720930115] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Epigenetic memory for signal-dependent transcription has remained elusive. So far, the concept of epigenetic memory has been largely limited to cell-autonomous, preprogrammed processes such as development and metabolism. Here we show that IFNβ stimulation creates transcriptional memory in fibroblasts, conferring faster and greater transcription upon restimulation. The memory was inherited through multiple cell divisions and led to improved antiviral protection. Of ∼2,000 IFNβ-stimulated genes (ISGs), about half exhibited memory, which we define as memory ISGs. The rest, designated nonmemory ISGs, did not show memory. Surprisingly, mechanistic analysis showed that IFN memory was not due to enhanced IFN signaling or retention of transcription factors on the ISGs. We demonstrated that this memory was attributed to accelerated recruitment of RNA polymerase II and transcription/chromatin factors, which coincided with acquisition of the histone H3.3 and H3K36me3 chromatin marks on memory ISGs. Similar memory was observed in bone marrow macrophages after IFNγ stimulation, suggesting that IFN stimulation modifies the shape of the innate immune response. Together, external signals can establish epigenetic memory in mammalian cells that imparts lasting adaptive performance upon various somatic cells.
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85
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Ramirez-Prado JS, Abulfaraj AA, Rayapuram N, Benhamed M, Hirt H. Plant Immunity: From Signaling to Epigenetic Control of Defense. TRENDS IN PLANT SCIENCE 2018; 23:833-844. [PMID: 29970339 DOI: 10.1016/j.tplants.2018.06.004] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 06/04/2018] [Accepted: 06/07/2018] [Indexed: 05/21/2023]
Abstract
Pathogen recognition by plants results in the activation of signaling pathways that induce defense reactions. There is growing evidence indicating that epigenetic mechanisms directly participate in plant immune memory. Here, we discuss current knowledge of diverse epigenomic processes and elements, such as noncoding RNAs, DNA and RNA methylation, histone post-translational modifications, and chromatin remodeling, that have been associated with the regulation of immune responses in plants. Furthermore, we discuss the currently limited evidence of transgenerational inheritance of pathogen-induced defense priming, together with its potentials, challenges, and limitations for crop improvement and biotechnological applications.
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Affiliation(s)
- Juan S Ramirez-Prado
- Desert Agriculture Initiative, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Institut des Sciences des Plantes de Paris Saclay, IPS2, Bâtiment 630, Plateau du Moulon, Rue Noetzlin CS 80004, 91192 Gif-sur-Yvette, France; These authors contributed equally
| | - Aala A Abulfaraj
- Desert Agriculture Initiative, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Department of Biology, Science and Arts College, Rabigh Campus, King Abdulaziz University, Jeddah 21589, Saudi Arabia; These authors contributed equally
| | - Naganand Rayapuram
- Desert Agriculture Initiative, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; These authors contributed equally
| | - Moussa Benhamed
- Institut des Sciences des Plantes de Paris Saclay, IPS2, Bâtiment 630, Plateau du Moulon, Rue Noetzlin CS 80004, 91192 Gif-sur-Yvette, France.
| | - Heribert Hirt
- Desert Agriculture Initiative, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Institut des Sciences des Plantes de Paris Saclay, IPS2, Bâtiment 630, Plateau du Moulon, Rue Noetzlin CS 80004, 91192 Gif-sur-Yvette, France.
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Recent advances in vertebrate and invertebrate transgenerational immunity in the light of ecology and evolution. Heredity (Edinb) 2018; 121:225-238. [PMID: 29915335 DOI: 10.1038/s41437-018-0101-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 05/06/2018] [Accepted: 05/31/2018] [Indexed: 12/18/2022] Open
Abstract
Parental experience with parasites and pathogens can lead to increased offspring resistance to infection, through a process known as transgenerational immune priming (TGIP). Broadly defined, TGIP occurs across a wide range of taxa, and can be viewed as a type of phenotypic plasticity, with hosts responding to the pressures of relevant local infection risk by altering their offspring's immune defenses. There are ever increasing examples of both invertebrate and vertebrate TGIP, which go beyond classical examples of maternal antibody transfer. Here we critically summarize the current evidence for TGIP in both invertebrates and vertebrates. Mechanisms underlying TGIP remain elusive in many systems, but while it is unlikely that they are conserved across the range of organisms with TGIP, recent insight into epigenetic modulation may challenge this view. We place TGIP into a framework of evolutionary ecology, discussing costs and relevant environmental variation. We highlight how the ecology of species or populations should affect if, where, when, and how TGIP is realized. We propose that the field can progress by incorporating evolutionary ecology focused designs to the study of the so far well chronicled, but mostly descriptive TGIP, and how rapidly developing -omic methods can be employed to further understand TGIP across taxa.
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87
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MLL5 suppresses antiviral innate immune response by facilitating STUB1-mediated RIG-I degradation. Nat Commun 2018; 9:1243. [PMID: 29593341 PMCID: PMC5871759 DOI: 10.1038/s41467-018-03563-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/23/2018] [Indexed: 12/27/2022] Open
Abstract
Trithorax group protein MLL5 is an important epigenetic modifier that controls cell cycle progression, chromatin architecture maintenance, and hematopoiesis. However, whether MLL5 has a role in innate antiviral immunity is largely unknown. Here we show that MLL5 suppresses the RIG-I-mediated anti-viral immune response. Mll5-deficient mice infected with vesicular stomatitis virus show enhanced anti-viral innate immunity, reduced morbidity, and viral load. Mechanistically, a fraction of MLL5 located in the cytoplasm interacts with both RIG-I and its E3 ubiquitin ligase STUB1, which promotes K48-linked polyubiquitination and proteasomal degradation of RIG-I. MLL5 deficiency attenuates the RIG-I and STUB1 association, reducing K48-linked polyubiquitination and accumulation of RIG-I protein in cells. Upon virus infection, nuclear MLL5 protein translocates from the nucleus to the cytoplasm inducing STUB1-mediated degradation of RIG-I. Our study uncovers a previously unrecognized role for MLL5 in antiviral innate immune responses and suggests a new target for controlling viral infection. MLL5 is an essential epigenetic modifier involved in cell cycle progression, chromatin architecture and hematopoiesis. Here the authors establish that MLL5 suppresses the innate immune response in a murine model of virus infection by targeting and promoting degradation of RIG-I.
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88
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Sacta MA, Tharmalingam B, Coppo M, Rollins DA, Deochand DK, Benjamin B, Yu L, Zhang B, Hu X, Li R, Chinenov Y, Rogatsky I. Gene-specific mechanisms direct glucocorticoid-receptor-driven repression of inflammatory response genes in macrophages. eLife 2018; 7:34864. [PMID: 29424686 PMCID: PMC5821458 DOI: 10.7554/elife.34864] [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: 01/07/2018] [Accepted: 01/28/2018] [Indexed: 01/13/2023] Open
Abstract
The glucocorticoid receptor (GR) potently represses macrophage-elicited inflammation, however, the underlying mechanisms remain obscure. Our genome-wide analysis in mouse macrophages reveals that pro-inflammatory paused genes, activated via global negative elongation factor (NELF) dissociation and RNA Polymerase (Pol)2 release from early elongation arrest, and non-paused genes, induced by de novo Pol2 recruitment, are equally susceptible to acute glucocorticoid repression. Moreover, in both cases the dominant mechanism involves rapid GR tethering to p65 at NF-kB-binding sites. Yet, specifically at paused genes, GR activation triggers widespread promoter accumulation of NELF, with myeloid cell-specific NELF deletion conferring glucocorticoid resistance. Conversely, at non-paused genes, GR attenuates the recruitment of p300 and histone acetylation, leading to a failure to assemble BRD4 and Mediator at promoters and enhancers, ultimately blocking Pol2 initiation. Thus, GR displays no preference for a specific pro-inflammatory gene class; however, it effects repression by targeting distinct temporal events and components of transcriptional machinery.
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Affiliation(s)
- Maria A Sacta
- Weill Cornell/ Rockefeller/ Sloan Kettering Tri-Institutional MD-PhD Program, New York, United States.,Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Bowranigan Tharmalingam
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Maddalena Coppo
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - David A Rollins
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
| | - Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Bradley Benjamin
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Li Yu
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Bin Zhang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xiaoyu Hu
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Rong Li
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, United States
| | - Yurii Chinenov
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosensweig Genomics Center, New York, United States.,Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, United States
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89
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MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A 2018; 115:E1012-E1021. [PMID: 29339515 PMCID: PMC5798318 DOI: 10.1073/pnas.1706928115] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ-dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]. Categorizing by function, we observed down-regulation of gene expression associated with antigen presentation following both H5N1-VN1203 and MERS-CoV infection. Further examination revealed global down-regulation of antigen-presentation gene expression, which was confirmed by proteomics for both H5N1-VN1203 and MERS-CoV infection. Importantly, epigenetic analysis suggested that DNA methylation, rather than histone modification, plays a crucial role in MERS-CoV-mediated antagonism of antigen-presentation gene expression; in contrast, H5N1-VN1203 likely utilizes a combination of epigenetic mechanisms to target antigen presentation. Together, the results indicate a common mechanism utilized by H5N1-VN1203 and MERS-CoV to modulate antigen presentation and the host adaptive immune response.
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90
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Weigert A, von Knethen A, Fuhrmann D, Dehne N, Brüne B. Redox-signals and macrophage biology. Mol Aspects Med 2018; 63:70-87. [PMID: 29329794 DOI: 10.1016/j.mam.2018.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/08/2018] [Accepted: 01/08/2018] [Indexed: 12/15/2022]
Abstract
Macrophages are known for their versatile role in biology. They sense and clear structures that contain exogenous or endogenous pathogen-associated molecular patterns. This process is tightly linked to the production of a mixture of potentially harmful oxidants and cytokines. Their inherent destructive behavior is directed against foreign material or structures of 'altered self', which explains the role of macrophages during innate immune reactions and inflammation. However, there is also another side of macrophages when they turn into a tissue regenerative, pro-resolving, and healing phenotype. Phenotype changes of macrophages are termed macrophage polarization, representing a continuum between classical and alternative activation. Macrophages as the dominating producers of superoxide/hydrogen peroxide and nitric oxide are not only prone to oxidative modifications but also to more subtle signaling properties of redox-active molecules conveying redox regulation. We review basic concepts of the enzymatic nitric oxide and superoxide production within macrophages, refer to their unique chemical reactions and outline biological consequences not only for macrophage biology but also for their communication with cells in the microenvironment. These considerations link hypoxia to the NO system, addressing feedforward as well as feedback circuits. Moreover, we summarize the role of redox-signaling affecting epigenetics and reflect the central role of mitochondrial-derived oxygen species in inflammation. To better understand the diverse functions of macrophages during initiation as well as resolution of inflammation and to decode their versatile roles during innate and adaptive immunity with the entire spectrum of cell protective towards cell destructive activities we need to appreciate the signaling properties of redox-active species. Herein we discuss macrophage responses in terms of nitric oxide and superoxide formation with the modulating impact of hypoxia.
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Affiliation(s)
- Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Andreas von Knethen
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Dominik Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Nathalie Dehne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt, Germany; Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology, IME, 60590 Frankfurt, Germany.
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91
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Soldi M, Mari T, Nicosia L, Musiani D, Sigismondo G, Cuomo A, Pavesi G, Bonaldi T. Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers. Nucleic Acids Res 2017; 45:12195-12213. [PMID: 28981749 PMCID: PMC5716071 DOI: 10.1093/nar/gkx821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/06/2017] [Indexed: 01/09/2023] Open
Abstract
The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type–specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K4me1/K36me2 marks transcribed enhancers, while H3K4me1/K36me3 and H3K4me1/K79me2 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Tommaso Mari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Daniele Musiani
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Giulio Pavesi
- Department of Biosciences, Milan University, Milan 20133, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
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92
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Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation. Nat Immunol 2017; 18:1104-1116. [PMID: 28825701 PMCID: PMC5605457 DOI: 10.1038/ni.3818] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 07/28/2017] [Indexed: 12/14/2022]
Abstract
Cross-regulation of Toll-like receptor responses by cytokines is
essential for effective host defense, avoidance of toxicity, and homeostasis,
but the underlying mechanisms are not well understood. A comprehensive
epigenomic approach in human macrophages showed that the proinflammatory
cytokines TNF and type I IFNs induce transcriptional cascades that alter
chromatin states to broadly reprogram TLR4-induced responses. TNF tolerized
inflammatory genes to prevent toxicity, while preserving antiviral and metabolic
gene induction. Type I IFNs potentiated TNF inflammatory function by priming
chromatin to prevent silencing of inflammatory NF-κB target genes.
Priming of chromatin enabled robust transcriptional responses to weak upstream
signals. Similar chromatin regulation occurred in human diseases. Our findings
reveal that signaling crosstalk between IFNs and TNF is integrated at the level
of chromatin to reprogram inflammatory responses, and identify new functions and
mechanisms of action of these cytokines.
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93
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Abstract
Epigenetic regulation in myeloid cells is crucial for cell differentiation and activation in response to developmental and environmental cues. Epigenetic control involves posttranslational modification of DNA or chromatin, and is also coupled to upstream signaling pathways and transcription factors. In this review, we summarize key epigenetic events and how dynamics in the epigenetic landscape of myeloid cells shape the development, immune activation, and innate immune memory.
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94
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Li X, Zhang Q, Shi Q, Liu Y, Zhao K, Shen Q, Shi Y, Liu X, Wang C, Li N, Ma Y, Cao X. Demethylase Kdm6a epigenetically promotes IL-6 and IFN-β production in macrophages. J Autoimmun 2017; 80:85-94. [DOI: 10.1016/j.jaut.2017.02.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 12/22/2022]
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95
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Arruda-Silva F, Bianchetto-Aguilera F, Gasperini S, Polletti S, Cosentino E, Tamassia N, Cassatella MA. Human Neutrophils Produce CCL23 in Response to Various TLR-Agonists and TNFα. Front Cell Infect Microbiol 2017; 7:176. [PMID: 28553619 PMCID: PMC5427542 DOI: 10.3389/fcimb.2017.00176] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/24/2017] [Indexed: 12/29/2022] Open
Abstract
CCL23, also known as myeloid progenitor inhibitory factor (MPIF)-1, macrophage inflammatory protein (MIP)-3, or CKβ8, is a member of the CC chemokine subfamily exerting its effects via CCR1 binding. By doing so, CCL23 selectively recruits resting T lymphocytes and monocytes, inhibits proliferation of myeloid progenitor cells and promotes angiogenesis. Previously, we and other groups have reported that human neutrophils are able to produce chemokines upon appropriate activation, including CCR1-binding CCL2, CCL3, and CCL4. Herein, we demonstrate that human neutrophils display the capacity to also express and release CCL23 when stimulated by R848 and, to a lesser extent, by other pro-inflammatory agonists, including LPS, Pam3CSK4, and TNFα. Notably, we show that, on a per cell basis, R848-activated neutrophils produce higher levels of CCL23 than autologous CD14+-monocytes activated under similar experimental conditions. By contrast, we found that, unlike CD14+-monocytes, neutrophils do not produce CCL23 in response to IL-4, thus indicating that they express CCL23 in a stimulus-specific fashion. Finally, we show that the production of CCL23 by R848-stimulated neutrophils is negatively modulated by IFNα, which instead enhances that of CCL2. Together, data extend our knowledge on the chemokines potentially produced by neutrophils. The ability of human neutrophils to produce CCL23 further supports the notion on the neutrophil capacity of orchestrating the recruitment of different cell types to the inflamed sites, in turn contributing to the control of the immune response.
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Affiliation(s)
- Fabio Arruda-Silva
- Section of General Pathology, Department of Medicine, University of VeronaVerona, Italy
| | | | - Sara Gasperini
- Section of General Pathology, Department of Medicine, University of VeronaVerona, Italy
| | - Sara Polletti
- Humanitas Clinical and Research CenterMilan, Italy.,Department of Biomedical Sciences, Humanitas UniversityMilan, Italy
| | - Emanuela Cosentino
- Functional Genomic Lab, Department of Biotechnology, University of VeronaVerona, Italy
| | - Nicola Tamassia
- Section of General Pathology, Department of Medicine, University of VeronaVerona, Italy
| | - Marco A Cassatella
- Section of General Pathology, Department of Medicine, University of VeronaVerona, Italy
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96
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Ma S, Wan X, Deng Z, Shi L, Hao C, Zhou Z, Zhou C, Fang Y, Liu J, Yang J, Chen X, Li T, Zang A, Yin S, Li B, Plumas J, Chaperot L, Zhang X, Xu G, Jiang L, Shen N, Xiong S, Gao X, Zhang Y, Xiao H. Epigenetic regulator CXXC5 recruits DNA demethylase Tet2 to regulate TLR7/9-elicited IFN response in pDCs. J Exp Med 2017; 214:1471-1491. [PMID: 28416650 PMCID: PMC5413332 DOI: 10.1084/jem.20161149] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 01/20/2017] [Accepted: 03/03/2017] [Indexed: 12/14/2022] Open
Abstract
Ma and colleagues identify CXXC5 as an epigenetic regulator required for maintaining the hypomethylation of a subset of CGIs, thereby promoting the expression of transcriptional factors such as IRF7 in pDCs to enable robust IFN response to viral infection. TLR7/9 signals are capable of mounting massive interferon (IFN) response in plasmacytoid dendritic cells (pDCs) immediately after viral infection, yet the involvement of epigenetic regulation in this process has not been documented. Here, we report that zinc finger CXXC family epigenetic regulator CXXC5 is highly expressed in pDCs, where it plays a crucial role in TLR7/9- and virus-induced IFN response. Notably, genetic ablation of CXXC5 resulted in aberrant methylation of the CpG-containing island (CGI) within the Irf7 gene and impaired IRF7 expression in steady-state pDCs. Mechanistically, CXXC5 is responsible for the recruitment of DNA demethylase Tet2 to maintain the hypomethylation of a subset of CGIs, a process coincident with active histone modifications and constitutive transcription of these CGI-containing genes. Consequently, CXXC5-deficient mice had compromised early IFN response and became highly vulnerable to infection by herpes simplex virus and vesicular stomatitis virus. Together, our results identify CXXC5 as a novel epigenetic regulator for pDC-mediated antiviral response.
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Affiliation(s)
- Shixin Ma
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Institute of Biology and Medical Sciences, Soochow University, Soochow, Jiangsu 215006, China
| | - Xiaoling Wan
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zihou Deng
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lei Shi
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Congfang Hao
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenyuan Zhou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Chun Zhou
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiyuan Fang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinghua Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing Yang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xia Chen
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Tiantian Li
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Aiping Zang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shigang Yin
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Li
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Joel Plumas
- Institute for Advanced Biosciences (IAB), Team Immunobiology and Immunotherapy in Chronic Diseases, Institut National de la Santé et de la Recherche Médicale U1209, Centre National de la Recherche Scientifique UMR5309, Université Grenoble Alpes, Etablissement Français du Sang-Rhone-Alpes, F-38700 Grenoble, France
| | - Laurence Chaperot
- Institute for Advanced Biosciences (IAB), Team Immunobiology and Immunotherapy in Chronic Diseases, Institut National de la Santé et de la Recherche Médicale U1209, Centre National de la Recherche Scientifique UMR5309, Université Grenoble Alpes, Etablissement Français du Sang-Rhone-Alpes, F-38700 Grenoble, France
| | - Xiaoming Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoliang Xu
- State Key Laboratory of Molecular Biology, CAS Excellence Center in Molecular Cell Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lubin Jiang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Sidong Xiong
- Institute of Biology and Medical Sciences, Soochow University, Soochow, Jiangsu 215006, China
| | - Xiaoming Gao
- Institute of Biology and Medical Sciences, Soochow University, Soochow, Jiangsu 215006, China
| | - Yan Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Xiao
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai; CAS Center for Excellence in Molecular Cell Sciences; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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97
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The NF-κB-dependent and -independent transcriptome and chromatin landscapes of human coronavirus 229E-infected cells. PLoS Pathog 2017; 13:e1006286. [PMID: 28355270 PMCID: PMC5386326 DOI: 10.1371/journal.ppat.1006286] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/10/2017] [Accepted: 03/09/2017] [Indexed: 12/20/2022] Open
Abstract
Coronavirus replication takes place in the host cell cytoplasm and triggers inflammatory gene expression by poorly characterized mechanisms. To obtain more insight into the signals and molecular events that coordinate global host responses in the nucleus of coronavirus-infected cells, first, transcriptome dynamics was studied in human coronavirus 229E (HCoV-229E)-infected A549 and HuH7 cells, respectively, revealing a core signature of upregulated genes in these cells. Compared to treatment with the prototypical inflammatory cytokine interleukin(IL)-1, HCoV-229E replication was found to attenuate the inducible activity of the transcription factor (TF) NF-κB and to restrict the nuclear concentration of NF-κB subunits by (i) an unusual mechanism involving partial degradation of IKKβ, NEMO and IκBα and (ii) upregulation of TNFAIP3 (A20), although constitutive IKK activity and basal TNFAIP3 expression levels were shown to be required for efficient virus replication. Second, we characterized actively transcribed genomic regions and enhancers in HCoV-229E-infected cells and systematically correlated the genome-wide gene expression changes with the recruitment of Ser5-phosphorylated RNA polymerase II and prototypical histone modifications (H3K9ac, H3K36ac, H4K5ac, H3K27ac, H3K4me1). The data revealed that, in HCoV-infected (but not IL-1-treated) cells, an extensive set of genes was activated without inducible p65 NF-κB being recruited. Furthermore, both HCoV-229E replication and IL-1 were shown to upregulate a small set of genes encoding immunomodulatory factors that bind p65 at promoters and require IKKβ activity and p65 for expression. Also, HCoV-229E and IL-1 activated a common set of 440 p65-bound enhancers that differed from another 992 HCoV-229E-specific enhancer regions by distinct TF-binding motif combinations. Taken together, the study shows that cytoplasmic RNA viruses fine-tune NF-κB signaling at multiple levels and profoundly reprogram the host cellular chromatin landscape, thereby orchestrating the timely coordinated expression of genes involved in multiple signaling, immunoregulatory and metabolic processes. Coronaviruses are major human and animal pathogens. They belong to a family of plus-strand RNA viruses that have extremely large genomes and encode a variety of proteins involved in virus-host interactions. The four common coronaviruses (HCoV-229E, NL63, OC43, HKU1) cause mainly upper respiratory tract infections, while zoonotic coronaviruses (SARS-CoV and MERS-CoV) cause severe lung disease, including acute respiratory distress syndrome (ARDS). The molecular basis for this fundamentally different pathology is incompletely understood. Our study provides a genome-wide investigation of epigenetic changes occurring in response to HCoV-229E. We identify at high resolution a large number of regulatory regions in the genome of infected cells that coordinate de novo gene transcription. Many of these genes have immunomodulatory functions and, most likely, contribute to limiting viral replication, while other factors may promote viral replication. The study provides an intriguing example of a virus that completes its entire life cycle in the cytoplasm while sending multiple signals to the nuclear chromatin compartment to adjust the host cell repertoire of transcribed genes. The approach taken in this study is expected to provide a suitable framework for future studies aimed at dissecting and comparing host responses to representative coronaviruses with different pathogenic potential in humans.
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98
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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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99
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Tartey S, Takeuchi O. Pathogen recognition and Toll-like receptor targeted therapeutics in innate immune cells. Int Rev Immunol 2017; 36:57-73. [PMID: 28060562 DOI: 10.1080/08830185.2016.1261318] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The innate immune system deploys a variety of pattern-recognition receptors (PRRs) which include Toll-like receptors (TLRs), RIG-I-like receptors, NOD-like receptors, and C-type lectin receptors to detect the invasion of pathogens and initiate protective responses. The intercellular and intracellular orchestration of signals from different PRRs, their endogenous or microbial ligands and accessory molecules determine the stimulatory or inhibitory responses. Progressing over the last two decades, considerable research on the molecular mechanisms underlying host-pathogen interactions has led to a paradigm shift of our understanding of TLR signaling in the innate immune system. Given that a significant amount of evidence implicates TLRs in the pathogenesis of immune diseases and cancer, and their activation occurs early in the inflammatory cascade, they are attractive targets for novel therapeutic agents. In this review, we discuss the recent advances in TLR signaling cross talks and the mechanism of pathogen recognition with special emphasis on the role of TLRs in tumor immunity and TLR-targeted therapeutics.
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Affiliation(s)
- Sarang Tartey
- a Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University , Kawara-Cho, Sakyo-Ku, Kyoto , Japan.,b AMED-CREST, Japan Agency for Medical Research and Development , Kyoto , Japan
| | - Osamu Takeuchi
- a Laboratory of Infection and Prevention, Institute for Virus Research, Kyoto University , Kawara-Cho, Sakyo-Ku, Kyoto , Japan.,b AMED-CREST, Japan Agency for Medical Research and Development , Kyoto , Japan
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100
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Tumor Associated Macrophages as Therapeutic Targets for Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1026:331-370. [PMID: 29282692 DOI: 10.1007/978-981-10-6020-5_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tumor-associated macrophages (TAMs) are the most abundant inflammatory infiltrates in the tumor stroma. TAMs promote tumor growth by suppressing immunocompetent cells, including neovascularization and supporting cancer stem cells. In the chapter, we discuss recent efforts in reprogramming or inhibiting tumor-protecting properties of TAMs, and developing potential strategies to increase the efficacy of breast cancer treatment.
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