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Rooney M, Duduskar SN, Ghait M, Reißing J, Stengel S, Reuken PA, Quickert S, Zipprich A, Bauer M, Russo AJ, Rathinam VA, Stallmach A, Rubio I, Bruns T. Type-I interferon shapes peritoneal immunity in cirrhosis and drives caspase-5-mediated progranulin release upon infection. J Hepatol 2024:S0168-8278(24)02325-0. [PMID: 38936554 DOI: 10.1016/j.jhep.2024.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 05/21/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND & AIMS Gut bacterial translocation contributes to immune dysfunction and spontaneous bacterial peritonitis (SBP) in cirrhosis. We hypothesized that exposure of peritoneal macrophages (PMs) to bacterial DNA results in type-I interferon (IFN) production, shaping subsequent immune responses, inflammasome activation, and the release of damage-associated molecular patterns (DAMPs). METHODS PMs from patients with cirrhosis were stimulated with E. coli single-stranded DNA (ssDNA), lipopolysaccharide LPS, and IFN or infected with E. coli, S. aureus, and Group B streptococcus in vitro. Cytokine release, inflammasome activation, and DAMP release were quantified by quantitative-PCR, ELISA, western blots, and reporter cells employing primary PMs, monocytes, and caspase-deficient THP-1 macrophages. Serum progranulin concentration was correlated with transplant-free survival in 77 patients with SBP. RESULTS E. coli ssDNA induced strong type-I IFN activity in PMs and monocytes, priming them for enhanced LPS-mediated tumor necrosis factor production without toll-like receptor 4 tolerance induction. During in vitro macrophage bacterial infection, type-I IFN release aligned with upregulated expression of IFN-regulatory factors (IRF)1/2 and guanylate binding proteins (GBP)2/5. PMs upregulated inflammasome-associated proteins and type-I IFN upon E. coli ssDNA exposure and released interleukin-1β upon bacterial infection. Proteomic screen in mouse macrophages revealed progranulin as being caspase-11-dependent during E. coli infection. PMs and THP-1 macrophages released significant amounts of progranulin when infected with S. aureus or E. coli via gasdermin-D in a type-I IFN and caspase-5-dependent manner. During SBP, PMs upregulated IRF1, GBP2/5 and caspase-5 and higher serum progranulin concentrations were indicative of lower 90-day transplant-free survival after SBP. CONCLUSIONS Type-I IFN shapes peritoneal immune responses and regulates caspase-5-mediated progranulin release during SBP. IMPACT AND IMPLICATIONS Patients with cirrhosis exhibit impaired immune responses and increased susceptibility to bacterial infections. This study reveals that type-I interferon responses, triggered by pathogen-associated molecular patterns, are crucial in regulating macrophage activation and priming them for inflammatory responses. Additionally, we elucidate the mechanisms by which type-I interferons promote the release of progranulin from macrophages during spontaneous bacterial peritonitis. Our findings enhance understanding of how bacterial translocation affects immune responses, identify novel biomarkers for inflammasome activation during infections, and point to potential therapeutic targets.
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Affiliation(s)
- Michael Rooney
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany; Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Shivalee N Duduskar
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Mohamed Ghait
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Johanna Reißing
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Sven Stengel
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany; Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
| | - Philipp A Reuken
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Stefanie Quickert
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Alexander Zipprich
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany; Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ashley J Russo
- Department of Immunology, University of Connecticut Health School of Medicine, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Vijay A Rathinam
- Department of Immunology, University of Connecticut Health School of Medicine, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Andreas Stallmach
- Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Ignacio Rubio
- Integrated Research and Treatment Center, Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany; Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Tony Bruns
- Department of Internal Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
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Yang B, Lin Y, Huang Y, Zhu N, Shen YQ. Extracellular vesicles modulate key signalling pathways in refractory wound healing. BURNS & TRAUMA 2023; 11:tkad039. [PMID: 38026441 PMCID: PMC10654481 DOI: 10.1093/burnst/tkad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 12/01/2023]
Abstract
Chronic wounds are wounds that cannot heal properly due to various factors, such as underlying diseases, infection or reinjury, and improper healing of skin wounds and ulcers can cause a serious economic burden. Numerous studies have shown that extracellular vesicles (EVs) derived from stem/progenitor cells promote wound healing, reduce scar formation and have significant advantages over traditional treatment methods. EVs are membranous particles that carry various bioactive molecules from their cellular origins, such as cytokines, nucleic acids, enzymes, lipids and proteins. EVs can mediate cell-to-cell communication and modulate various physiological processes, such as cell differentiation, angiogenesis, immune response and tissue remodelling. In this review, we summarize the recent advances in EV-based wound healing, focusing on the signalling pathways that are regulated by EVs and their cargos. We discuss how EVs derived from different types of stem/progenitor cells can promote wound healing and reduce scar formation by modulating the Wnt/β-catenin, phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin, vascular endothelial growth factor, transforming growth factor β and JAK-STAT pathways. Moreover, we also highlight the challenges and opportunities for engineering or modifying EVs to enhance their efficacy and specificity for wound healing.
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Affiliation(s)
- Bowen Yang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yumeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Yibo Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Nanxi Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
| | - Ying-Qiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, No. 14, Section 3, Renmin South Road, Wuhou District, Chengdu 610041, China
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Lynall ME, Soskic B, Hayhurst J, Schwartzentruber J, Levey DF, Pathak GA, Polimanti R, Gelernter J, Stein MB, Trynka G, Clatworthy MR, Bullmore E. Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells. Nat Commun 2022; 13:6102. [PMID: 36243721 PMCID: PMC9569335 DOI: 10.1038/s41467-022-33885-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/06/2022] [Indexed: 02/06/2023] Open
Abstract
Multiple psychiatric disorders have been associated with abnormalities in both the innate and adaptive immune systems. The role of these abnormalities in pathogenesis, and whether they are driven by psychiatric risk variants, remains unclear. We test for enrichment of GWAS variants associated with multiple psychiatric disorders (cross-disorder or trans-diagnostic risk), or 5 specific disorders (cis-diagnostic risk), in regulatory elements in immune cells. We use three independent epigenetic datasets representing multiple organ systems and immune cell subsets. Trans-diagnostic and cis-diagnostic risk variants (for schizophrenia and depression) are enriched at epigenetically active sites in brain tissues and in lymphoid cells, especially stimulated CD4+ T cells. There is no evidence for enrichment of either trans-risk or cis-risk variants for schizophrenia or depression in myeloid cells. This suggests a possible model where environmental stimuli activate T cells to unmask the effects of psychiatric risk variants, contributing to the pathogenesis of mental health disorders.
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Affiliation(s)
- Mary-Ellen Lynall
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK.
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK.
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Blagoje Soskic
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Human Technopole, Milan, Italy
| | | | | | - Daniel F Levey
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Gita A Pathak
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Joel Gelernter
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Murray B Stein
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Ed Bullmore
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
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Trained innate immunity, long-lasting epigenetic modulation, and skewed myelopoiesis by heme. Proc Natl Acad Sci U S A 2021; 118:2102698118. [PMID: 34663697 PMCID: PMC8545490 DOI: 10.1073/pnas.2102698118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 12/19/2022] Open
Abstract
During infection, extracellular “labile” heme, released from damaged red blood or parenchymal cells, acts as prototypical alarmin stimulating myeloid cells. A characteristic hallmark of myeloid cell activation is the development of trained immunity, specified as long-lasting adaptations based on transcriptional and epigenetic modifications. In vivo, this is maintained by the rerouting of hematopoiesis. We found that heme is a previously unrecognized trained immunity inducer promoting resistance to bacterial infection in mice. This goes along with extensive long-lasting epigenetic memory in hematopoietic stem cells provoking drastic changes in the transcription factor–binding landscape of myeloid progenitor cells. Given the critical role of heme during infections, we propose that trained immunity is a more general component of innate immunity than previously suggested. Trained immunity defines long-lasting adaptations of innate immunity based on transcriptional and epigenetic modifications of myeloid cells and their bone marrow progenitors [M. Divangahi et al., Nat. Immunol. 22, 2–6 (2021)]. Innate immune cells, however, do not exclusively differentiate between foreign and self but also react to host-derived molecules referred to as alarmins. Extracellular “labile” heme, released during infections, is a bona fide alarmin promoting myeloid cell activation [M. P. Soares, M. T. Bozza, Curr. Opin. Immunol. 38, 94–100 (2016)]. Here, we report that labile heme is a previously unrecognized inducer of trained immunity that confers long-term regulation of lineage specification of hematopoietic stem cells and progenitor cells. In contrast to previous reports on trained immunity, essentially mediated by pathogen-associated molecular patterns, heme training depends on spleen tyrosine kinase signal transduction pathway acting upstream of c-Jun N-terminal kinases. Heme training promotes resistance to sepsis, is associated with the expansion of self-renewing hematopoetic stem cells primed toward myelopoiesis and to the occurrence of a specific myeloid cell population. This is potentially evoked by sustained activity of Nfix, Runx1, and Nfe2l2 and dissociation of the transcriptional repressor Bach2. Previously reported trained immunity inducers are, however, infrequently present in the host, whereas heme abundantly occurs during noninfectious and infectious disease. This difference might explain the vanishing protection exerted by heme training in sepsis over time with sustained long-term myeloid adaptations. Hence, we propose that trained immunity is an integral component of innate immunity with distinct functional differences on infectious disease outcome depending on its induction by pathogenic or endogenous molecules.
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Steiner SE, Choong FX, Antypas H, Morado-Urbina CE, Schulz A, Bersellini Farinotti A, Bas DB, Svensson CI, Richter-Dahlfors A, Melican K. UPEC kidney infection triggers neuro-immune communication leading to modulation of local renal inflammation by splenic IFNγ. PLoS Pathog 2021; 17:e1009553. [PMID: 34015044 PMCID: PMC8136731 DOI: 10.1371/journal.ppat.1009553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial infection results in a veritable cascade of host responses, both local and systemic. To study the initial stages of host-pathogen interaction in living tissue we use spatially-temporally controlled in vivo models. Using this approach, we show here that within 4 h of a uropathogenic Escherichia coli (UPEC) infection in the kidney, an IFNγ response is triggered in the spleen. This rapid infection-mediated inter-organ communication was found to be transmitted via nerve signalling. Bacterial expression of the toxin α-hemolysin directly and indirectly activated sensory neurons, which were identified in the basement membrane of renal tubules. Nerve activation was transmitted via the splenic nerve, inducing upregulation of IFNγ in the marginal zones of the spleen that led to increasing concentrations of IFNγ in the circulation. We found that IFNγ modulated the inflammatory signalling generated by renal epithelia cells in response to UPEC infection. This demonstrates a new concept in the host response to kidney infection; the role of nerves in sensing infection and rapidly triggering a systemic response which can modulate inflammation at the site of infection. The interplay between the nervous and immune systems is an exciting, developing field with the appealing prospect of non-pharmaceutical interventions. Our study identifies an important role for systemic neuro-immune communication in modulating inflammation during the very first hours of a local bacterial infection in vivo.
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Affiliation(s)
- Svava E. Steiner
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinand X. Choong
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Haris Antypas
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Carlos E. Morado-Urbina
- Department for Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anette Schulz
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alex Bersellini Farinotti
- Department for Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Duygu B. Bas
- Department for Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Camilla I. Svensson
- Department for Physiology and Pharmacology, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agneta Richter-Dahlfors
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (AR-D); (KM)
| | - Keira Melican
- AIMES—Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (AR-D); (KM)
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Jasenosky LD, Nambu A, Tsytsykova AV, Ranjbar S, Haridas V, Kruidenier L, Tough DF, Goldfeld AE. Identification of a Distal Locus Enhancer Element That Controls Cell Type-Specific TNF and LTA Gene Expression in Human T Cells. THE JOURNAL OF IMMUNOLOGY 2020; 205:2479-2488. [PMID: 32978279 DOI: 10.4049/jimmunol.1901311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
The human TNF/LT locus genes TNF, LTA, and LTB are expressed in a cell type-specific manner. In this study, we show that a highly conserved NFAT binding site within the distal noncoding element hHS-8 coordinately controls TNF and LTA gene expression in human T cells. Upon activation of primary human CD4+ T cells, hHS-8 and the TNF and LTA promoters display increased H3K27 acetylation and nuclease sensitivity and coordinate induction of TNF, LTA, and hHS-8 enhancer RNA transcription occurs. Functional analyses using CRISPR/dead(d)Cas9 targeting of the hHS-8-NFAT site in the human T cell line CEM demonstrate significant reduction of TNF and LTA mRNA synthesis and of RNA polymerase II recruitment to their promoters. These studies elucidate how a distal element regulates the inducible cell type-specific gene expression program of the human TNF/LT locus and provide an approach for modulation of TNF and LTA transcription in human disease using CRISPR/dCas9.
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Affiliation(s)
- Luke D Jasenosky
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Aya Nambu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Alla V Tsytsykova
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115.,Program in Hematology, Boston Children's Hospital, Boston, MA 02115
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Viraga Haridas
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | | | - David F Tough
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, United Kingdom
| | - Anne E Goldfeld
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115;
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Abou El Hassan M, Huang K, Xu Z, Yu T, Bremner R. Frequent interferon regulatory factor 1 (IRF1) binding at remote elements without histone modification. J Biol Chem 2018; 293:10353-10362. [PMID: 29748386 DOI: 10.1074/jbc.ra118.002889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Transcriptional activators bind DNA and recruit cofactors to modify chromatin. The extent to which these two events are separable is unclear. Here, using a custom ChIP tiling array to map chromatin modifications, we show that interferon-γ-induced DNA binding of signal transducer and activator of transcription 1 (STAT1), typically associated with the transcription factor interferon regulatory factor 1 (IRF1), causes histone acetylation (H3ac, H4ac). In contrast, among IRF1 sites lacking concomitant STAT1 recruitment, only 25% underwent inducible histone acetylation, 31% exhibited constitutive histone acetylation, and 44% had no histone acetylation. These latter "orphan sites" also lacked other activating modifications (e.g. H3K4me1, H3K4me2) and were typically remote from transcription start sites. In these cases the closest gene was typically an IFNγ-inducible locus that did not respond to IFNγ in this setting. Orphan sites were detected in different cell types, suggesting broad relevance. Despite an atypical downstream response (i.e. no histone modifications), IRF1 binding depended on SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4 or BRG1), as is typical of active IRF1 enhancers. Although SMARCA4 permitted IRF1 access to the orphan sites, there was no corecruitment of the histone acetyltransferases CREB-binding protein (CBP) and p300. Orphan sites were constitutively unacetylated, and several were marked with repressive chromatin modifications (e.g. H3K27me3). In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.
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Affiliation(s)
- Mohamed Abou El Hassan
- From the Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada.,the Clinical Chemistry Division, Provincial Laboratory Services, Queen Elizabeth Hospital, Charlottetown, Prince Edward Island C1A 8T5, Canada.,the Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada, and
| | - Katherine Huang
- From the Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Zhaodong Xu
- From the Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Tao Yu
- From the Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Rod Bremner
- From the Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada, .,the Departments of Lab Medicine and Pathobiology and.,Ophthalmology and Vision Science, University of Toronto, Toronto, Ontario M5S 1A1, Canada
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8
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Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Nat Genet 2018; 50:424-431. [PMID: 29379200 DOI: 10.1038/s41588-018-0046-7] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/22/2017] [Indexed: 01/25/2023]
Abstract
Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs) for chromatin accessibility and gene expression in human macrophages exposed to IFNγ, Salmonella and IFNγ plus Salmonella. We observed that ~60% of stimulus-specific expression QTLs with a detectable effect on chromatin altered the chromatin accessibility in naive cells, thus suggesting that they perturb enhancer priming. Such variants probably influence binding of cell-type-specific transcription factors, such as PU.1, which can then indirectly alter the binding of stimulus-specific transcription factors, such as NF-κB or STAT2. Thus, although chromatin accessibility assays are powerful for fine-mapping causal regulatory variants, detecting their downstream effects on gene expression will be challenging, requiring profiling of large numbers of stimulated cellular states and time points.
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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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10
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Higher-Order Chromatin Regulation of Inflammatory Gene Expression. Mediators Inflamm 2017; 2017:7848591. [PMID: 28490839 PMCID: PMC5401750 DOI: 10.1155/2017/7848591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Whether it is caused by viruses and bacteria infection, or low-grade chronic inflammation of atherosclerosis and cellular senescence, the transcription factor (TF) NF-κB plays a central role in the inducible expression of inflammatory genes. Accumulated evidence has indicated that the chromatin environment is the main determinant of TF binding in gene expression regulation, including the stimulus-responsive NF-κB. Dynamic changes in intra- and interchromosomes are the key regulatory mechanisms promoting the binding of TFs. When an inflammatory process is triggered, NF-κB binds to enhancers or superenhancers, triggering the transcription of enhancer RNA (eRNA), driving the chromatin of the NF-κB-binding gene locus to construct transcriptional factories, and forming intra- or interchromosomal contacts. These processes reveal a mechanism in which intrachromosomal contacts appear to be cis-control enhancer-promoter communications, whereas interchromosomal regulatory elements construct trans-form relationships with genes on other chromosomes. This article will review emerging evidence on the genome organization hierarchy underlying the inflammatory response.
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11
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Lyroni K, Patsalos A, Daskalaki MG, Doxaki C, Soennichsen B, Helms M, Liapis I, Zacharioudaki V, Kampranis SC, Tsatsanis C. Epigenetic and Transcriptional Regulation of IRAK-M Expression in Macrophages. THE JOURNAL OF IMMUNOLOGY 2016; 198:1297-1307. [DOI: 10.4049/jimmunol.1600009] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 11/21/2016] [Indexed: 12/16/2022]
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12
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Józefowski S, Śróttek M. Lipid raft-dependent endocytosis negatively regulates responsiveness of J774 macrophage-like cells to LPS by down regulating the cell surface expression of LPS receptors. Cell Immunol 2016; 312:42-50. [PMID: 27908440 DOI: 10.1016/j.cellimm.2016.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/13/2016] [Accepted: 11/22/2016] [Indexed: 01/07/2023]
Abstract
Acting through CD14 and TLR4/MD-2, lipopolysaccharide (LPS) triggers strong pro-inflammatory activation of macrophages, which, if not appropriately controlled, may lead to lethal septic shock. Therefore, numerous mechanisms of negative regulation of responses to LPS exist, but whether they include down-regulation of LPS receptors is not clear. We have found that in J774 cells, the clathrin-dependent endocytic pathway enables activation of TRIF-dependent TLR4 signaling within endosomes, but is not associated with the down-regulation of TLR4 or CD14 surface expression. In contrast, lipid raft-dependent endocytosis negatively regulates the basal cell surface expression of LPS receptors and, consequently, responsiveness to LPS. Together with observations that treatments, known to selectively disrupt lipid rafts, do not inhibit LPS-stimulated cytokine production, our results suggest that lipid rafts may serve as sites in which LPS receptors are sorted for endocytosis, rather than being platforms for the assembly of TLR4-centered signaling complexes, as suggested previously.
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Affiliation(s)
- Szczepan Józefowski
- Department of Immunology, Jagiellonian University Medical College, Czysta Street 18, 31-121 Kraków, Poland.
| | - Małgorzata Śróttek
- Department of Immunology, Jagiellonian University Medical College, Czysta Street 18, 31-121 Kraków, Poland
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Salerno F, Guislain A, Cansever D, Wolkers MC. TLR-Mediated Innate Production of IFN-γ by CD8+ T Cells Is Independent of Glycolysis. THE JOURNAL OF IMMUNOLOGY 2016; 196:3695-705. [PMID: 27016606 DOI: 10.4049/jimmunol.1501997] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 02/24/2016] [Indexed: 01/23/2023]
Abstract
CD8(+) T cells can respond to unrelated infections in an Ag-independent manner. This rapid innate-like immune response allows Ag-experienced T cells to alert other immune cell types to pathogenic intruders. In this study, we show that murine CD8(+) T cells can sense TLR2 and TLR7 ligands, resulting in rapid production of IFN-γ but not of TNF-α and IL-2. Importantly, Ag-experienced T cells activated by TLR ligands produce sufficient IFN-γ to augment the activation of macrophages. In contrast to Ag-specific reactivation, TLR-dependent production of IFN-γ by CD8(+) T cells relies exclusively on newly synthesized transcripts without inducing mRNA stability. Furthermore, transcription of IFN-γ upon TLR triggering depends on the activation of PI3K and serine-threonine kinase Akt, and protein synthesis relies on the activation of the mechanistic target of rapamycin. We next investigated which energy source drives the TLR-induced production of IFN-γ. Although Ag-specific cytokine production requires a glycolytic switch for optimal cytokine release, glucose availability does not alter the rate of IFN-γ production upon TLR-mediated activation. Rather, mitochondrial respiration provides sufficient energy for TLR-induced IFN-γ production. To our knowledge, this is the first report describing that TLR-mediated bystander activation elicits a helper phenotype of CD8(+) T cells. It induces a short boost of IFN-γ production that leads to a significant but limited activation of Ag-experienced CD8(+) T cells. This activation suffices to prime macrophages but keeps T cell responses limited to unrelated infections.
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Affiliation(s)
- Fiamma Salerno
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands
| | - Aurelie Guislain
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands
| | - Dilay Cansever
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands
| | - Monika C Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands
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Sumoylation coordinates the repression of inflammatory and anti-viral gene-expression programs during innate sensing. Nat Immunol 2015; 17:140-9. [PMID: 26657003 DOI: 10.1038/ni.3342] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 11/02/2015] [Indexed: 12/13/2022]
Abstract
Innate sensing of pathogens initiates inflammatory cytokine responses that need to be tightly controlled. We found here that after engagement of Toll-like receptors (TLRs) in myeloid cells, deficient sumoylation caused increased secretion of transcription factor NF-κB-dependent inflammatory cytokines and a massive type I interferon signature. In mice, diminished sumoylation conferred susceptibility to endotoxin shock and resistance to viral infection. Overproduction of several NF-κB-dependent inflammatory cytokines required expression of the type I interferon receptor, which identified type I interferon as a central sumoylation-controlled hub for inflammation. Mechanistically, the small ubiquitin-like modifier SUMO operated from a distal enhancer of the gene encoding interferon-β (Ifnb1) to silence both basal and stimulus-induced activity of the Ifnb1 promoter. Therefore, sumoylation restrained inflammation by silencing Ifnb1 expression and by strictly suppressing an unanticipated priming by type I interferons of the TLR-induced production of inflammatory cytokines.
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