51
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Hurtado-Tamayo J, Requena-Platek R, Enjuanes L, Bello-Perez M, Sola I. Contribution to pathogenesis of accessory proteins of deadly human coronaviruses. Front Cell Infect Microbiol 2023; 13:1166839. [PMID: 37197199 PMCID: PMC10183600 DOI: 10.3389/fcimb.2023.1166839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/19/2023] Open
Abstract
Coronaviruses (CoVs) are enveloped and positive-stranded RNA viruses with a large genome (∼ 30kb). CoVs include essential genes, such as the replicase and four genes coding for structural proteins (S, M, N and E), and genes encoding accessory proteins, which are variable in number, sequence and function among different CoVs. Accessory proteins are non-essential for virus replication, but are frequently involved in virus-host interactions associated with virulence. The scientific literature on CoV accessory proteins includes information analyzing the effect of deleting or mutating accessory genes in the context of viral infection, which requires the engineering of CoV genomes using reverse genetics systems. However, a considerable number of publications analyze gene function by overexpressing the protein in the absence of other viral proteins. This ectopic expression provides relevant information, although does not acknowledge the complex interplay of proteins during virus infection. A critical review of the literature may be helpful to interpret apparent discrepancies in the conclusions obtained by different experimental approaches. This review summarizes the current knowledge on human CoV accessory proteins, with an emphasis on their contribution to virus-host interactions and pathogenesis. This knowledge may help the search for antiviral drugs and vaccine development, still needed for some highly pathogenic human CoVs.
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Affiliation(s)
| | | | | | | | - Isabel Sola
- *Correspondence: Melissa Bello-Perez, ; Isabel Sola,
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52
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Lesha E, George H, Zaki MM, Smith CJ, Khoshakhlagh P, Ng AHM. A Survey of Transcription Factors in Cell Fate Control. Methods Mol Biol 2023; 2594:133-141. [PMID: 36264493 DOI: 10.1007/978-1-0716-2815-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Transcription factors (TFs) play a cardinal role in the development and maintenance of human physiology by acting as mediators of gene expression and cell state control. Recent advancements have broadened our knowledge on the potency of TFs in governing cell physiology and have deepened our understanding of the mechanisms through which they exert this control. The ability of TFs to program cell fates has gathered significant interest in recent decades, and high-throughput technologies now allow for the systematic discovery of forward programming factors to convert pluripotent stem cells into numerous differentiated cell types. The next generation of these technologies has the potential to improve our understanding and control of cell fates and states and provide advanced therapeutic modalities to address many medical conditions.
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Affiliation(s)
- Emal Lesha
- GC Therapeutics Inc., Cambridge, MA, USA
- Department of Neurosurgery, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Haydy George
- GC Therapeutics Inc., Cambridge, MA, USA
- School of Medicine, St. George's University, West Indies, Grenada
| | - Mark M Zaki
- GC Therapeutics Inc., Cambridge, MA, USA
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
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53
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Application of Bioinformatics Tools for the Prediction of Helper MicroRNAs for Improvement of Oncolytic Virus Efficacy. Cell Microbiol 2022. [DOI: 10.1155/2022/5756131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Purpose. Oncolytic Reoviruses, as a self-limiting virus, can be used in cancer treatment, because they have the ability to replicate in tumor cells selectively and destroy them. Studies show that some immune response proteins may interfere with the virus life cycle. So, the main aim of this bioinformatic study is to check which microRNA is able to target some reovirus inhibitory proteins. Experimental Design. By use of online bioinformatics software, the microRNAs that could target inhibitory genes were selected. Then, other features like content ++ score and cell type were checked and finally the eligible microRNAs were determined. Results. After choosing 15 inhibitory proteins, analysis was performed and finally 37 microRNAs which could target inhibitory proteins in colorectal cell lines were selected. In the end, by investigation of web-based tools, just two microRNAs were finalized. Conclusions and Clinical Relevance. This bioinformatic study shows that microRNA-140 and microRNA-92a have the potential to target some inhibitory proteins which interfere with oncolytic Reovirus replication and it may help in the optimal use of this virus as a cancer treatment. Because selective reproduction of Reovirus in tumor cells, as a nonchemical therapy, can be a good way to overcome this disease with broad advantages.
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54
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Pinto MV, Neves JF. Precision medicine: The use of tailored therapy in primary immunodeficiencies. Front Immunol 2022; 13:1029560. [PMID: 36569887 PMCID: PMC9773086 DOI: 10.3389/fimmu.2022.1029560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Primary immunodeficiencies (PID) are rare, complex diseases that can be characterised by a spectrum of phenotypes, from increased susceptibility to infections to autoimmunity, allergy, auto-inflammatory diseases and predisposition to malignancy. With the introduction of genetic testing in these patients and wider use of next-Generation sequencing techniques, a higher number of pathogenic genetic variants and conditions have been identified, allowing the development of new, targeted treatments in PID. The concept of precision medicine, that aims to tailor the medical interventions to each patient, allows to perform more precise diagnosis and more importantly the use of treatments directed to a specific defect, with the objective to cure or achieve long-term remission, minimising the number and type of side effects. This approach takes particular importance in PID, considering the nature of causative defects, disease severity, short- and long-term complications of disease but also of the available treatments, with impact in life-expectancy and quality of life. In this review we revisit how this approach can or is already being implemented in PID and provide a summary of the most relevant treatments applied to specific diseases.
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Affiliation(s)
- Marta Valente Pinto
- Primary Immunodeficiencies Unit, Hospital Dona Estefânia, CHULC-EPE, Lisbon, Portugal,Centro de Investigação Egas Moniz (CiiEM), Instituto Universitário Egas Moniz (IUEM), Quinta da Granja, Monte da Caparica, Caparica, Portugal
| | - João Farela Neves
- Primary Immunodeficiencies Unit, Hospital Dona Estefânia, CHULC-EPE, Lisbon, Portugal,CHRC, Comprehensive Health Research Centre, Nova Medical School, Lisbon, Portugal,*Correspondence: João Farela Neves,
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55
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Larrieux A, Sanjuán R. Cellular resistance to an oncolytic virus is driven by chronic activation of innate immunity. iScience 2022; 26:105749. [PMID: 36590165 PMCID: PMC9794979 DOI: 10.1016/j.isci.2022.105749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/23/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The emergence of cellular resistances to oncolytic viruses is an underexplored process that could compromise the efficacy of cancer virotherapy. Here, we isolated and characterized B16 mouse melanoma cells that evolved resistance to an oncolytic vesicular stomatitis virus (VSV-D51). RNA-seq revealed that resistance was associated to broad changes in gene expression, which typically involved chronic upregulation of interferon-stimulated genes. Innate immunity activation was maintained in the absence of the virus or other infection signals, and conferred cross-resistance to wild-type VSV and the unrelated Sindbis virus. Furthermore, we identified differentially expressed genes with no obvious role in antiviral immunity, such as Mnda, Psmb8 and Btn2a2, suggesting novel functions for these genes. Transcriptomic changes associated to VSV resistance were similar among B16 clones and in some clones derived from the mouse colon carcinoma cell line CT26, suggesting that oncolytic virus resistance involves certain conserved mechanisms and is therefore a potentially predictable process.
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Affiliation(s)
- Alejandra Larrieux
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, València 46980, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, València 46980, Spain,Corresponding author
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56
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Tian T, Sun W, Du J, Sun Y. Analysis of co-expression gene network associated with intracranial aneurysm and type 2 diabetes mellitus. Front Neurol 2022; 13:1032038. [PMID: 36561297 PMCID: PMC9763588 DOI: 10.3389/fneur.2022.1032038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
To screen for common target genes in intracranial aneurysms (IA) and type 2 diabetes mellitus (T2DM), construct a common transcriptional regulatory network to predict clusters of candidate genes involved in the pathogenesis of T2DM and IA, and identify the common neurovascular markers and pathways in T2DM causing IA. Microarray datasets (GSE55650, GSE25462, GSE26969, GSE75436, and GSE13353) from the GEO database were analyzed in this research. Screening of the IA and the T2DM datasets yielded a total of 126 DEGs, among which 78 were upregulated and 138 were downregulated. Functional enrichment analysis revealed that these DEGs were enriched for a total of 68 GO pathways, including extracellular matrix composition, coagulation regulation, hemostasis regulation, and collagen fiber composition pathways. We also constructed transcriptional regulatory networks, and identified key transcription factors involved in both the conditions. Univariate logistic regression analysis showed that ARNTL2 and STAT1 were significantly associated with the development of T2DM and IA, acting as the common neurovascular markers for both the diseases. In cellular experiments, hyperglycemic microenvironments exhibited upregulated STAT1 expression. STAT1 may be involved in the pathogenesis of IA in T2DM patients. Being the common neurovascular markers, STAT1 may acts as novel therapeutic targets for the treatment of IA and T2DM.
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Affiliation(s)
- Tian Tian
- Department of Neurological Surgery, Chengde Medical University Affiliated Hospital, Chengde, China
| | - Wenhao Sun
- Department of Neurological Surgery, Chengde Medical University Affiliated Hospital, Chengde, China
| | - Jia Du
- Department of Neurological Surgery, Cangzhou Center Hospital, Cangzhou, China
| | - Yafei Sun
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, China,*Correspondence: Yafei Sun
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57
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Slonchak A, Wang X, Aguado J, Sng JDJ, Chaggar H, Freney ME, Yan K, Torres FJ, Amarilla AA, Balea R, Setoh YX, Peng N, Watterson D, Wolvetang E, Suhrbier A, Khromykh AA. Zika virus noncoding RNA cooperates with the viral protein NS5 to inhibit STAT1 phosphorylation and facilitate viral pathogenesis. SCIENCE ADVANCES 2022; 8:eadd8095. [PMID: 36449607 PMCID: PMC9710884 DOI: 10.1126/sciadv.add8095] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/13/2022] [Indexed: 05/25/2023]
Abstract
All flaviviruses, including Zika virus, produce noncoding subgenomic flaviviral RNA (sfRNA), which plays an important role in viral pathogenesis. However, the exact mechanism of how sfRNA enables viral evasion of antiviral response is not well defined. Here, we show that sfRNA is required for transplacental virus dissemination in pregnant mice and subsequent fetal brain infection. We also show that sfRNA promotes apoptosis of neural progenitor cells in human brain organoids, leading to their disintegration. In infected human placental cells, sfRNA inhibits multiple antiviral pathways and promotes apoptosis, with signal transducer and activator of transcription 1 (STAT1) identified as a key shared factor. We further show that the production of sfRNA leads to reduced phosphorylation and nuclear translocation of STAT1 via a mechanism that involves sfRNA binding to and stabilizing viral protein NS5. Our results suggest the cooperation between viral noncoding RNA and a viral protein as a novel strategy for counteracting antiviral responses.
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Affiliation(s)
- Andrii Slonchak
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Xiaohui Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Julio Aguado
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Julian D. J. Sng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Harman Chaggar
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Morgan E. Freney
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Kexin Yan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Francisco J. Torres
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Rickyle Balea
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yin Xiang Setoh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Nias Peng
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas Suhrbier
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
| | - Alexander A. Khromykh
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Australian Infectious Diseases Research Centre, Global Virus Network Center of Excellence, Brisbane, QLD, Australia
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58
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Illig D, Kotlarz D. Dysregulated inflammasome activity in intestinal inflammation - Insights from patients with very early onset IBD. Front Immunol 2022; 13:1027289. [PMID: 36524121 PMCID: PMC9744759 DOI: 10.3389/fimmu.2022.1027289] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a multifactorial disorder triggered by imbalances of the microbiome and immune dysregulations in genetically susceptible individuals. Several mouse and human studies have demonstrated that multimeric inflammasomes are critical regulators of host defense and gut homeostasis by modulating immune responses to pathogen- or damage-associated molecular patterns. In the context of IBD, excessive production of pro-inflammatory Interleukin-1β has been detected in patient-derived intestinal tissues and correlated with the disease severity or failure to respond to anti-tumor necrosis factor therapy. Correspondingly, genome-wide association studies have suggested that single nucleotide polymorphisms in inflammasome components might be associated with risk of IBD development. The relevance of inflammasomes in controlling human intestinal homeostasis has been further exemplified by the discovery of very early onset IBD (VEO-IBD) patients with monogenic defects affecting different molecules in the complex regulatory network of inflammasome activity. This review provides an overview of known causative monogenic entities of VEO-IBD associated with altered inflammasome activity. A better understanding of the molecular mechanisms controlling inflammasomes in monogenic VEO-IBD may open novel therapeutic avenues for rare and common inflammatory diseases.
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Affiliation(s)
- David Illig
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, Ludwig-Maximilians-University (LMU), Munich, Germany,Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany,*Correspondence: Daniel Kotlarz,
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59
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Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LA, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC. Human variation in population-wide gene expression data predicts gene perturbation phenotype. iScience 2022; 25:105328. [PMID: 36310583 PMCID: PMC9614568 DOI: 10.1016/j.isci.2022.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function "in population" experiment. We describe here an approach, huva (human variation), taking advantage of population-scale multi-layered data to infer gene function and relationships between phenotypes and expression. Within a reference dataset, huva derives two experimental groups with LOW or HIGH expression of the GOI, enabling the subsequent comparison of their transcriptional profile and functional parameters. We demonstrate that this approach robustly identifies the phenotypic relevance of a GOI allowing the stratification of genes according to biological functions, and we generalize this concept to almost 16,000 genes in the human transcriptome. Additionally, we describe how huva predicts monocytes to be the major cell type in the pathophysiology of STAT1 mutations, evidence validated in a clinical cohort.
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Affiliation(s)
- Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Laura L. Sun
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | | | - Ioanna Gemünd
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010 VIC, Australia
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Peer Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, 5000 SA, Australia
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Medical Genetics, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Immunology and Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
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60
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Çetin G, Studencka-Turski M, Venz S, Schormann E, Junker H, Hammer E, Völker U, Ebstein F, Krüger E. Immunoproteasomes control activation of innate immune signaling and microglial function. Front Immunol 2022; 13:982786. [PMID: 36275769 PMCID: PMC9584546 DOI: 10.3389/fimmu.2022.982786] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Microglia are the resident immune cells of the central nervous system (CNS) and play a major role in the regulation of brain homeostasis. To maintain their cellular protein homeostasis, microglia express standard proteasomes and immunoproteasomes (IP), a proteasome isoform that preserves protein homeostasis also in non-immune cells under challenging conditions. The impact of IP on microglia function in innate immunity of the CNS is however not well described. Here, we establish that IP impairment leads to proteotoxic stress and triggers the unfolded and integrated stress responses in mouse and human microglia models. Using proteomic analysis, we demonstrate that IP deficiency in microglia results in profound alterations of the ubiquitin-modified proteome among which proteins involved in the regulation of stress and immune responses. In line with this, molecular analysis revealed chronic activation of NF-κB signaling in IP-deficient microglia without further stimulus. In addition, we show that IP impairment alters microglial function based on markers for phagocytosis and motility. At the molecular level IP impairment activates interferon signaling promoted by the activation of the cytosolic stress response protein kinase R. The presented data highlight the importance of IP function for the proteostatic potential as well as for precision proteolysis to control stress and immune signaling in microglia function.
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Affiliation(s)
- Gonca Çetin
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Maja Studencka-Turski
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Simone Venz
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Eileen Schormann
- Institute of Biochemistry, Charité – University Medicine Berlin, Berlin, Germany
| | - Heike Junker
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
- *Correspondence: Elke Krüger,
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61
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Hayes LN, An K, Carloni E, Li F, Vincent E, Trippaers C, Paranjpe M, Dölen G, Goff LA, Ramos A, Kano SI, Sawa A. Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry. Nature 2022; 610:327-334. [PMID: 36171283 DOI: 10.1038/s41586-022-05274-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/24/2022] [Indexed: 01/12/2023]
Abstract
Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function1,2. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood3,4. Several maternal environmental factors-such as an aberrant microbiome, immune activation and poor nutrition-can influence prenatal brain development5,6. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that, after maternal immune activation (MIA) in mice, microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was accompanied by changes in chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single-cell RNA-sequencing analysis revealed that MIA does not induce a distinct subpopulation but, rather, decreases the contribution to inflammatory microglia states. Prenatal replacement of microglia from MIA offspring with physiological infiltration of naive microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment affect the long-term microglia reactivity and proper striatal circuit development.
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Affiliation(s)
- Lindsay N Hayes
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kyongman An
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elisa Carloni
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Fangze Li
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Vincent
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chloë Trippaers
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - Manish Paranjpe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gül Dölen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Loyal A Goff
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adriana Ramos
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shin-Ichi Kano
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Akira Sawa
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Mental Health, Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Douglas K, Logan SM, Storey KB. Status of the Janus Kinase-Signal Transducer and Activator of Transcription (JAK-STAT) pathway in liver and skin of the freeze tolerant wood frog. Cryobiology 2022; 108:27-33. [PMID: 36100073 DOI: 10.1016/j.cryobiol.2022.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/21/2022] [Accepted: 08/19/2022] [Indexed: 11/03/2022]
Abstract
The wood frog (Rana sylvatica) has adapted full-body freezing and thawing as a means of sub-zero winter survival and early-breeding in ephemeral pools. One such protective process implicated recently in freeze-thaw tolerance is that of anti-apoptotic signaling, which has been proposed to play a cytoprotective role by modulating stress-induced death signals. This study employed the use of immunoblotting to examine response of a potent cell cycle and apoptosis regulator, known as the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway, to freezing and thawing in the liver and skin of the wood frog. This pathway demonstrably exhibits factor- and tissue-specific changes between non-frozen, 24 h-frozen, and 8 h-thawed conditions. There were few changes in JAK-STAT proteins in frozen frogs, but protective changes were observed upon thaw: Elevated levels of pJAK3 and nuclear localization of pSTAT3 and pSTAT5 suggested an increase in anti-apoptotic signaling after thaw. By contrast, both STAT1 and STAT3 signaling appeared to increase in frozen skin, suggesting frogs use homeostatic regulation of apoptotic- and anti-apoptotic signals, in an antagonistic and compensatory manner. As such, these findings support that JAK-STAT pathway signaling modulation is a plausible adaptation that contributes to fast and reversible manipulation of anti-apoptotic signals, thus assisting in freeze survival of the wood frog.
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Affiliation(s)
- Kurtis Douglas
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Samantha M Logan
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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Wu T, Sui GQ, Teng DK, Luo Q, Wang H, Lin YQ. Study on Changes in Immune Function After Microwave Ablation of Papillary Thyroid Microcarcinoma. Cancer Manag Res 2022; 14:2861-2868. [PMID: 36171864 PMCID: PMC9510695 DOI: 10.2147/cmar.s358649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background In recent years, papillary thyroid microcarcinoma (PTMC) has been a main cause of the high incidence of thyroid carcinoma. No existing study has reported whether microwave ablation (MWA) affects patients' immunity. Therefore, this study explored the effects of MWA treatment on the immune functions of patients with PTMC. Methods This study included 50 patients diagnosed with PTMC who received MWA treatment under ultrasound guidance at the ultrasound department of our hospital from January 2019 to October 2020. Changes in immune function after MWA treatment in PTMC patients were detected by T lymphocyte subsets and cytokines secreted by T helper cells. Results At 1 day and 2 weeks after MWA treatment, the proportions of CD3+, CD4+ and CD4+/CD8+ T lymphocyte subsets and the levels of the cytokines interleukin (IL)-2 and interferon (IFN)-γ in the peripheral blood of the patients were significantly higher than those before MWA treatment (P<0.05). The levels of CD8+ T lymphocytes, tumour necrosis factor (TNF)-α, IL-4, IL-6, IL-10 and IL-17A were not significantly different from those before MWA treatment (P>0.05). One month after MWA treatment, the proportions of CD3+, CD4+, CD8+ and CD4+/CD8+ T lymphocytes and the levels of the cytokines IL-2, IL-4, IL-6, IL-10, IFN-γ, TNF-α and IL-17A were not significantly different from those before MWA treatment (P>0.05). Conclusion The immune functions of patients with PTMC are temporarily enhanced after MWA treatment, which has important clinical significance for patients' anti-PTMC ability.
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Affiliation(s)
- Ting Wu
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
| | - Guo-Qing Sui
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
| | - Deng-Ke Teng
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
| | - Qiang Luo
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
| | - Hui Wang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
| | - Yuan-Qiang Lin
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, Jilin, 130000, People's Republic of China
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Invading Bacterial Pathogens Activate Transcription Factor EB in Epithelial Cells through the Amino Acid Starvation Pathway of mTORC1 Inhibition. Mol Cell Biol 2022; 42:e0024122. [PMID: 36005752 PMCID: PMC9476939 DOI: 10.1128/mcb.00241-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upon pathogen infection, intricate innate signaling cascades are induced to initiate the transcription of immune effectors, including cytokines and chemokines. Transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy genes, was found recently to be a novel regulator of innate immunity in both Caenorhabditis elegans and mammals. Despite TFEB participating in critical mechanisms of pathogen recognition and in the transcriptional response to infection in mammalian macrophages, little is known about its roles in the infected epithelium or infected nonimmune cells in general. Here, we demonstrate that TFEB is activated in nonimmune cells upon infection with bacterial pathogens through a pathway dependent on mTORC1 inhibition and RAG-GTPase activity, reflecting the importance of membrane damage and amino acid starvation responses during infection. Additionally, we present data demonstrating that although TFEB does not affect bacterial killing or load in nonimmune cells, it alters the host transcriptome upon infection, thus promoting an antibacterial transcriptomic landscape. Elucidating the roles of TFEB in infected nonimmune cells and the upstream signaling cascade provides critical insight into understanding how cells recognize and respond to bacterial pathogens.
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Lu X, Zhang K, Jiang W, Li H, Huang Y, Du M, Wan J, Cao Y, Du L, Liu X, Pan W. Single-cell RNA sequencing combined with whole exome sequencing reveals the landscape of the immune pathogenic response to chronic mucocutaneous candidiasis with STAT1 GOF mutation. Front Immunol 2022; 13:988766. [PMID: 36225936 PMCID: PMC9549386 DOI: 10.3389/fimmu.2022.988766] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic mucocutaneous candidiasis (CMC) is characterized by recurrent or persistent infections with Candida of the skin, nails, and mucous membranes (e.g., mouth, esophagus, and vagina). Compared with that of other infectious diseases, the immune pathogenic mechanism of CMC is still poorly understood. We identified a signal transducer and activator of transcription 1 gain-of-function (c.Y289C) mutation in a CMC patient. Single-cell transcriptional profiling on peripheral blood mononuclear cells from this patient revealed decreases in immature B cells and monocytes. Further analysis revealed several differentially expressed genes related to immune regulation, including RGS1, TNFAIP3, S100A8/A9, and CTSS. In our review of the literature on signal transducer and activator of transcription 1 gain-of-function (c.Y289C) mutations, we identified seven cases in total. The median age of onset for CMC (n=4, data lacking for three cases) was 10.5 years (range: birth to 11 years), with an average onset age of 8 years. There were no reports linking tumors to the c.Y289C mutation, and the incidence of pre-existing clinical disease in patients with the c.Y289C mutation was similar to previous data.
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Affiliation(s)
- Xiaodi Lu
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
| | - Keming Zhang
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
| | - Weiwei Jiang
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
- Department of Dermatology, 72nd Group Army Hospital of People’s Liberation Army (PLA), Huzhou, China
| | - Hang Li
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
| | - Yue Huang
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
| | - Mingwei Du
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
| | - Jian Wan
- Department of Dermatology, Pudong New Area People’s Hospital, Shanghai, China
| | - Yanyun Cao
- Department of Dermatology, Pudong New Area People’s Hospital, Shanghai, China
- Shanghai Key Laboratory of Pathogenic Fungi Medical Testing, Pudong New Area People’s Hospital, Shanghai, China
| | - Lin Du
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
- *Correspondence: Lin Du, ; Xiaogang Liu, ; Weihua Pan,
| | - Xiaogang Liu
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
- *Correspondence: Lin Du, ; Xiaogang Liu, ; Weihua Pan,
| | - Weihua Pan
- Shanghai Key Laboratory of Molecular Medicine Mycology, Naval Medical University, Shanghai, China
- *Correspondence: Lin Du, ; Xiaogang Liu, ; Weihua Pan,
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Ezeonwumelu IJ, García-Vidal E, Felip E, Puertas MC, Oriol-Tordera B, Gutiérrez-Chamorro L, Gohr A, Ruiz-Riol M, Massanella M, Clotet B, Martinez-Picado J, Badia R, Riveira-Muñoz E, Ballana E. IRF7 expression correlates with HIV latency reversal upon specific blockade of immune activation. Front Immunol 2022; 13:1001068. [PMID: 36131914 PMCID: PMC9484258 DOI: 10.3389/fimmu.2022.1001068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The persistence of latent HIV reservoirs allows for viral rebound upon antiretroviral therapy interruption, hindering effective HIV-1 cure. Emerging evidence suggests that modulation of innate immune stimulation could impact viral latency and contribute to the clearing of HIV reservoir. Here, the latency reactivation capacity of a subclass of selective JAK2 inhibitors was characterized as a potential novel therapeutic strategy for HIV-1 cure. Notably, JAK2 inhibitors reversed HIV-1 latency in non-clonal lymphoid and myeloid in vitro models of HIV-1 latency and also ex vivo in CD4+ T cells from ART+ PWH, albeit its function was not dependent on JAK2 expression. Immunophenotypic characterization and whole transcriptomic profiling supported reactivation data, showing common gene expression signatures between latency reactivating agents (LRA; JAK2i fedratinib and PMA) in contrast to other JAK inhibitors, but with significantly fewer affected gene sets in the pathway analysis. In depth evaluation of differentially expressed genes, identified a significant upregulation of IRF7 expression despite the blockade of the JAK-STAT pathway and downregulation of proinflammatory cytokines and chemokines. Moreover, IRF7 expression levels positively correlated with HIV latency reactivation capacity of JAK2 inhibitors and also other common LRAs. Collectively, these results represent a promising step towards HIV eradication by demonstrating the potential of innate immune modulation for reducing the viral reservoir through a novel pathway driven by IRF7.
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Affiliation(s)
- Ifeanyi Jude Ezeonwumelu
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Edurne García-Vidal
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eudald Felip
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Medical Oncology Department, Catalan Institute of Oncology (ICO)-Badalona, B-ARGO (Badalona Applied Research Group in Oncology) and IGTP (Health Research Institute Germans Trias i Pujol), Universitat Autònoma de Barcelona, Badalona, Spain
| | - Maria C. Puertas
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Lucía Gutiérrez-Chamorro
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - André Gohr
- Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Massanella
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
- Consorcio Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic – Central University of Catalonia (UVic – UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Roger Badia
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eva Riveira-Muñoz
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute – IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Saffari M, Rahimzada M, Mirhosseini A, Ghezaldasht SA, Valizadeh N, Moshfegh M, Moradi MT, Rezaee SA. Coevolution of HTLV-1-HBZ, Tax, and proviral load with host IRF-1 and CCNA-2 in HAM/TSP patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105337. [PMID: 35835355 DOI: 10.1016/j.meegid.2022.105337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 06/25/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Background HTLV-1-associated myelopathy (HAM/TSP) is a progressive neurodegenerative inflammatory condition of HTLV-1 infection. Viral-host interactions are a significant contributor to the symptoms of HTLV-1-associated diseases. Therefore, in this study, the expression of the main regulatory viral factors and proviral load (PVL) and two host transcription molecules were evaluated in HAM/TSP patients. Materials and methods The study population included 17 HAM/TSP patients, 20 asymptomatic carriers (ACs), and 19 healthy controls (HCs). RNA and DNA were extracted from PBMCs for assessment of the gene expressions and PVL assessment using RT-qPCR and TaqMan method. Results HTLV-1-PVL was higher in HAM/TSPs (395.80 ± 99.69) than ACs (92.92 ± 29.41) (P = 0.001). The Tax expression in HAM/TSPs (7.8 ± 5.7) was strongly higher than ACs (0.06 ± 0.04) (P = 0.02), while HTLV-1-HBZ was only increased around three times in HAM/TSPs (3.17), compared to ACs (1.20) and not significant. The host IRF1 expression in HAM/TSPs (0.4 ± 0.31) was higher than ACs (0.09 ± 0.05) (P = 0.02) and also HCs (0.16 ± 0.07) (P = 0.5), but lower in ACs than HCs (p = 0.01). Although, in HAM/TSPs (0.13 ± 0.09) and ACs (0.03 ± 0.02) CCNA-2 expression was statistically fewer than HCs (0.18 ± 0.06) (P = 0.03, P = 0.001, respectively), in HAM/TSP was higher than ACs (P = 0.1), but did not meet a 95% confidence interval. Conclusion The study showed that HTLV-1-PVL and Tax, along with host IRF-1, could be considered biomarkers in HAM/TSP development. Furthermore, IRF-1, as an essential transcription factor, can be considered a pivotal target in HAM/TSPs treatment.
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Affiliation(s)
- Mona Saffari
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Masooma Rahimzada
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Mirhosseini
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sanaz Ahmadi Ghezaldasht
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan Branch, Mashhad, Iran
| | - Narges Valizadeh
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohammad-Taghi Moradi
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Seyed Abdolrahim Rezaee
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran.
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Silva RCMC, Vasconcelos LR, Travassos LH. The different facets of heme-oxygenase 1 in innate and adaptive immunity. Cell Biochem Biophys 2022; 80:609-631. [PMID: 36018440 DOI: 10.1007/s12013-022-01087-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 07/20/2022] [Indexed: 11/26/2022]
Abstract
Heme oxygenase (HO) enzymes are responsible for the main oxidative step in heme degradation, generating equimolar amounts of free iron, biliverdin and carbon monoxide. HO-1 is induced as a crucial stress response protein, playing protective roles in physiologic and pathological conditions, due to its antioxidant, anti-apoptotic and anti-inflammatory effects. The mechanisms behind HO-1-mediated protection are being explored by different studies, affecting cell fate through multiple ways, such as reduction in intracellular levels of heme and ROS, transcriptional regulation, and through its byproducts generation. In this review we focus on the interplay between HO-1 and immune-related signaling pathways, which culminate in the activation of transcription factors important in immune responses and inflammation. We also discuss the dual interaction of HO-1 and inflammatory mediators that govern resolution and tissue damage. We highlight the dichotomy of HO-1 in innate and adaptive immune cells development and activation in different disease contexts. Finally, we address different known anti-inflammatory pharmaceuticals that are now being described to modulate HO-1, and the possible contribution of HO-1 in their anti-inflammatory effects.
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Affiliation(s)
- Rafael Cardoso Maciel Costa Silva
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Luiz Ricardo Vasconcelos
- Cellular Signaling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, UK
| | - Leonardo Holanda Travassos
- Laboratory of Immunoreceptors and Signaling, Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Yi R, Cho K, Bonneau R. NetTIME: a Multitask and Base-pair Resolution Framework for Improved Transcription Factor Binding Site Prediction. Bioinformatics 2022; 38:4762-4770. [PMID: 35997560 PMCID: PMC9563695 DOI: 10.1093/bioinformatics/btac569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 12/05/2022] Open
Abstract
Motivation Machine learning models for predicting cell-type-specific transcription factor (TF) binding sites have become increasingly more accurate thanks to the increased availability of next-generation sequencing data and more standardized model evaluation criteria. However, knowledge transfer from data-rich to data-limited TFs and cell types remains crucial for improving TF binding prediction models because available binding labels are highly skewed towards a small collection of TFs and cell types. Transfer prediction of TF binding sites can potentially benefit from a multitask learning approach; however, existing methods typically use shallow single-task models to generate low-resolution predictions. Here, we propose NetTIME, a multitask learning framework for predicting cell-type-specific TF binding sites with base-pair resolution. Results We show that the multitask learning strategy for TF binding prediction is more efficient than the single-task approach due to the increased data availability. NetTIME trains high-dimensional embedding vectors to distinguish TF and cell-type identities. We show that this approach is critical for the success of the multitask learning strategy and allows our model to make accurate transfer predictions within and beyond the training panels of TFs and cell types. We additionally train a linear-chain conditional random field (CRF) to classify binding predictions and show that this CRF eliminates the need for setting a probability threshold and reduces classification noise. We compare our method’s predictive performance with two state-of-the-art methods, Catchitt and Leopard, and show that our method outperforms previous methods under both supervised and transfer learning settings. Availability and implementation NetTIME is freely available at https://github.com/ryi06/NetTIME and the code is also archived at https://doi.org/10.5281/zenodo.6994897. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ren Yi
- Department of Computer Science, New York University, New York, NY, 10011, USA
| | - Kyunghyun Cho
- Department of Computer Science, New York University, New York, NY, 10011, USA.,Center for Data Science, New York University, New York, NY, 10011, USA.,Prescient Design, a Genentech accelerator, New York, NY, 10010, USA
| | - Richard Bonneau
- Department of Computer Science, New York University, New York, NY, 10011, USA.,Center for Data Science, New York University, New York, NY, 10011, USA.,Department of Biology, New York University, New York, NY, 10003, USA.,Prescient Design, a Genentech accelerator, New York, NY, 10010, USA
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A Comprehensive Analysis of Interferon Regulatory Factor Expression: Correlation with Immune Cell Infiltration and Patient Prognosis in Endometrial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7948898. [PMID: 35993041 PMCID: PMC9381850 DOI: 10.1155/2022/7948898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022]
Abstract
As a family of transcription factors, the correlations between expression pattern of nine interferon regulatory factor (IRF) family members, the immune invasion pattern, and the associated patient survival rate in endometrial carcinoma (EC) remain to be elucidated. Based on The Cancer Genome Atlas (TCGA), the expression profiles of the high and low IRF mRNA expression groups were analyzed using R (3.6.3) statistical software. Gene annotation and pathway analyses were performed using Metascape. GSEA was performed using the R package clusterProfiler (3.6.3). The single-sample gene set enrichment analysis (ssGSEA) was used to quantify the relative tumor infiltration levels of immune cell types. Immunohistochemistry data provided by HPA database was used to study the expression of the IRF proteins. Using the GEPIA dataset, the correlation between the expression of IRFs and the tumor stage of EC was analyzed. The correlations between the different IRFs were analyzed using cBioPortal. The expression of IRF2, IRF3, IRF5, IRF6, IRF7, IRF8, and IRF9 was different when comparing EC and normal endometrial samples. IRF2, IRF6, IRF7, and IRF8 were indicated to be potential diagnostic markers for EC. In combination with receiver operating characteristic analysis results, IRF2, IRF6, IRF7, and IRF8 were indicated to be potential diagnostic markers for EC. Levels of individual IRFs were associated with alternate outcomes, with the expression of IRF3 being correlated with the stage of EC and high expression of IRF4 being positively correlated with overall survival (OS); conversely, high expression of IRF5 was negatively correlated with OS. Additionally, high expression levels of both IRF2 and IRF4 were positively correlated with the disease-specific survival rate, and high expression of IRF4 was positively correlated with the progression-free interval. These data suggest a role for IRF2, IRF4, and IRF5 in the prognosis of EC. The expression of IRFs is associated with immune infiltration.
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Nilsen KE, Skjesol A, Frengen Kojen J, Espevik T, Stenvik J, Yurchenko M. TIRAP/Mal Positively Regulates TLR8-Mediated Signaling via IRF5 in Human Cells. Biomedicines 2022; 10:biomedicines10071476. [PMID: 35884781 PMCID: PMC9312982 DOI: 10.3390/biomedicines10071476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Toll-like receptor 8 (TLR8) recognizes single-stranded RNA of viral and bacterial origin as well as mediates the secretion of pro-inflammatory cytokines and type I interferons by human monocytes and macrophages. TLR8, as other endosomal TLRs, utilizes the MyD88 adaptor protein for initiation of signaling from endosomes. Here, we addressed the potential role of the Toll-interleukin 1 receptor domain-containing adaptor protein (TIRAP) in the regulation of TLR8 signaling in human primary monocyte-derived macrophages (MDMs). To accomplish this, we performed TIRAP gene silencing, followed by the stimulation of cells with synthetic ligands or live bacteria. Cytokine-gene expression and secretion were analyzed by quantitative PCR or Bioplex assays, respectively, while nuclear translocation of transcription factors was addressed by immunofluorescence and imaging, as well as by cell fractionation and immunoblotting. Immunoprecipitation and Akt inhibitors were also used to dissect the signaling mechanisms. Overall, we show that TIRAP is recruited to the TLR8 Myddosome signaling complex, where TIRAP contributes to Akt-kinase activation and the nuclear translocation of interferon regulatory factor 5 (IRF5). Recruitment of TIRAP to the TLR8 signaling complex promotes the expression and secretion of the IRF5-dependent cytokines IFNβ and IL-12p70 as well as, to a lesser degree, TNF. These findings reveal a new and unconventional role of TIRAP in innate immune defense.
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Affiliation(s)
- Kaja Elisabeth Nilsen
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Astrid Skjesol
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - June Frengen Kojen
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Terje Espevik
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Jørgen Stenvik
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Department of Infectious Diseases, Clinic of Medicine, St. Olavs Hospital HF, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Maria Yurchenko
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; (K.E.N.); (A.S.); (J.F.K.); (T.E.); (J.S.)
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Department of Infectious Diseases, Clinic of Medicine, St. Olavs Hospital HF, Trondheim University Hospital, NO-7006 Trondheim, Norway
- Correspondence:
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Abstract
The cardiac vascular and perivascular niche are of major importance in homeostasis and during disease, but we lack a complete understanding of its cellular heterogeneity and alteration in response to injury as a major driver of heart failure. Using combined genetic fate tracing with confocal imaging and single-cell RNA sequencing of this niche in homeostasis and during heart failure, we unravel cell type specific transcriptomic changes in fibroblast, endothelial, pericyte and vascular smooth muscle cell subtypes. We characterize a specific fibroblast subpopulation that exists during homeostasis, acquires Thbs4 expression and expands after injury driving cardiac fibrosis, and identify the transcription factor TEAD1 as a regulator of fibroblast activation. Endothelial cells display a proliferative response after injury, which is not sustained in later remodeling, together with transcriptional changes related to hypoxia, angiogenesis, and migration. Collectively, our data provides an extensive resource of transcriptomic changes in the vascular niche in hypertrophic cardiac remodeling. The cardiac vascular niche is of major importance in homeostasis and disease, but knowledge of its complexity in response to injury remains limited. Here we combine lineage tracing with single cell RNA sequencing to show alterations in fibroblasts, endothelial and mural cells in hypertrophic remodeling.
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Choi S, Jeon SA, Heo BY, Kang JG, Jung Y, Duong PTT, Song IC, Kim JH, Kim SY, Kwon J. Gene Set Enrichment Analysis Reveals That Fucoidan Induces Type I IFN Pathways in BMDC. Nutrients 2022; 14:nu14112242. [PMID: 35684042 PMCID: PMC9182765 DOI: 10.3390/nu14112242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Fucoidan, a sulfated polysaccharide extracted from brown seaweed, has been proposed to effectively treat and prevent various viral infections. However, the mechanisms behind its antiviral activity are not completely understood. We investigate here the global transcriptional changes in bone marrow-derived dendritic cells (BMDCs) using RNA-Seq technology. Through both analysis of differentially expressed genes (DEG) and gene set enrichment analysis (GSEA), we found that fucoidan-treated BMDCs were enriched in virus-specific response pathways, including that of SARS-CoV-2, as well as pathways associated with nucleic acid-sensing receptors (RLR, TLR, NLR, STING), and type I interferon (IFN) production. We show that these transcriptome changes are driven by well-known regulators of the inflammatory response against viruses, including IRF, NF-κB, and STAT family transcription factors. Furthermore, 435 of the 950 upregulated DEGs are classified as type I IFN-stimulated genes (ISGs). Flow cytometric analysis additionally showed that fucoidan increased MHCII, CD80, and CD40 surface markers in BMDCs, indicative of greater antigen presentation and co-stimulation functionality. Our current study suggests that fucoidan transcriptionally activates PRR signaling, type I IFN production and signaling, ISGs production, and DC maturation, highlighting a potential mechanism of fucoidan-induced antiviral activity.
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Affiliation(s)
- Suyoung Choi
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
| | - Sol A Jeon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.A.J.); (J.-H.K.)
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Korea
| | - Bu Yeon Heo
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
| | - Ju-Gyeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea;
| | - Yunju Jung
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Pham Thi Thuy Duong
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
| | - Ik-Chan Song
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
- Department of Internal Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Jeong-Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.A.J.); (J.-H.K.)
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; (S.A.J.); (J.-H.K.)
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Korea
- Correspondence: (S.-Y.K.); (J.K.); Tel.: +82-42-280-6937 (J.K); Fax: +82-42-583-8216 (J.K.)
| | - Jaeyul Kwon
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea; (S.C.); (B.Y.H.); (Y.J.); (P.T.T.D.); (I.-C.S.)
- Department of Infection Biology, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Brain Korea 21 FOUR Project for Medical Science, Chungnam National University, Daejeon 35015, Korea
- Department of Medical Education, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Translational Immunology Institute, Chungnam National University, Daejeon 35015, Korea
- Correspondence: (S.-Y.K.); (J.K.); Tel.: +82-42-280-6937 (J.K); Fax: +82-42-583-8216 (J.K.)
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Tissue-Specific Variations in Transcription Factors Elucidate Complex Immune System Regulation. Genes (Basel) 2022; 13:genes13050929. [PMID: 35627314 PMCID: PMC9140347 DOI: 10.3390/genes13050929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Gene expression plays a key role in health and disease. Estimating the genetic components underlying gene expression can thus help understand disease etiology. Polygenic models termed “transcriptome imputation” are used to estimate the genetic component of gene expression, but these models typically consider only the cis regions of the gene. However, these cis-based models miss large variability in expression for multiple genes. Transcription factors (TFs) that regulate gene expression are natural candidates for looking for additional sources of the missing variability. We developed a hypothesis-driven approach to identify second-tier regulation by variability in TFs. Our approach tested two models representing possible mechanisms by which variations in TFs can affect gene expression: variability in the expression of the TF and genetic variants within the TF that may affect the binding affinity of the TF to the TF-binding site. We tested our TF models in whole blood and skeletal muscle tissues and identified TF variability that can partially explain missing gene expression for 1035 genes, 76% of which explains more than the cis-based models. While the discovered regulation patterns were tissue-specific, they were both enriched for immune system functionality, elucidating complex regulation patterns. Our hypothesis-driven approach is useful for identifying tissue-specific genetic regulation patterns involving variations in TF expression or binding.
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75
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Genetic Associations and Differential mRNA Expression Levels of Host Genes Suggest a Viral Trigger for Endemic Pemphigus Foliaceus. Viruses 2022; 14:v14050879. [PMID: 35632621 PMCID: PMC9144834 DOI: 10.3390/v14050879] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
The long search for the environmental trigger of the endemic pemphigus foliaceus (EPF, fogo selvagem) has not yet resulted in any tangible findings. Here, we searched for genetic associations and the differential expression of host genes involved in early viral infections and innate antiviral defense. Genetic variants could alter the structure, expression sites, or levels of the gene products, impacting their functions. By analyzing 3063 variants of 166 candidate genes in 227 EPF patients and 194 controls, we found 12 variants within 11 genes associated with differential susceptibility (p < 0.005) to EPF. The products of genes TRIM5, TPCN2, EIF4E, EIF4E3, NUP37, NUP50, NUP88, TPR, USP15, IRF8, and JAK1 are involved in different mechanisms of viral control, for example, the regulation of viral entry into the host cell or recognition of viral nucleic acids and proteins. Only two of nine variants were also associated in an independent German cohort of sporadic PF (75 patients, 150 controls), aligning with our hypothesis that antiviral host genes play a major role in EPF due to a specific virus−human interaction in the endemic region. Moreover, CCL5, P4HB, and APOBEC3G mRNA levels were increased (p < 0.001) in CD4+ T lymphocytes of EPF patients. Because there is limited or no evidence that these genes are involved in autoimmunity, their crucial role in antiviral responses and the associations that we observed support the hypothesis of a viral trigger for EPF, presumably a still unnoticed flavivirus. This work opens new frontiers in searching for the trigger of EPF, with the potential to advance translational research that aims for disease prevention and treatment.
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76
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STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming. Nat Commun 2022; 13:1859. [PMID: 35388001 PMCID: PMC8986786 DOI: 10.1038/s41467-022-29541-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/22/2022] [Indexed: 02/02/2023] Open
Abstract
The cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization, especially the long-range enhancer-promoter contacts and subsequent gene expression control in cancer, remains poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of acetylated histone H3 lysine 27 (H3K27ac)-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-seq, STAG2 ChIP-seq and H3K27ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may enhance the immune evasion potential in STAG2-mutant cancer.
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77
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Al Hamrashdi M, Brady G. Regulation of IRF3 activation in Human Antiviral Signalling Pathways. Biochem Pharmacol 2022; 200:115026. [PMID: 35367198 DOI: 10.1016/j.bcp.2022.115026] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022]
Abstract
The interferon regulatory factor (IRF) family of transcription factors play a vital role in the human innate antiviral immune responses with production of interferons (IFNs) as a hallmark outcome of activation. In recent years, IRF3 has been considered a principal early regulator of type I IFNs (TI-IFNs) directly downstream of intracellular virus sensing. Despite decades of research on IRF-activating pathways, many questions remain on the regulation of IRF3 activation. The kinases IκB kinase epsilon (IKKε) and TANK-binding kinase-1 (TBK1) and the scaffold proteins TRAF family member-associated NF-kappa-B activator (TANK), NF-kappa-B-activating kinase-associated protein 1 (NAP1) and TANK-binding kinase 1-binding protein 1 (TBKBP1)/similar to NAP1 TBK1 adaptor (SINTBAD) are believed to be core components of an IRF3-activation complex yet their contextual involvement and complex composition are still unclear. This review will give an overview of antiviral signaling pathways leading to the activation of IRF3 and discuss recent developments in our understanding of its proximal regulation.
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Affiliation(s)
- Mariya Al Hamrashdi
- Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Dublin, Ireland.
| | - Gareth Brady
- Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Dublin, Ireland.
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Chen C, Man N, Liu F, Martin GM, Itonaga H, Sun J, Nimer SD. Epigenetic and transcriptional regulation of innate immunity in cancer. Cancer Res 2022; 82:2047-2056. [PMID: 35320354 DOI: 10.1158/0008-5472.can-21-3503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/16/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
Innate immune cells participate in the detection of tumor cells via complex signaling pathways mediated by pattern-recognition receptors, such as Toll-like receptors (TLR) and NOD-like receptors (NLR). These pathways are finely tuned via multiple mechanisms, including epigenetic regulation. It is well established that hematopoietic progenitors generate innate immune cells that can regulate cancer cell behavior, and the disruption of normal hematopoiesis in pathologic states may lead to altered immunity and the development of cancer. In this review, we discuss the epigenetic and transcriptional mechanisms that underlie the initiation and amplification of innate immune signaling in cancer. We also discuss new targeting possibilities for cancer control that exploit innate immune cells and signaling molecules, potentially heralding the next generation of immunotherapy.
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Affiliation(s)
- Chuan Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Na Man
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Fan Liu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Gloria Mas Martin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Hidehiro Itonaga
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Jun Sun
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
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Hu Y, Pan Q, Zhou K, Ling Y, Wang H, Li Y. RUNX1 inhibits the antiviral immune response against influenza A virus through attenuating type I interferon signaling. Virol J 2022; 19:39. [PMID: 35248104 PMCID: PMC8897766 DOI: 10.1186/s12985-022-01764-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background Influenza A viruses (IAVs) are zoonotic, segmented negative-stranded RNA viruses. The rapid mutation of IAVs results in host immune response escape and antiviral drug and vaccine resistance. RUNX1 is a transcription factor that not only plays essential roles in hematopoiesis, but also functions as a regulator in inflammation. However, its role in the innate immunity to IAV infection has not been well studied. Methods To investigate the effects of RUNX1 on IAV infection and explore the mechanisms that RUNX1 uses during IAV infection. We infected the human alveolar epithelial cell line (A549) with influenza virus A/Puerto Rico/8/34 (H1N1) (PR8) and examined RUNX1 expression by Western blot and qRT-PCR. We also knocked down or overexpressed RUNX1 in A549 cells, then evaluated viral replication by Western blot, qRT-PCR, and viral titration. Results We found RUNX1 expression is induced by IAV H1N1 PR8 infection, but not by poly(I:C) treatment, in the human alveolar epithelial cell line A549. Knockdown of RUNX1 significantly inhibited IAV infection. Conversely, overexpression of RUNX1 efficiently promoted production of progeny viruses. Additionally, RUNX1 knockdown increased IFN-β and ISGs production while RUNX1 overexpression compromised IFN-β and ISGs production upon PR8 infection in A549 cells. We further showed that RUNX1 may attenuate the interferon signaling transduction by hampering the expression of IRF3 and STAT1 during IAV infection. Conclusions Taken together, we found RUNX1 attenuates type I interferon signaling to facilitate IAV infection in A549 cells.
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Zou PF, Li KQ, Li Y, Shen YJ, Zhang ZP, Wang YL. Molecular cloning and functional characterization of RIP1 in large yellow croaker Larimichthys crocea. FISH & SHELLFISH IMMUNOLOGY 2022; 122:386-398. [PMID: 35181446 DOI: 10.1016/j.fsi.2022.02.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
Receptor interacting protein 1 (RIP1) plays important roles not only in cell-death pathways but also in host innate immune responses. In the present study, a RIP1 ortholog named Lc-RIP1 was cloned and characterized in large yellow croaker (Larimichthys crocea). The open reading frame (ORF) of Lc-RIP1 is 2,046 bp, encoding a protein of 681 amino acids (aa), with an N-terminal kinase domain, an RHIM domain, and a C-terminal death domain. Subcellular localization analysis revealed that Lc-RIP1 was a cytosolic protein, which was broadly expressed in examined tissues/organs, and could be up-regulated under poly I:C, LPS, PGN, and Pseudomonas plecoglossicida stimulation in vivo based on qRT-PCR analysis. Notably, Lc-RIP1 could induce NF-κB, but not IRF3, IRF7 or type I IFN promoter activation. In addition, Lc-RIP1 overexpression could enhance Lc-MAVS, Lc-TRAF3, and Lc-TRAF6 mediated NF-κB promoter activation, and also Lc-TRIF and Lc-MAVS mediated IRF3 promoter activation, whereas suppress Lc-TRIF mediated NF-κB and type I IFN promoter activation, as well as Lc-TRAF3 and Lc-IRF3 mediated IRF3 promoter activation, Lc-IRF3 mediated type I IFN promoter activation and Lc-IRF7 mediated IRF7 promoter activation. These results collectively indicated that Lc-RIP1 function importantly in regulation of host innate immune signaling.
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Affiliation(s)
- Peng Fei Zou
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, Fujian Province, 361021, China.
| | - Kai Qing Li
- College of the Environment and Ecology, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Ying Li
- Key Laboratory of Estuarine Ecological Security and Environmental Health, Tan Kah Kee College, Xiamen University, Zhangzhou, Fujian Province, 363105, China.
| | - Ying Jia Shen
- College of the Environment and Ecology, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Zi Ping Zhang
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, 350002, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian Province, 352103, China
| | - Yi Lei Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen, Fujian Province, 361021, China; State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian Province, 352103, China
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81
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Kamyshna I, Kamyshnyi A. Transcription factors and regulators pathway-focused genes expression analysis in patients with different forms of thyroid pathology. Curr Pharm Biotechnol 2022; 23:1396-1404. [PMID: 35176984 DOI: 10.2174/1389201023666220217123454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Autoimmune thyroiditis (AIT) is a T cell-mediated organ-specific disorder and transcription factors have a critical role in the regulation of immune responses, especially in the fate of T-helper cells. OBJECTIVE This study aims to investigate changes in the gene expression profile of transcription factors and regulators in patients with different forms of thyroid pathology Methods. We used the pathway-specific real-time PCR array (Neurotrophins and Receptors RT2 Profiler PCR Array, QIAGEN, Germany) to identify and verify transcription factors and regulators pathway-focused genes expression in peripheral white blood cells of patients with postoperative hypothyroidism, hypothyroidism as a result of AIT and AIT with elevated serum an anti-thyroglobulin (anti-Tg) and anti-thyroid peroxidase (anti-TPO) antibodies. RESULTS It was shown that in patients with postoperative hypothyroidism FOS, NR1I2, STAT4, and TP53 significantly increased their expression whereas the expression of STAT1, STAT2, and STAT3 decreased. In patients with hypothyroidism as a result of AIT, we have found increased expression of NR1I2, STAT2, and STAT3. In contrast, the expression of STAT1 and TP53 decreased. FOS and STAT4 mRNAs did not change their expression. In patients with AIT and elevated serum anti-Tg and anti-TPO antibodies, the expression of FOS and NR1I2 reduced whereas the mRNA level of STAT3 increased. STAT1, STAT2, and STAT4 mRNAs did not change their expression. MYC did not change its expression in all groups of patients. CONCLUSIONS The results of this study demonstrate that autoimmune thyroiditis and hypothyroidism affect the mRNA-level expression of transcription factors and regulators genes in a gene-specific manner and that these changes to genes expression can be among the triggers of autoimmune inflammation progression in the thyroid gland.
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Affiliation(s)
- Iryna Kamyshna
- Department of Medical Rehabilitation, I. Horbachevsky Ternopil National Medical University, Majdan Voli 1, Ternopil, Ukraine
| | - Aleksandr Kamyshnyi
- Department of Microbiology, Virology, and Immunology, I. Horbachevsky Ternopil National Medical University, Majdan Voli 1, Ternopil, Ukraine
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Alfaro R, Martínez-Banaclocha H, Llorente S, Jimenez-Coll V, Galián JA, Botella C, Moya-Quiles MR, Parrado A, Muro-Perez M, Minguela A, Legaz I, Muro M. Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection. Front Immunol 2022; 12:800968. [PMID: 34975915 PMCID: PMC8714745 DOI: 10.3389/fimmu.2021.800968] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023] Open
Abstract
Background The diagnosis of graft rejection in kidney transplantation (KT) patients is made by evaluating the histological characteristics of biopsy samples. The evolution of omics sciences and bioinformatics techniques has contributed to the advancement in searching and predicting biomarkers, pathways, and new target drugs that allow a more precise and less invasive diagnosis. The aim was to search for differentially expressed genes (DEGs) in patients with/without antibody-mediated rejection (AMR) and find essential cells involved in AMR, new target drugs, protein-protein interactions (PPI), and know their functional and biological analysis. Material and Methods Four GEO databases of kidney biopsies of kidney transplantation with/without AMR were analyzed. The infiltrating leukocyte populations in the graft, new target drugs, protein-protein interactions (PPI), functional and biological analysis were studied by different bioinformatics tools. Results Our results show DEGs and the infiltrating leukocyte populations in the graft. There is an increase in the expression of genes related to different stages of the activation of the immune system, antigenic presentation such as antibody-mediated cytotoxicity, or leukocyte migration during AMR. The importance of the IRF/STAT1 pathways of response to IFN in controlling the expression of genes related to humoral rejection. The genes of this biological pathway were postulated as potential therapeutic targets and biomarkers of AMR. These biological processes correlated showed the infiltration of NK cells and monocytes towards the allograft. Besides the increase in dendritic cell maturation, it plays a central role in mediating the damage suffered by the graft during AMR. Computational approaches to the search for new therapeutic uses of approved target drugs also showed that imatinib might theoretically be helpful in KT for the prevention and/or treatment of AMR. Conclusion Our results suggest the importance of the IRF/STAT1 pathways in humoral kidney rejection. NK cells and monocytes in graft damage have an essential role during rejection, and imatinib improves KT outcomes. Our results will have to be validated for the potential use of overexpressed genes as rejection biomarkers that can be used as diagnostic and prognostic markers and as therapeutic targets to avoid graft rejection in patients undergoing kidney transplantation.
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Affiliation(s)
- Rafael Alfaro
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Helios Martínez-Banaclocha
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Santiago Llorente
- Nephrology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Victor Jimenez-Coll
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - José Antonio Galián
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Carmen Botella
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - María Rosa Moya-Quiles
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Antonio Parrado
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Manuel Muro-Perez
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Alfredo Minguela
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), University of Murcia, Murcia, Spain
| | - Manuel Muro
- Immunology Services, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
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Lažetić V, Wu F, Cohen LB, Reddy KC, Chang YT, Gang SS, Bhabha G, Troemel ER. The transcription factor ZIP-1 promotes resistance to intracellular infection in Caenorhabditis elegans. Nat Commun 2022; 13:17. [PMID: 35013162 PMCID: PMC8748929 DOI: 10.1038/s41467-021-27621-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Defense against intracellular infection has been extensively studied in vertebrate hosts, but less is known about invertebrate hosts; specifically, the transcription factors that induce defense against intracellular intestinal infection in the model nematode Caenorhabditis elegans remain understudied. Two different types of intracellular pathogens that naturally infect the C. elegans intestine are the Orsay virus, which is an RNA virus, and microsporidia, which comprise a phylum of fungal pathogens. Despite their molecular differences, these pathogens induce a common host transcriptional response called the intracellular pathogen response (IPR). Here we show that zip-1 is an IPR regulator that functions downstream of all known IPR-activating and regulatory pathways. zip-1 encodes a putative bZIP transcription factor, and we show that zip-1 controls induction of a subset of genes upon IPR activation. ZIP-1 protein is expressed in the nuclei of intestinal cells, and is at least partially required in the intestine to upregulate IPR gene expression. Importantly, zip-1 promotes resistance to infection by the Orsay virus and by microsporidia in intestinal cells. Altogether, our results indicate that zip-1 represents a central hub for triggers of the IPR, and that this transcription factor has a protective function against intracellular pathogen infection in C. elegans. Intestinal immune responses to intracellular infection of Caenorhabditis elegans and other Invertebrate hosts are not well understood. Here the authors show a key role for the transcription factor ZIP-1 during intestinal intracellular infection.
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Affiliation(s)
- Vladimir Lažetić
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA
| | - Fengting Wu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA
| | - Lianne B Cohen
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA
| | - Kirthi C Reddy
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA
| | - Ya-Ting Chang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Spencer S Gang
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Emily R Troemel
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, CA, USA.
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84
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The Immunogenetics of Systemic Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:259-298. [DOI: 10.1007/978-3-030-92616-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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85
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Onyedibe KI, Elmanfi S, Aryal UK, Könönen E, Gürsoy UK, Sintim HO. Global proteomics of fibroblast cells treated with bacterial cyclic dinucleotides, c-di-GMP and c-di-AMP. J Oral Microbiol 2021; 14:2003617. [PMID: 34992733 PMCID: PMC8725719 DOI: 10.1080/20002297.2021.2003617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/04/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Constant exposure of human gingival fibroblasts (HGFs) to oral pathogens trigger selective immune responses. Recently, the activation of immune response to cyclic dinucleotides (CDNs) via STING has come to the forefront. Reports show that other proteins outside the STING-TBK1-IRF3 axis respond to CDNs but a global view of impacted proteome in diverse cells is lacking. HGFs are constantly exposed to bacterial-derived cyclic-di-adenosine monophosphate (c-di-AMP) and cyclic-di-guanosine monophosphate (c-di-GMP). AIM To understand the response of HGFs to bacterial-derived CDNs, we carried out a global proteomics analysis of HGFs treated with c-di-AMP or c-di-GMP. METHODS The expression levels of several proteins modulated by CDNs were examined. RESULTS Interferon signaling proteins such as Ubiquitin-like protein ISG15 (ISG15), Interferon-induced GTP-binding protein Mx1 (MX1), Interferon-induced protein with tetratricopeptide repeats (IFIT) 1 (IFIT1), and (IFIT3) were significantly upregulated. Interestingly, other pathways not fully characterized to be regulated by CDNs, such as necroptosis signaling, iron homeostasis signaling, protein ubiquitination, EIF2 signaling, sumoylation and nucleotide excision repair pathways were also modulated by the bacterial-derived CDNs. CONCLUSION This study has added to the increasing appreciation that beyond the regulation of cytokine production via STING, cyclic dinucleotides also broadly affect many critical processes in human cells.
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Affiliation(s)
- Kenneth I. Onyedibe
- Department of Chemistry, Purdue University, West Lafayette, USA
- Immunology and Infectious Disease, Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Purdue University, West Lafayette, USA
| | - Samira Elmanfi
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Uma K. Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, USA
- Department of Comparative Pathobiology, Purdue University, West Lafayette, USA
| | - Eija Könönen
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Ulvi Kahraman Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Herman O. Sintim
- Department of Chemistry, Purdue University, West Lafayette, USA
- Immunology and Infectious Disease, Purdue Institute for Drug Discovery and Purdue Institute of Inflammation, Purdue University, West Lafayette, USA
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86
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Stati G, Passaretta F, Gindraux F, Centurione L, Di Pietro R. The Role of the CREB Protein Family Members and the Related Transcription Factors in Radioresistance Mechanisms. Life (Basel) 2021; 11:life11121437. [PMID: 34947968 PMCID: PMC8706059 DOI: 10.3390/life11121437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/02/2021] [Accepted: 12/16/2021] [Indexed: 02/05/2023] Open
Abstract
In the framework of space flight, the risk of radiation carcinogenesis is considered a "red" risk due to the high likelihood of occurrence as well as the high potential impact on the quality of life in terms of disease-free survival after space missions. The cyclic AMP response element-binding protein (CREB) is overexpressed both in haematological malignancies and solid tumours and its expression and function are modulated following irradiation. The CREB protein is a transcription factor and member of the CREB/activating transcription factor (ATF) family. As such, it has an essential role in a wide range of cell processes, including cell survival, proliferation, and differentiation. Among the CREB-related nuclear transcription factors, NF-κB and p53 have a relevant role in cell response to ionising radiation. Their expression and function can decide the fate of the cell by choosing between death or survival. The aim of this review was to define the role of the CREB/ATF family members and the related transcription factors in the response to ionising radiation of human haematological malignancies and solid tumours.
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Affiliation(s)
- Gianmarco Stati
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
- Correspondence: ; Tel.: +39-08713554567
| | - Francesca Passaretta
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Florelle Gindraux
- Laboratoire de Nanomédecine, Imagerie, Thérapeutique EA 4662, Université Bourgogne Franche-Comté, 25030 Besançon, France;
- Service de Chirurgie Orthopédique, Traumatologique et Plastique, CHU, 25030 Besançon, France
| | - Lucia Centurione
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Roberta Di Pietro
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
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87
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Wen TH, Tsai KW, Wu YJ, Liao MT, Lu KC, Hu WC. The Framework for Human Host Immune Responses to Four Types of Parasitic Infections and Relevant Key JAK/STAT Signaling. Int J Mol Sci 2021; 22:ijms222413310. [PMID: 34948112 PMCID: PMC8705408 DOI: 10.3390/ijms222413310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 02/07/2023] Open
Abstract
The human host immune responses to parasitic infections are complex. They can be categorized into four immunological pathways mounted against four types of parasitic infections. For intracellular protozoa, the eradicable host immunological pathway is TH1 immunity involving macrophages (M1), interferon gamma (IFNγ) CD4 T cells, innate lymphoid cells 1 (NKp44+ ILC1), CD8 T cells (Effector-Memory4, EM4), invariant natural killer T cells 1 (iNKT1) cells, and immunoglobulin G3 (IgG3) B cells. For intracellular protozoa, the tolerable host immunological pathway is TH1-like immunity involving macrophages (M2), interferon gamma (IFNγ)/TGFβ CD4 T cells, innate lymphoid cells 1 (NKp44- ILC1), CD8 T cells (EM3), invariant natural killer T 1 (iNKT1) cells, and immunoglobulin A1 (IgA1) B cells. For free-living extracellular protozoa, the eradicable host immunological pathway is TH22 immunity involving neutrophils (N1), interleukin-22 CD4 T cells, innate lymphoid cells 3 (NCR+ ILC3), iNKT17 cells, and IgG2 B cells. For free-living extracellular protozoa, the tolerable host immunological pathway is TH17 immunity involving neutrophils (N2), interleukin-17 CD4 T cells, innate lymphoid cells 3 (NCR- ILC3), iNKT17 cells, and IgA2 B cells. For endoparasites (helminths), the eradicable host immunological pathway is TH2a immunity with inflammatory eosinophils (iEOS), interleukin-5/interleukin-4 CD4 T cells, interleukin-25 induced inflammatory innate lymphoid cells 2 (iILC2), tryptase-positive mast cells (MCt), iNKT2 cells, and IgG4 B cells. For ectoparasites (parasitic insects and arachnids), the eradicable host immunological pathway is TH2b immunity with inflammatory basophils, chymase- and tryptase-positive mast cells (MCct), interleukin-3/interleukin-4 CD4 T cells, interleukin-33 induced nature innate lymphoid cells 2 (nILC2), iNKT2 cells, and immunoglobulin E (IgE) B cells. The tolerable host immunity against ectoparasites and endoparasites is TH9 immunity with regulatory eosinophils, regulatory basophils, interleukin-9 mast cells (MMC9), thymic stromal lymphopoietin induced innate lymphoid cells 2, interleukin-9 CD4 T cells, iNKT2 cells, and IgA2 B cells. In addition, specific transcription factors important for specific immune responses were listed. This JAK/STAT signaling is key to controlling or inducing different immunological pathways. In sum, Tfh is related to STAT5β, and BCL6 expression. Treg is related to STAT5α, STAT5β, and FOXP3. TH1 immunity is related to STAT1α, STAT4, and T-bet. TH2a immunity is related to STAT6, STAT1α, GATA1, and GATA3. TH2b immunity is related to STAT6, STAT3, GATA2, and GATA3. TH22 immunity is associated with both STAT3α and AHR. THαβ immunity is related to STAT1α, STAT1β, STAT2, STAT3β, and ISGF. TH1-like immunity is related to STAT1α, STAT4, STAT5α, and STAT5β. TH9 immunity is related to STAT6, STAT5α, STAT5β, and PU.1. TH17 immunity is related to STAT3α, STAT5α, STAT5β, and RORG. TH3 immunity is related to STAT1α, STAT1β, STAT2, STAT3β, STAT5α, STAT5β, and ISGF. This categorization provides a complete framework of immunological pathways against four types of parasitic infections. This framework as well as relevant JAK/STAT signaling can provide useful knowledge to control allergic hypersensitivities and parasitic infections via development of vaccines or drugs in the near future.
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Affiliation(s)
- Tsung-Han Wen
- Department of Anatomical Pathology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan;
| | - Kuo-Wang Tsai
- Department of Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan;
| | - Yan-Jun Wu
- Department of Pediatrics, Taoyuan Armed Forces General Hospital, Taoyuan City 325, Taiwan; (Y.-J.W.); (M.-T.L.)
| | - Min-Tser Liao
- Department of Pediatrics, Taoyuan Armed Forces General Hospital, Taoyuan City 325, Taiwan; (Y.-J.W.); (M.-T.L.)
| | - Kuo-Cheng Lu
- Division of Nephrology, Department of Medicine, Fu-Jen Catholic University Hospital, School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan;
| | - Wan-Chung Hu
- Department of Clinical Pathology & Medical Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation No. 289, Jianguo Road, Xindian District, New Taipei City 231, Taiwan
- Correspondence: ; Tel.: +886-2-89676779
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Awasthi N, Liongue C, Ward AC. STAT proteins: a kaleidoscope of canonical and non-canonical functions in immunity and cancer. J Hematol Oncol 2021; 14:198. [PMID: 34809691 PMCID: PMC8607625 DOI: 10.1186/s13045-021-01214-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/09/2021] [Indexed: 12/24/2022] Open
Abstract
STAT proteins represent an important family of evolutionarily conserved transcription factors that play key roles in diverse biological processes, notably including blood and immune cell development and function. Classically, STAT proteins have been viewed as inducible activators of transcription that mediate cellular responses to extracellular signals, particularly cytokines. In this 'canonical' paradigm, latent STAT proteins become tyrosine phosphorylated following receptor activation, typically via downstream JAK proteins, facilitating their dimerization and translocation into the nucleus where they bind to specific sequences in the regulatory region of target genes to activate transcription. However, growing evidence has challenged this paradigm and identified alternate 'non-canonical' functions, such as transcriptional repression and roles outside the nucleus, with both phosphorylated and unphosphorylated STATs involved. This review provides a revised framework for understanding the diverse kaleidoscope of STAT protein functional modalities. It further discusses the implications of this framework for our understanding of STAT proteins in normal blood and immune cell biology and diseases such as cancer, and also provides an evolutionary context to place the origins of these alternative functional modalities.
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Affiliation(s)
- Nagendra Awasthi
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia.,Institue of Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
| | - Clifford Liongue
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia.,Institue of Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia
| | - Alister C Ward
- School of Medicine, Deakin University, Pigdons Road, Geelong, VIC, 3216, Australia. .,Institue of Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, VIC, Australia.
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牟 斐, 陈 曦, 杜 希, 焦 倩, 毕 明, 姜 宏. [Regulatory mechanism of interferon regulatory factor 1 by α-synuclein in mouse Parkinson's disease model]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1641-1648. [PMID: 34916189 PMCID: PMC8685704 DOI: 10.12122/j.issn.1673-4254.2021.11.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To investigate the molecular mechanism by which α-synuclein (α-Syn) regulates interferon regulatory factor 1 (IRF-1) expression. METHODS SH-SY5Y cells overexpressing α-Syn and transgenic mouse model carrying human α-Syn gene with A53T mutation (3 and 6 months old) were examined for IRF-1 mRNA and protein expressions using real-time PCR and Western blotting, respectively. The subcellular localization of IRF-1 was determined with immunofluorescence staining and cytoplasmic/nuclear protein isolation. The optimal concentrations of the proteasome inhibitor MG132 (0.01-2.0 μmol/L) and lysosomal inhibitor chloroquine (5-200 μmol/L) for treatment of SH-SY5Y cells for 24 h were determined by examining the cell viability. SH-SY5Y cells were treated with 0.2 μmol/L MG132 and 30 μmol/L chloroquine for 24 h (the maximum dose that did not cause cell damage), and the changes of IRF-1 protein expressions was analyzed. The effects of α-Syn on MDM2 protein expression and IRF-1 ubiquitylation were analyzed using Western blotting and ubiquitylation assay. RESULTS α-Syn overexpression did not affect the mRNA level of IRF-1 but significantly increased its protein level (P < 0.01). In α-Synoverexpressing SH-SY5Y cells, IRF-1 translocation was observed from the cytoplasm to the nucleus (P < 0.001). Treatment of the cells with 0.2 μmol/L MG132 significantly aggravated α-Syn-induced increase of IRF-1 protein expression (P < 0.01) while 30 μmol/L chloroquine produced no significant changes in IRF-1 level. α-Syn overexpression caused an obvious decrease of MDM2 protein level and further inhibited the ubiquitylation of IRF-1 (P < 0.01). CONCLUSION α-Syn blocks MDM2-mediated ubiquitylation of IRF-1 through ubiquitin proteasome pathway, thereby enhancing IRF-1 protein expression.
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Affiliation(s)
- 斐斐 牟
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
| | - 曦 陈
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
| | - 希恂 杜
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
| | - 倩 焦
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
| | - 明霞 毕
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
| | - 宏 姜
- />青岛大学国家生理学重点(培育)学科,山东 青岛 266071State Key Disciplines of Physiology (Incubation), Department of Physiology, Qingdao University, Qingdao 266071, China
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90
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Goswami DG, Walker WE. Aged IRF3-KO Mice are Protected from Sepsis. J Inflamm Res 2021; 14:5757-5767. [PMID: 34764669 PMCID: PMC8573150 DOI: 10.2147/jir.s335203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/30/2021] [Indexed: 12/29/2022] Open
Abstract
Purpose Sepsis is a leading cause of hospital admissions and deaths. Older adults (>65 years) are particularly susceptible to sepsis and experience higher morbidity and mortality rates than younger people. We previously showed that interferon regulatory factor 3 (IRF3) contributes to sepsis pathogenesis in young mice subject to cecal ligation and puncture (CLP). In this study, we investigated if IRF3 contributes to sepsis in the context of aging. Methods Sepsis was induced in aged wild-type (WT) and IRF3-knock-out (KO) mice, using a clinically-relevant CLP-sepsis model including fluids and antibiotics. Animal survival, disease score and hypothermia were evaluated as indicators of sepsis pathogenesis. Serum cytokines and serum enzymes indicative of organ damage were also measured. Results Aged WT mice were highly susceptible to sepsis (90% mortality). In comparison, aged IRF3-KO mice were significantly protected (20% mortality). Aged IRF3-KO mice showed a lower disease score and reduced hypothermia following CLP, compared to WT mice. Serum cytokines interleukin (IL)-6, IL-12/23p40 and macrophage chemoattractant protein (MCP)-1, and creatinine kinase (CK) were lower in aged IRF3-KO septic mice compared to WT counterparts. Aged male mice were found to be more susceptible to sepsis compared to females. Female mice, however, produced higher levels of serum cytokines and CK. Conclusion These results demonstrate that IRF3 plays a detrimental role in sepsis in aged mice and highlight the impact of biological sex.
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Affiliation(s)
- Dinesh G Goswami
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Wendy E Walker
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
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91
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Xiong Y, Tang YD, Zheng C. The crosstalk between the caspase family and the cGAS‒STING signaling pathway. J Mol Cell Biol 2021; 13:739-747. [PMID: 34718659 PMCID: PMC8718194 DOI: 10.1093/jmcb/mjab071] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Edited by Jiarui Wu Cytosolic nucleic acid sensors are critical for sensing nucleic acids and initiating innate immunity during microbial infections and/or cell death. Over the last decade, several key studies have characterized the conserved mechanism of cyclic guanosine monophosphate‒adenosine monophosphate synthase (cGAS) and the downstream signaling adaptor stimulator of interferon genes (STING) initiating the innate immune signaling pathways. Aside from its primary involvement in microbial infections and inflammatory diseases, there is growing interest in the alternate roles of cGAS‒STING-mediated signaling. Caspase family members are powerful functional proteins that respond to cellular stress, including cell death signals, inflammation, and innate immunity. Recent studies have uncovered how the caspase family cooperates with the cGAS‒STING signaling pathway. Most caspase family members negatively regulate the cGAS‒STING signaling pathway. In turn, some caspase family members can also be modulated by cGAS‒STING. This review gives a detailed account of the interplay between the caspase family and the cGAS‒STING signaling pathway, which will shed light on developing novel therapeutics targeting the caspase family and cGAS‒STING signaling in antiviral innate immunity, cancer, inflammatory, and autoimmunity.
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Affiliation(s)
- Yongai Xiong
- Department of Pharmaceutics, Key Laboratory of Basic Pharmacology of Guizhou Province and School of Pharmacy, Zunyi Medical University, Zunyi, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Yan-Dong Tang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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92
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RIP3 Associates with RIP1, TRIF, MAVS, and Also IRF3/7 in Host Innate Immune Signaling in Large Yellow Croaker Larimichthys crocea. Antibiotics (Basel) 2021; 10:antibiotics10101199. [PMID: 34680780 PMCID: PMC8533023 DOI: 10.3390/antibiotics10101199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 02/06/2023] Open
Abstract
Receptor-interacting protein 3 (RIP3) has been demonstrated to be a key regulator not only in cell death pathways including apoptosis and necroptosis but also in inflammation and host immune responses. In this study, a RIP3 ortholog named Lc-RIP3 is identified in large yellow croaker (Larimichthys crocea). The open reading frame (ORF) of Lc-RIP3 is 1524 bp long and encodes a protein of 507 amino acids (aa). The deduced Lc-RIP3 protein has an N-terminal kinase domain and a C-terminal RHIM domain, and the genome organization of Lc-RIP3 is conserved in teleosts with 12 exons and 11 introns but is different from that in mammals, which comprises 10 exons and 9 introns. Confocal microscopy revealed that Lc-RIP3 is a cytosolic protein. The expression analysis at the mRNA level indicated that Lc-RIP3 is ubiquitously distributed in various tissues/organs, and could be up-regulated under poly I:C, LPS, PGN, and Pseudomonas plecoglossicida stimulation in vivo. Notably, Lc-RIP3 could induce NF-κB but not IRF3 activation. In addition, Lc-RIP3 co-expression with Lc-TRIF, Lc-MAVS, or Lc-IRF3 significantly abolishes the activation of NF-κB but enhances the induction of IRF3 activity. Moreover, NF-κB activity could be up-regulated when Lc-RIP3 is co-expressed with Lc-RIP1 or Lc-IRF7. These results collectively indicate that Lc-RIP3 acts as an important regulator in host innate immune signaling in teleosts.
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93
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Classification Criteria for Acute Retinal Necrosis Syndrome. Am J Ophthalmol 2021; 228:237-244. [PMID: 33845012 PMCID: PMC8675365 DOI: 10.1016/j.ajo.2021.03.057] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 01/29/2021] [Accepted: 03/31/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE To determine classification criteria for acute retinal necrosis (ARN). DESIGN Machine learning of cases with ARN and 4 other infectious posterior uveitides / panuveitides. METHODS Cases of infectious posterior uveitides / panuveitides were collected in an informatics-designed preliminary database, and a final database was constructed of cases achieving supermajority agreement on diagnosis, using formal consensus techniques. Cases were split into a training set and a validation set. Machine learning using multinomial logistic regression was used on the training set to determine a parsimonious set of criteria that minimized the misclassification rate among the infectious posterior uveitides / panuveitides. The resulting criteria were evaluated on the validation set. RESULTS Eight hundred three cases of infectious posterior uveitides / panuveitides, including 186 cases of ARN, were evaluated by machine learning. Key criteria for ARN included (1) peripheral necrotizing retinitis and either (2) polymerase chain reaction assay of an intraocular fluid specimen positive for either herpes simplex virus or varicella zoster virus or (3) a characteristic clinical appearance with circumferential or confluent retinitis, retinal vascular sheathing and/or occlusion, and more than minimal vitritis. Overall accuracy for infectious posterior uveitides / panuveitides was 92.1% in the training set and 93.3% (95% confidence interval 88.2, 96.3) in the validation set. The misclassification rates for ARN were 15% in the training set and 11.5% in the validation set. CONCLUSIONS The criteria for ARN had a reasonably low misclassification rate and seemed to perform sufficiently well for use in clinical and translational research.
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94
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Liu S, Ma H, Zhang H, Deng C, Xin P. Recent advances on signaling pathways and their inhibitors in rheumatoid arthritis. Clin Immunol 2021; 230:108793. [PMID: 34242749 DOI: 10.1016/j.clim.2021.108793] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is characterized by systemic synovitis leading to joint destruction in which imbalances in pro-inflammatory and anti-inflammatory cytokines promote the induction of autoimmunity. Some pro-inflammatory cytokines can trigger the signaling pathways which responsible for immune-mediated inflammation in RA, and the activated signaling pathways produce pro-inflammatory cytokines, resulting in aggravation of RA. Hence, understanding of the signaling pathways and their inhibitors might be advantageous in the development of therapeutic targets and new drugs for RA. In the current review, we summarize the signaling pathways involved in the pathogenesis of RA as well as the potential role of specific inhibitors in its management. We hope this paper may serve a reference for future studies on signaling pathways implicated in the pathogenesis of RA and benefit the treatment of RA.
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Affiliation(s)
- Shuang Liu
- College of Pharmacy, Harbin Medical University-Daqing, Daqing 163319, China
| | - Hongxing Ma
- Clinical Laboratory Department, Nanjing Lishui People's Hospital, Zhongda Hospital Lishui Branch, Southeast University, Nanjing 211200, China
| | - Huaxi Zhang
- College of Pharmacy, Harbin Medical University-Daqing, Daqing 163319, China
| | - Chengjie Deng
- College of Pharmacy, Harbin Medical University-Daqing, Daqing 163319, China
| | - Ping Xin
- College of Pharmacy, Harbin Medical University-Daqing, Daqing 163319, China.
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95
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Manes NP, Nita-Lazar A. Molecular Mechanisms of the Toll-Like Receptor, STING, MAVS, Inflammasome, and Interferon Pathways. mSystems 2021; 6:e0033621. [PMID: 34184910 PMCID: PMC8269223 DOI: 10.1128/msystems.00336-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pattern recognition receptors (PRRs) form the front line of defense against pathogens. Many of the molecular mechanisms that facilitate PRR signaling have been characterized in detail, which is critical for the development of accurate PRR pathway models at the molecular interaction level. These models could support the development of therapeutics for numerous diseases, including sepsis and COVID-19. This review describes the molecular mechanisms of the principal signaling interactions of the Toll-like receptor, STING, MAVS, and inflammasome pathways. A detailed molecular mechanism network is included as Data Set S1 in the supplemental material.
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Affiliation(s)
- Nathan P. Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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96
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Dat NQ, Thuy LTT, Hieu VN, Hai H, Hoang DV, Thi Thanh Hai N, Thuy TTV, Komiya T, Rombouts K, Dong MP, Hanh NV, Hoang TH, Sato‐Matsubara M, Daikoku A, Kadono C, Oikawa D, Yoshizato K, Tokunaga F, Pinzani M, Kawada N. Hexa Histidine-Tagged Recombinant Human Cytoglobin Deactivates Hepatic Stellate Cells and Inhibits Liver Fibrosis by Scavenging Reactive Oxygen Species. Hepatology 2021; 73:2527-2545. [PMID: 33576020 PMCID: PMC8251927 DOI: 10.1002/hep.31752] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/25/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Antifibrotic therapy remains an unmet medical need in human chronic liver disease. We report the antifibrotic properties of cytoglobin (CYGB), a respiratory protein expressed in hepatic stellate cells (HSCs), the main cell type involved in liver fibrosis. APPROACH AND RESULTS Cygb-deficient mice that had bile duct ligation-induced liver cholestasis or choline-deficient amino acid-defined diet-induced steatohepatitis significantly exacerbated liver damage, fibrosis, and reactive oxygen species (ROS) formation. All of these manifestations were attenuated in Cygb-overexpressing mice. We produced hexa histidine-tagged recombinant human CYGB (His-CYGB), traced its biodistribution, and assessed its function in HSCs or in mice with advanced liver cirrhosis using thioacetamide (TAA) or 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). In cultured HSCs, extracellular His-CYGB was endocytosed and accumulated in endosomes through a clathrin-mediated pathway. His-CYGB significantly impeded ROS formation spontaneously or in the presence of ROS inducers in HSCs, thus leading to the attenuation of collagen type 1 alpha 1 production and α-smooth muscle actin expression. Replacement the iron center of the heme group with cobalt nullified the effect of His-CYGB. In addition, His-CYGB induced interferon-β secretion by HSCs that partly contributed to its antifibrotic function. Momelotinib incompletely reversed the effect of His-CYGB. Intravenously injected His-CYGB markedly suppressed liver inflammation, fibrosis, and oxidative cell damage in mice administered TAA or DDC mice without adverse effects. RNA-sequencing analysis revealed the down-regulation of inflammation- and fibrosis-related genes and the up-regulation of antioxidant genes in both cell culture and liver tissues. The injected His-CYGB predominantly localized to HSCs but not to macrophages, suggesting specific targeting effects. His-CYGB exhibited no toxicity in chimeric mice with humanized livers. CONCLUSIONS His-CYGB could have antifibrotic clinical applications for human chronic liver diseases.
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Affiliation(s)
- Ninh Quoc Dat
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan,Department of PediatricsHanoi Medical UniversityHanoiVietnam
| | - Le Thi Thanh Thuy
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Vu Ngoc Hieu
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Hoang Hai
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Dinh Viet Hoang
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | | | - Tuong Thi Van Thuy
- Biological Resources Vinmec Tissue BankVinmec Healthcare SystemHanoiVietnam
| | - Tohru Komiya
- Department of BiologyFaculty of ScienceOsaka City UniversityOsakaJapan
| | - Krista Rombouts
- Regenerative Medicine and Fibrosis GroupInstitute for Liver and Digestive HealthUniversity College LondonRoyal Free HospitalLondonUnited Kingdom
| | - Minh Phuong Dong
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Ngo Vinh Hanh
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Truong Huu Hoang
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | | | - Atsuko Daikoku
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Chiho Kadono
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Daisuke Oikawa
- Department of PathobiochemistryGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Katsutoshi Yoshizato
- Academic Advisor’s OfficePhoenixBio Co., Ltd.HiroshimaJapan,Endowed Laboratory of Synthetic BiologyGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Fuminori Tokunaga
- Department of PathobiochemistryGraduate School of MedicineOsaka City UniversityOsakaJapan
| | - Massimo Pinzani
- Regenerative Medicine and Fibrosis GroupInstitute for Liver and Digestive HealthUniversity College LondonRoyal Free HospitalLondonUnited Kingdom
| | - Norifumi Kawada
- Department of HepatologyGraduate School of MedicineOsaka City UniversityOsakaJapan,Regenerative Medicine and Fibrosis GroupInstitute for Liver and Digestive HealthUniversity College LondonRoyal Free HospitalLondonUnited Kingdom
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Parra-Izquierdo I, Sánchez-Bayuela T, Castaños-Mollor I, López J, Gómez C, San Román JA, Sánchez Crespo M, García-Rodríguez C. Clinically used JAK inhibitor blunts dsRNA-induced inflammation and calcification in aortic valve interstitial cells. FEBS J 2021; 288:6528-6542. [PMID: 34009721 DOI: 10.1111/febs.16026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 01/25/2023]
Abstract
Calcific aortic valve disease (CAVD) is the most prevalent valvulopathy worldwide. Growing evidence supports a role for viral and cell-derived double-stranded (ds)-RNA in cardiovascular pathophysiology. Poly(I:C), a dsRNA surrogate, has been shown to induce inflammation, type I interferon (IFN) responses, and osteogenesis through Toll-like receptor 3 in aortic valve interstitial cells (VIC). Here, we aimed to determine whether IFN signaling via Janus kinase (JAK)/Signal transducers and activators of transcription (STAT) mediates dsRNA-induced responses in primary human VIC. Western blot, ELISA, qPCR, calcification, flow cytometry, and enzymatic assays were performed to evaluate the mechanisms of dsRNA-induced inflammation and calcification. Poly(I:C) triggered a type I IFN response characterized by IFN-regulatory factors gene upregulation, IFN-β secretion, and STAT1 activation. Additionally, Poly(I:C) promoted VIC inflammation via NF-κB and subsequent adhesion molecule expression, and cytokine secretion. Pretreatment with ruxolitinib, a clinically used JAK inhibitor, abrogated these responses. Moreover, Poly(I:C) promoted a pro-osteogenic phenotype and increased VIC calcification to a higher extent in cells from males. Inhibition of JAK with ruxolitinib or a type I IFN receptor blocking antibody blunted Poly(I:C)-induced calcification. Mechanistically, Poly(I:C) promoted VIC apoptosis in calcification medium, which was inhibited by ruxolitinib. Moreover, Poly(I:C) co-operated with IFN-γ to increase VIC calcification by synergistically activating extracellular signal-regulated kinases and hypoxia-inducible factor-1α pathways. In conclusion, JAK/STAT signaling mediates dsRNA-triggered inflammation, apoptosis, and calcification and may contribute to a positive autocrine loop in human VIC in the presence of IFN-γ. Blockade of dsRNA responses with JAK inhibitors may be a promising therapeutic avenue for CAVD.
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Affiliation(s)
- Iván Parra-Izquierdo
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain
| | - Tania Sánchez-Bayuela
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain
| | - Irene Castaños-Mollor
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain
| | - Javier López
- ICICOR, Hospital Clínico Universitario, Valladolid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Cristina Gómez
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain
| | - J Alberto San Román
- ICICOR, Hospital Clínico Universitario, Valladolid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain
| | - Carmen García-Rodríguez
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Spain.,CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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98
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Declerck K, Novo CP, Grielens L, Van Camp G, Suter A, Vanden Berghe W. Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences. BMC Complement Med Ther 2021; 21:141. [PMID: 33980308 PMCID: PMC8114977 DOI: 10.1186/s12906-021-03310-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Herbal remedies of Echinacea purpurea tinctures are widely used today to reduce common cold respiratory tract infections. Methods Transcriptome, epigenome and kinome profiling allowed a systems biology level characterisation of genomewide immunomodulatory effects of a standardized Echinacea purpurea (L.) Moench extract in THP1 monocytes. Results Gene expression and DNA methylation analysis revealed that Echinaforce® treatment triggers antiviral innate immunity pathways, involving tonic IFN signaling, activation of pattern recognition receptors, chemotaxis and immunometabolism. Furthermore, phosphopeptide based kinome activity profiling and pharmacological inhibitor experiments with filgotinib confirm a key role for Janus Kinase (JAK)-1 dependent gene expression changes in innate immune signaling. Finally, Echinaforce® treatment induces DNA hypermethylation at intergenic CpG, long/short interspersed nuclear DNA repeat elements (LINE, SINE) or long termininal DNA repeats (LTR). This changes transcription of flanking endogenous retroviral sequences (HERVs), involved in an evolutionary conserved (epi) genomic protective response against viral infections. Conclusions Altogether, our results suggest that Echinaforce® phytochemicals strengthen antiviral innate immunity through tonic IFN regulation of pattern recognition and chemokine gene expression and DNA repeat hypermethylated silencing of HERVs in monocytes. These results suggest that immunomodulation by Echinaforce® treatment holds promise to reduce symptoms and duration of infection episodes of common cold corona viruses (CoV), Severe Acute Respiratory Syndrome (SARS)-CoV, and new occurring strains such as SARS-CoV-2, with strongly impaired interferon (IFN) response and weak innate antiviral defense. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03310-5.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Claudina Perez Novo
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Lisa Grielens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, Department of Biomedical Sciences, University of Antwerp (UA) and University Hospital Antwerp (UZA), Antwerp, Belgium
| | | | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Antwerp, Belgium.
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99
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Sogkas G, Atschekzei F, Adriawan IR, Dubrowinskaja N, Witte T, Schmidt RE. Cellular and molecular mechanisms breaking immune tolerance in inborn errors of immunity. Cell Mol Immunol 2021; 18:1122-1140. [PMID: 33795850 PMCID: PMC8015752 DOI: 10.1038/s41423-020-00626-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/11/2020] [Indexed: 02/01/2023] Open
Abstract
In addition to susceptibility to infections, conventional primary immunodeficiency disorders (PIDs) and inborn errors of immunity (IEI) can cause immune dysregulation, manifesting as lymphoproliferative and/or autoimmune disease. Autoimmunity can be the prominent phenotype of PIDs and commonly includes cytopenias and rheumatological diseases, such as arthritis, systemic lupus erythematosus (SLE), and Sjogren's syndrome (SjS). Recent advances in understanding the genetic basis of systemic autoimmune diseases and PIDs suggest an at least partially shared genetic background and therefore common pathogenic mechanisms. Here, we explore the interconnected pathogenic pathways of autoimmunity and primary immunodeficiency, highlighting the mechanisms breaking the different layers of immune tolerance to self-antigens in selected IEI.
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Affiliation(s)
- Georgios Sogkas
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany.
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany.
| | - Faranaz Atschekzei
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany
| | - Ignatius Ryan Adriawan
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany
| | - Natalia Dubrowinskaja
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany
| | - Torsten Witte
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany
| | - Reinhold Ernst Schmidt
- Department of Rheumatology and Immunology, Hannover Medical School, Hanover, Germany
- Hannover Medical School, Cluster of Excellence RESIST (EXC 2155), Hanover, Germany
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100
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Mishra R, Banerjea AC. SARS-CoV-2 Spike Targets USP33-IRF9 Axis via Exosomal miR-148a to Activate Human Microglia. Front Immunol 2021; 12:656700. [PMID: 33936086 PMCID: PMC8079643 DOI: 10.3389/fimmu.2021.656700] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2, the novel coronavirus infection has consistently shown an association with neurological anomalies in patients, in addition to its usual respiratory distress syndrome. Multi-organ dysfunctions including neurological sequelae during COVID-19 persist even after declining viral load. We propose that SARS-CoV-2 gene product, Spike, is able to modify the host exosomal cargo, which gets transported to distant uninfected tissues and organs and can initiate a catastrophic immune cascade within Central Nervous System (CNS). SARS-CoV-2 Spike transfected cells release a significant amount of exosomes loaded with microRNAs such as miR-148a and miR-590. microRNAs gets internalized by human microglia and suppress target gene expression of USP33 (Ubiquitin Specific peptidase 33) and downstream IRF9 levels. Cellular levels of USP33 regulate the turnover time of IRF9 via deubiquitylation. Our results also demonstrate that absorption of modified exosomes effectively regulate the major pro-inflammatory gene expression profile of TNFα, NF-κB and IFN-β. These results uncover a bystander pathway of SARS-CoV-2 mediated CNS damage through hyperactivation of human microglia. Our results also attempt to explain the extra-pulmonary dysfunctions observed in COVID-19 cases when active replication of virus is not supported. Since Spike gene and mRNAs have been extensively picked up for vaccine development; the knowledge of host immune response against spike gene and protein holds a great significance. Our study therefore provides novel and relevant insights regarding the impact of Spike gene on shuttling of host microRNAs via exosomes to trigger the neuroinflammation.
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Affiliation(s)
- Ritu Mishra
- Laboratory of Virology, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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