1
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Jia P, Peng S, Zhang Y, Zhao J, Zhao Q, Wu X, Shen F, Sun K, Yu L, Cen S. Identification of immune-associated genes involved in latent Mycobacterium marinum infection. Microbes Infect 2024:105407. [PMID: 39178982 DOI: 10.1016/j.micinf.2024.105407] [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: 03/19/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024]
Abstract
Tuberculosis (TB) is a high mortality infectious disease caused by Mycobacterium tuberculosis (Mtb), and often develops into latent infection. About 5~10% of latent infections turn into active tuberculosis when the host immune system becomes deficient. Therefore, exploring the latent infection mechanism of Mtb is pivotal for the prevention and treatment of tuberculosis. We first established the zebrafish latent infection model and the chronic infection model utilizing Mycobacterium marinum, which has the highly similar gene background to Mtb. Using the latent infection model, we characterized the gene expression profiles and found 462 genes expressed differentially in the latent period and chronic tuberculosis infection. These differentially expressed genes are involved in various biological processes including transcription, transcriptional regulation, organism development, and immune responses. Among them, nineteen immune-related genes were found to express differentially in the latent period. By analyzing immune related protein network, the genes in the center of the network, including Nos2b, TNFα, IL1, TNFβ, TLR1, TLR2, and TLR4b, displayed significant deferential expression in latent infection and chronic infection period of zebrafish, suggesting that these genes might play an important role in controlling latent infection of Mtb. Identifying immune biomarker related to the status of tuberculosis latent infection might lead to novel strategy for diagnosis and treatment.
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Affiliation(s)
- Pingping Jia
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China.
| | - Shize Peng
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Zhang
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, China
| | - Jianyuan Zhao
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, China
| | - Qianqian Zhao
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Xiaoxiao Wu
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Fangqi Shen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Kai Sun
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Cancer FSMP for State Market Regulation, Beijing, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences, Beijing, China.
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2
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Tufan T, Comertpay G, Villani A, Nelson GM, Terekhova M, Kelley S, Zakharov P, Ellison RM, Shpynov O, Raymond M, Sun J, Chen Y, Bockelmann E, Stremska M, Peterson LW, Boeckaerts L, Goldman SR, Etchegaray JI, Artyomov MN, Peri F, Ravichandran KS. Rapid unleashing of macrophage efferocytic capacity via transcriptional pause release. Nature 2024; 628:408-415. [PMID: 38480883 DOI: 10.1038/s41586-024-07172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/07/2024] [Indexed: 03/18/2024]
Abstract
During development, inflammation or tissue injury, macrophages may successively engulf and process multiple apoptotic corpses via efferocytosis to achieve tissue homeostasis1. How macrophages may rapidly adapt their transcription to achieve continuous corpse uptake is incompletely understood. Transcriptional pause/release is an evolutionarily conserved mechanism, in which RNA polymerase (Pol) II initiates transcription for 20-60 nucleotides, is paused for minutes to hours and is then released to make full-length mRNA2. Here we show that macrophages, within minutes of corpse encounter, use transcriptional pause/release to unleash a rapid transcriptional response. For human and mouse macrophages, the Pol II pause/release was required for continuous efferocytosis in vitro and in vivo. Interestingly, blocking Pol II pause/release did not impede Fc receptor-mediated phagocytosis, yeast uptake or bacterial phagocytosis. Integration of data from three genomic approaches-precision nuclear run-on sequencing, RNA sequencing, and assay for transposase-accessible chromatin using sequencing (ATAC-seq)-on efferocytic macrophages at different time points revealed that Pol II pause/release controls expression of select transcription factors and downstream target genes. Mechanistic studies on transcription factor EGR3, prominently regulated by pause/release, uncovered EGR3-related reprogramming of other macrophage genes involved in cytoskeleton and corpse processing. Using lysosomal probes and a new genetic fluorescent reporter, we identify a role for pause/release in phagosome acidification during efferocytosis. Furthermore, microglia from egr3-deficient zebrafish embryos displayed reduced phagocytosis of apoptotic neurons and fewer maturing phagosomes, supporting defective corpse processing. Collectively, these data indicate that macrophages use Pol II pause/release as a mechanism to rapidly alter their transcriptional programs for efficient processing of the ingested apoptotic corpses and for successive efferocytosis.
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Affiliation(s)
- Turan Tufan
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gamze Comertpay
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ambra Villani
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Marina Terekhova
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Shannon Kelley
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Pavel Zakharov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rochelle M Ellison
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Oleg Shpynov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- JetBrains Research, Munich, Germany
| | - Michael Raymond
- Department of Neuroscience and MIC, University of Virginia, Charlottesville, VA, USA
| | - Jerry Sun
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yitan Chen
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Enno Bockelmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Marta Stremska
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lance W Peterson
- Department of Pediatrics, Division of Rheumatology and Immunology, Washington University in St. Louis, St. Louis, MO, USA
| | - Laura Boeckaerts
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research and the Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Seth R Goldman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - J Iker Etchegaray
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Francesca Peri
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Kodi S Ravichandran
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Neuroscience and MIC, University of Virginia, Charlottesville, VA, USA.
- Unit for Cell Clearance in Health and Disease, VIB-UGent Center for Inflammation Research and the Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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3
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Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
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Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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4
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Butto T, Mungikar K, Baumann P, Winter J, Lutz B, Gerber S. Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing. Cells 2023; 12:cells12071051. [PMID: 37048124 PMCID: PMC10093037 DOI: 10.3390/cells12071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.
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Affiliation(s)
- Tamer Butto
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
| | - Kanak Mungikar
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
| | - Peter Baumann
- Faculty of Biology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
| | - Beat Lutz
- Leibniz Institute for Resilience Research (LIR), 55122 Mainz, Germany
- Institute of Physiological Chemistry, University Medical Center Mainz, 55128 Mainz, Germany
| | - Susanne Gerber
- Institute of Human Genetics, University Medical Center Mainz, 55131 Mainz, Germany
- Correspondence: (T.B.); (S.G.); Tel.: +49-(0)6131-39-27331 (S.G.)
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5
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Leiba J, Özbilgiç R, Hernández L, Demou M, Lutfalla G, Yatime L, Nguyen-Chi M. Molecular Actors of Inflammation and Their Signaling Pathways: Mechanistic Insights from Zebrafish. BIOLOGY 2023; 12:153. [PMID: 36829432 PMCID: PMC9952950 DOI: 10.3390/biology12020153] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
Inflammation is a hallmark of the physiological response to aggressions. It is orchestrated by a plethora of molecules that detect the danger, signal intracellularly, and activate immune mechanisms to fight the threat. Understanding these processes at a level that allows to modulate their fate in a pathological context strongly relies on in vivo studies, as these can capture the complexity of the whole process and integrate the intricate interplay between the cellular and molecular actors of inflammation. Over the years, zebrafish has proven to be a well-recognized model to study immune responses linked to human physiopathology. We here provide a systematic review of the molecular effectors of inflammation known in this vertebrate and recapitulate their modes of action, as inferred from sterile or infection-based inflammatory models. We present a comprehensive analysis of their sequence, expression, and tissue distribution and summarize the tools that have been developed to study their function. We further highlight how these tools helped gain insights into the mechanisms of immune cell activation, induction, or resolution of inflammation, by uncovering downstream receptors and signaling pathways. These progresses pave the way for more refined models of inflammation, mimicking human diseases and enabling drug development using zebrafish models.
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6
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Margaroli C, Moncada-Giraldo D, Gulick DA, Dobosh B, Giacalone VD, Forrest OA, Sun F, Gu C, Gaggar A, Kissick H, Wu R, Gibson G, Tirouvanziam R. Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils. Cell Rep Med 2021; 2:100239. [PMID: 33948572 PMCID: PMC8080108 DOI: 10.1016/j.xcrm.2021.100239] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 11/15/2020] [Accepted: 03/15/2021] [Indexed: 02/06/2023]
Abstract
Neutrophils are often considered terminally differentiated and poised for bacterial killing. In chronic diseases such as cystic fibrosis (CF), an unexplained paradox pits massive neutrophil presence against prolonged bacterial infections. Here, we show that neutrophils recruited to CF airways in vivo and in an in vitro transmigration model display rapid and broad transcriptional firing, leading to an upregulation of anabolic genes and a downregulation of antimicrobial genes. Newly transcribed RNAs are mirrored by the appearance of corresponding proteins, confirming active translation in these cells. Treatment by the RNA polymerase II and III inhibitor α-amanitin restores the expression of key antimicrobial genes and increases the bactericidal capacity of CF airway neutrophils in vitro and in short-term sputum cultures ex vivo. Broadly, our findings show that neutrophil plasticity is regulated at the site of inflammation via RNA and protein synthesis, leading to adaptations that affect their canonical functions (i.e., bacterial clearance).
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Affiliation(s)
- Camilla Margaroli
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Diego Moncada-Giraldo
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Dalia Arafat Gulick
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Brian Dobosh
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Vincent D. Giacalone
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Osric A. Forrest
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Fangxu Sun
- Department of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chunhui Gu
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Amit Gaggar
- Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Birmingham VA Medical Center, Birmingham, AL, USA
| | - Haydn Kissick
- Department of Urology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ronghu Wu
- Department of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Greg Gibson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Center for CF & Airways Disease Research, Children’s Healthcare of Atlanta, Atlanta, GA, USA
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7
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Campbell JS, Davidson AJ, Todd H, Rodrigues FSLM, Elliot AM, Early JJ, Lyons DA, Feng Y, Wood W. PTPN21/Pez Is a Novel and Evolutionarily Conserved Key Regulator of Inflammation In Vivo. Curr Biol 2021; 31:875-883.e5. [PMID: 33296680 PMCID: PMC7902905 DOI: 10.1016/j.cub.2020.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/09/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022]
Abstract
Drosophila provides a powerful model in which to study inflammation in vivo, and previous studies have revealed many of the key signaling events critical for recruitment of immune cells to tissue damage. In the fly, wounding stimulates the rapid production of hydrogen peroxide (H2O2).1,2 This then acts as an activation signal by triggering a signaling pathway within responding macrophages by directly activating the Src family kinase (SFK) Src42A,3 which in turn phosphorylates the damage receptor Draper. Activated Draper then guides macrophages to the wound through the detection of an as-yet unidentified chemoattractant.3-5 Similar H2O2-activated signaling pathways are also critical for leukocyte recruitment following wounding in larval zebrafish,6-9 where H2O2 activates the SFK Lyn to drive neutrophil chemotaxis. In this study, we combine proteomics, live imaging, and genetics in the fly to identify a novel regulator of inflammation in vivo; the PTP-type phosphatase Pez. Pez is expressed in macrophages and is critical for their efficient migration to wounds. Pez functions within activated macrophages downstream of damage-induced H2O2 and operates, via its band 4.1 ezrin, radixin, and moesin (FERM) domain, together with Src42A and Draper to ensure effective inflammatory cell recruitment to wounds. We show that this key role is conserved in vertebrates, because "crispant" zebrafish larvae of the Draper ortholog (MEGF10) or the Pez ortholog (PTPN21) exhibit a failure in leukocyte recruitment to wounds. This study demonstrates evolutionary conservation of inflammatory signaling and identifies MEGF10 and PTPN21 as potential therapeutic targets for the treatment of inflammatory disorders.
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Affiliation(s)
- Jennie S Campbell
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK; School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK.
| | - Andrew J Davidson
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Henry Todd
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Frederico S L M Rodrigues
- School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Abigail M Elliot
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Jason J Early
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Yi Feng
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Will Wood
- Centre for Inflammation Research, University of Edinburgh, Queens Medical Research Institute, 47 Little France Crescent, Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK.
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8
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Elliot A, Myllymäki H, Feng Y. Inflammatory Responses during Tumour Initiation: From Zebrafish Transgenic Models of Cancer to Evidence from Mouse and Man. Cells 2020; 9:cells9041018. [PMID: 32325966 PMCID: PMC7226149 DOI: 10.3390/cells9041018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
The zebrafish is now an important model organism for cancer biology studies and provides unique and complementary opportunities in comparison to the mammalian equivalent. The translucency of zebrafish has allowed in vivo live imaging studies of tumour initiation and progression at the cellular level, providing novel insights into our understanding of cancer. Here we summarise the available transgenic zebrafish tumour models and discuss what we have gleaned from them with respect to cancer inflammation. In particular, we focus on the host inflammatory response towards transformed cells during the pre-neoplastic stage of tumour development. We discuss features of tumour-associated macrophages and neutrophils in mammalian models and present evidence that supports the idea that these inflammatory cells promote early stage tumour development and progression. Direct live imaging of tumour initiation in zebrafish models has shown that the intrinsic inflammation induced by pre-neoplastic cells is tumour promoting. Signals mediating leukocyte recruitment to pre-neoplastic cells in zebrafish correspond to the signals that mediate leukocyte recruitment in mammalian tumours. The activation state of macrophages and neutrophils recruited to pre-neoplastic cells in zebrafish appears to be heterogenous, as seen in mammalian models, which provides an opportunity to study the plasticity of innate immune cells during tumour initiation. Although several potential mechanisms are described that might mediate the trophic function of innate immune cells during tumour initiation in zebrafish, there are several unknowns that are yet to be resolved. Rapid advancement of genetic tools and imaging technologies for zebrafish will facilitate research into the mechanisms that modulate leukocyte function during tumour initiation and identify targets for cancer prevention.
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Affiliation(s)
| | | | - Yi Feng
- Correspondence: ; Tel.: +44-(0)131-242-6685
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9
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Harjula SKE, Saralahti AK, Ojanen MJT, Rantapero T, Uusi-Mäkelä MIE, Nykter M, Lohi O, Parikka M, Rämet M. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 103:103523. [PMID: 31626817 DOI: 10.1016/j.dci.2019.103523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Tuberculosis remains a major global health challenge. To gain information about genes important for defense against tuberculosis, we used a well-established tuberculosis model; Mycobacterium marinum infection in adult zebrafish. To characterize the immunological response to mycobacterial infection at 14 days post infection, we performed a whole-genome level transcriptome analysis using cells from kidney, the main hematopoietic organ of adult zebrafish. Among the upregulated genes, those associated with immune signaling and regulation formed the largest category, whereas the largest group of downregulated genes had a metabolic role. We also performed a forward genetic screen in adult zebrafish and identified a fish line with severely impaired survival during chronic mycobacterial infection. Based on transcriptome analysis, these fish have decreased expression of several immunological genes. Taken together, these results give new information about the genes involved in the defense against mycobacterial infection in zebrafish.
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Affiliation(s)
- Sanna-Kaisa E Harjula
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Anni K Saralahti
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Markus J T Ojanen
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Laboratory of Immunoregulation, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Tommi Rantapero
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Meri I E Uusi-Mäkelä
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Matti Nykter
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Olli Lohi
- Tampere Center for Child Health Research, Tampere University and Tays Cancer Center, Tampere University Hospital, FI-33014, Tampere University, Finland.
| | - Mataleena Parikka
- Laboratory of Infection Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Oral and Maxillofacial Unit, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland.
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Department of Pediatrics, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland; PEDEGO Research Unit, Medical Research Center Oulu, P.O. Box 8000, FI-90014, University of Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, P.O. Box 10, FI-90029, OYS, Finland.
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10
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Zebrafish in Inflammasome Research. Cells 2019; 8:cells8080901. [PMID: 31443239 PMCID: PMC6721725 DOI: 10.3390/cells8080901] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Inflammasomes are cytosolic multiprotein complexes that regulate inflammatory responses to danger stimuli and infection, and their dysregulation is associated with an increasing number of autoinflammatory diseases. In recent years, zebrafish models of human pathologies to study inflammasome function in vivo have started to emerge. Here, we discuss inflammasome research in zebrafish in light of current knowledge about mammalian inflammasomes. We summarize the evolutionary conservation of inflammasome components between zebrafish and mammals, highlighting the similarities and possible divergence in functions of these components. We present new insights into the evolution of the caspase-1 family in the teleost lineage, and how its evolutionary origin may help contextualize its functions. We also review existing infectious and non-infectious models in zebrafish in which inflammasomes have been directly implicated. Finally, we discuss the advantages of zebrafish larvae for intravital imaging of inflammasome activation and summarize available tools that will help to advance inflammasome research.
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11
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Murdoch CC, Espenschied ST, Matty MA, Mueller O, Tobin DM, Rawls JF. Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization. PLoS Pathog 2019; 15:e1007381. [PMID: 30845179 PMCID: PMC6405052 DOI: 10.1371/journal.ppat.1007381] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/09/2019] [Indexed: 12/25/2022] Open
Abstract
The intestinal microbiota influences the development and function of myeloid lineages such as neutrophils, but the underlying molecular mechanisms are unresolved. Using gnotobiotic zebrafish, we identified the immune effector Serum amyloid A (Saa) as one of the most highly induced transcripts in digestive tissues following microbiota colonization. Saa is a conserved secreted protein produced in the intestine and liver with described effects on neutrophils in vitro, however its in vivo functions remain poorly defined. We engineered saa mutant zebrafish to test requirements for Saa on innate immunity in vivo. Zebrafish mutant for saa displayed impaired neutrophil responses to wounding but augmented clearance of pathogenic bacteria. At baseline, saa mutants exhibited moderate neutrophilia and altered neutrophil tissue distribution. Molecular and functional analyses of isolated neutrophils revealed that Saa suppresses expression of pro-inflammatory markers and bactericidal activity. Saa's effects on neutrophils depended on microbiota colonization, suggesting this protein mediates the microbiota's effects on host innate immunity. To test tissue-specific roles of Saa on neutrophil function, we over-expressed saa in the intestine or liver and found that sufficient to partially complement neutrophil phenotypes observed in saa mutants. These results indicate Saa produced by the intestine in response to microbiota serves as a systemic signal to neutrophils to restrict aberrant activation, decreasing inflammatory tone and bacterial killing potential while simultaneously enhancing their ability to migrate to wounds.
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Affiliation(s)
- Caitlin C. Murdoch
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott T. Espenschied
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Molly A. Matty
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Olaf Mueller
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - John F. Rawls
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
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12
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Intelectin 3 is dispensable for resistance against a mycobacterial infection in zebrafish (Danio rerio). Sci Rep 2019; 9:995. [PMID: 30700796 PMCID: PMC6353920 DOI: 10.1038/s41598-018-37678-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/07/2018] [Indexed: 12/20/2022] Open
Abstract
Tuberculosis is a multifactorial bacterial disease, which can be modeled in the zebrafish (Danio rerio). Abdominal cavity infection with Mycobacterium marinum, a close relative of Mycobacterium tuberculosis, leads to a granulomatous disease in adult zebrafish, which replicates the different phases of human tuberculosis, including primary infection, latency and spontaneous reactivation. Here, we have carried out a transcriptional analysis of zebrafish challenged with low-dose of M. marinum, and identified intelectin 3 (itln3) among the highly up-regulated genes. In order to clarify the in vivo significance of Itln3 in immunity, we created nonsense itln3 mutant zebrafish by CRISPR/Cas9 mutagenesis and analyzed the outcome of M. marinum infection in both zebrafish embryos and adult fish. The lack of functional itln3 did not affect survival or the mycobacterial burden in the zebrafish. Furthermore, embryonic survival was not affected when another mycobacterial challenge responsive intelectin, itln1, was silenced using morpholinos either in the WT or itln3 mutant fish. In addition, M. marinum infection in dexamethasone-treated adult zebrafish, which have lowered lymphocyte counts, resulted in similar bacterial burden in both WT fish and homozygous itln3 mutants. Collectively, although itln3 expression is induced upon M. marinum infection in zebrafish, it is dispensable for protective mycobacterial immune response.
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13
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Trinh LA, Chong-Morrison V, Sauka-Spengler T. Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods 2018; 150:24-31. [DOI: 10.1016/j.ymeth.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
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14
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Kenyon A, Gavriouchkina D, Zorman J, Chong-Morrison V, Napolitani G, Cerundolo V, Sauka-Spengler T. Generation of a double binary transgenic zebrafish model to study myeloid gene regulation in response to oncogene activation in melanocytes. Dis Model Mech 2018; 11:dmm030056. [PMID: 29666124 PMCID: PMC5963855 DOI: 10.1242/dmm.030056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
A complex network of inflammatory genes is closely linked to somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. Here, we describe the development of a double binary zebrafish model that enables regulatory programming of the myeloid cells as they respond to oncogene-activated melanocytes to be explored, focussing on the initial phase when cells become the precursors of cancer. A hormone-inducible binary system allows for temporal control of expression of different Ras oncogenes (NRasQ61K, HRasG12V and KRasG12V) in melanocytes, leading to proliferation and changes in morphology of the melanocytes. This model was coupled to binary cell-specific biotagging models allowing in vivo biotinylation and subsequent isolation of macrophage or neutrophil nuclei for regulatory profiling of their active transcriptomes. Nuclear transcriptional profiling of neutrophils, performed as they respond to the earliest precursors of melanoma in vivo, revealed an intricate landscape of regulatory factors that may promote progression to melanoma, including Serpinb1l4, Fgf1, Fgf6, Cathepsin H, Galectin 1 and Galectin 3. The model presented here provides a powerful platform to study the myeloid response to the earliest precursors of melanoma.
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Affiliation(s)
- Amy Kenyon
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Daria Gavriouchkina
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Jernej Zorman
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Giorgio Napolitani
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vincenzo Cerundolo
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
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15
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Torraca V, Mostowy S. Zebrafish Infection: From Pathogenesis to Cell Biology. Trends Cell Biol 2018; 28:143-156. [PMID: 29173800 PMCID: PMC5777827 DOI: 10.1016/j.tcb.2017.10.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
Abstract
The study of host-pathogen interactions has illuminated fundamental research avenues in both infection and cell biology. Zebrafish (Danio rerio) larvae are genetically tractable, optically accessible, and present a fully functional innate immune system with macrophages and neutrophils that mimic their mammalian counterparts. A wide variety of pathogenic bacteria have been investigated using zebrafish models, providing unprecedented resolution of the cellular response to infection in vivo. In this review, we illustrate how zebrafish models have contributed to our understanding of cellular microbiology by providing an in vivo platform to study host-pathogen interactions from the single cell to whole animal level. We also highlight discoveries made from zebrafish infection that hold great promise for translation into novel therapies for humans.
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Affiliation(s)
- Vincenzo Torraca
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Serge Mostowy
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
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16
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Higashi Y, Yamakuchi M, Fukushige T, Ibusuki A, Hashiguchi T, Kanekura T. High-fat diet exacerbates imiquimod-induced psoriasis-like dermatitis in mice. Exp Dermatol 2018; 27:178-184. [PMID: 29247486 DOI: 10.1111/exd.13484] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 02/07/2023]
Abstract
Psoriasis, a chronic inflammatory skin disease, is closely related to systemic metabolism. An elevated body mass index (BMI) is a risk factor for psoriasis; inflammasomes are activated by adipose tissue macrophages in obese subjects. We hypothesized that hyperlipidaemia is involved in the pathogenesis of psoriasis and examined the role of a high-fat diet (HFD) in the development of psoriasis in imiquimod (IMQ)-treated mice. The body weight and serum level of cholesterol were significantly higher in mice fed an HFD than in a regular diet (RD). HFD mice had higher psoriasis skin scores, and the number of neutrophils infiltrating into the lesional skin was elevated. IL-17A mRNA expression was significantly increased in the skin of IMQ-treated HFD mice; the expression of IL-22, IL-23 and TNF-α mRNA was not enhanced. Caspase-1 and IL-1β were activated in the skin of IMQ-treated HFD mice, and their serum level of IL-17A, TNF-α and IL-1β was significantly upregulated. Our findings strongly suggest that hyperlipidaemia is involved in the development and progression of psoriasis via systemic inflammation and inflammasome activation.
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Affiliation(s)
- Yuko Higashi
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Munekazu Yamakuchi
- Department of Laboratory and Vascular Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoko Fukushige
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Atsuko Ibusuki
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Teruto Hashiguchi
- Department of Laboratory and Vascular Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Takuro Kanekura
- Department of Dermatology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
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Cardenal-Muñoz E, Barisch C, Lefrançois LH, López-Jiménez AT, Soldati T. When Dicty Met Myco, a (Not So) Romantic Story about One Amoeba and Its Intracellular Pathogen. Front Cell Infect Microbiol 2018; 7:529. [PMID: 29376033 PMCID: PMC5767268 DOI: 10.3389/fcimb.2017.00529] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/18/2017] [Indexed: 01/06/2023] Open
Abstract
In recent years, Dictyostelium discoideum has become an important model organism to study the cell biology of professional phagocytes. This amoeba not only shares many molecular features with mammalian macrophages, but most of its fundamental signal transduction pathways are conserved in humans. The broad range of existing genetic and biochemical tools, together with its suitability for cell culture and live microscopy, make D. discoideum an ideal and versatile laboratory organism. In this review, we focus on the use of D. discoideum as a phagocyte model for the study of mycobacterial infections, in particular Mycobacterium marinum. We look in detail at the intracellular cycle of M. marinum, from its uptake by D. discoideum to its active or passive egress into the extracellular medium. In addition, we describe the molecular mechanisms that both the mycobacterial invader and the amoeboid host have developed to fight against each other, and compare and contrast with those developed by mammalian phagocytes. Finally, we introduce the methods and specific tools that have been used so far to monitor the D. discoideum-M. marinum interaction.
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Affiliation(s)
- Elena Cardenal-Muñoz
- Department of Biochemistry, Sciences II, Faculty of Sciences, University of Geneva, Geneva, Switzerland
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