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de Sena-Tomás C, Rebola Lameira L, Rebocho da Costa M, Naique Taborda P, Laborde A, Orger M, de Oliveira S, Saúde L. Neutrophil immune profile guides spinal cord regeneration in zebrafish. Brain Behav Immun 2024; 120:514-531. [PMID: 38925414 DOI: 10.1016/j.bbi.2024.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/15/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
Spinal cord injury triggers a strong innate inflammatory response in both non-regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet, their role in the repair process, particularly in a regenerative context, remains largely unknown. Here, we show that, following rapid recruitment to the injured spinal cord, neutrophils mostly reverse migrate throughout the zebrafish body. In addition, promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil-specific RNA-seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf-α expression in macrophage/microglia populations. Conversely, blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether, these findings provide new insights into the role of neutrophils in spinal cord regeneration, emphasizing the significant impact of their immune profile on the outcome of the repair process.
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Affiliation(s)
- Carmen de Sena-Tomás
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Leonor Rebola Lameira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Mariana Rebocho da Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Patrícia Naique Taborda
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Alexandre Laborde
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisboa, Portugal
| | - Michael Orger
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisboa, Portugal
| | - Sofia de Oliveira
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine (Hepatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA; Harold and Muriel Block Institute for Clinical and Translational Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Montefiore-Einstein Comprehensive Cancer Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Leonor Saúde
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; Instituto de Histologia e Biologia de Desenvolvimento, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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2
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Speirs ZC, Loynes CA, Mathiessen H, Elks PM, Renshaw SA, Jørgensen LVG. What can we learn about fish neutrophil and macrophage response to immune challenge from studies in zebrafish. FISH & SHELLFISH IMMUNOLOGY 2024; 148:109490. [PMID: 38471626 DOI: 10.1016/j.fsi.2024.109490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Fish rely, to a high degree, on the innate immune system to protect them against the constant exposure to potential pathogenic invasion from the surrounding water during homeostasis and injury. Zebrafish larvae have emerged as an outstanding model organism for immunity. The cellular component of zebrafish innate immunity is similar to the mammalian innate immune system and has a high degree of sophistication due to the needs of living in an aquatic environment from early embryonic stages of life. Innate immune cells (leukocytes), including neutrophils and macrophages, have major roles in protecting zebrafish against pathogens, as well as being essential for proper wound healing and regeneration. Zebrafish larvae are visually transparent, with unprecedented in vivo microscopy opportunities that, in combination with transgenic immune reporter lines, have permitted visualisation of the functions of these cells when zebrafish are exposed to bacterial, viral and parasitic infections, as well as during injury and healing. Recent findings indicate that leukocytes are even more complex than previously anticipated and are essential for inflammation, infection control, and subsequent wound healing and regeneration.
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Affiliation(s)
- Zoë C Speirs
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Catherine A Loynes
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Heidi Mathiessen
- Laboratory of Experimental Fish Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark
| | - Philip M Elks
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Stephen A Renshaw
- The Bateson Centre, School of Medicine and Population Health, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Louise von Gersdorff Jørgensen
- Laboratory of Experimental Fish Models, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C., Denmark.
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3
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Ellett F, Kacamak NI, Alvarez CR, Oliveira EH, Hasturk H, Paster BJ, Kantarci A, Irimia D. Fusobacterium nucleatum dissemination by neutrophils. J Oral Microbiol 2023; 15:2217067. [PMID: 37283724 PMCID: PMC10240972 DOI: 10.1080/20002297.2023.2217067] [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: 02/01/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Recent studies uncovered that Fusobacterium nucleatum (Fn), a common, opportunistic bacterium in the oral cavity, is associated with a growing number of systemic diseases, ranging from colon cancer to Alzheimer's disease. However, the pathological mechanisms responsible for this association are still poorly understood. Here, we leverage recent technological advances to study the interactions between Fn and neutrophils. We show that Fn survives within human neutrophils after phagocytosis. Using in vitro microfluidic devices, we determine that human neutrophils can protect and transport Fn over large distances. Moreover, we validate these observations in vivo by showing that neutrophils disseminate Fn using a zebrafish model. Our data support the emerging hypothesis that bacterial dissemination by neutrophils is a mechanistic link between oral and systemic diseases. Furthermore, our results may ultimately lead to therapeutic approaches that target specific host-bacteria interactions, including the dissemination process.
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Affiliation(s)
- Felix Ellett
- Department of Surgery, Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, MA, USA
- Shriners Hospital for Children, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nazli I. Kacamak
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Carla R. Alvarez
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Eduardo H.S. Oliveira
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Hatice Hasturk
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Bruce J. Paster
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Alpdogan Kantarci
- The Forsyth Institute, Cambridge, MA, USA
- Harvard School of Dental Medicine, Boston, MA, USA
| | - Daniel Irimia
- Department of Surgery, Center for Engineering in Medicine and Surgery, Massachusetts General Hospital, Boston, MA, USA
- Shriners Hospital for Children, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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4
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Dowdell A, Paschke PI, Thomason PA, Tweedy L, Insall RH. Competition between chemoattractants causes unexpected complexity and can explain negative chemotaxis. Curr Biol 2023; 33:1704-1715.e3. [PMID: 37001521 DOI: 10.1016/j.cub.2023.03.006] [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: 12/06/2022] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 05/11/2023]
Abstract
Negative chemotaxis, where eukaryotic cells migrate away from repellents, is important throughout biology, for example, in nervous system patterning and resolution of inflammation. However, the mechanisms by which molecules repel migrating cells are unknown. Here, we use predictive modeling and experiments with Dictyostelium cells to show that competition between different ligands that bind to the same receptor leads to effective chemorepulsion. 8-CPT-cAMP, widely described as a simple chemorepellent, is inactive on its own and only repels cells when it acts in combination with the attractant cAMP. If cells degrade either competing ligand, the pattern of migration becomes more complex; cells may be repelled in one part of a gradient but attracted elsewhere, leading to populations moving in different directions in the same assay or converging in an arbitrary place. More counterintuitively still, two chemicals that normally attract cells can become repellent when combined. Computational models of chemotaxis are now accurate enough to predict phenomena that have not been anticipated by experiments. We have used them to identify new mechanisms that drive reverse chemotaxis, which we have confirmed through experiments with real cells. These findings are important whenever multiple ligands compete for the same receptors.
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Affiliation(s)
- Adam Dowdell
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK; CRUK Beatson Institute, Switchback Road, Glasgow G63 9AE, UK
| | - Peggy I Paschke
- CRUK Beatson Institute, Switchback Road, Glasgow G63 9AE, UK
| | | | - Luke Tweedy
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK; CRUK Beatson Institute, Switchback Road, Glasgow G63 9AE, UK
| | - Robert H Insall
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow G61 1QH, UK; CRUK Beatson Institute, Switchback Road, Glasgow G63 9AE, UK.
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5
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Xu Q, Zhao W, Yan M, Mei H. Neutrophil reverse migration. J Inflamm (Lond) 2022; 19:22. [PMID: 36424665 PMCID: PMC9686117 DOI: 10.1186/s12950-022-00320-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
The behavior of neutrophils is very important for the resolution of inflammation and tissue repair. People have used advanced imaging techniques to observe the phenomenon of neutrophils leaving the injured or inflammatory site and migrating back into blood vessels in transgenic zebrafish and mice, which is called neutrophil reverse migration. Numerous studies have shown that neutrophil reverse migration is a double-edged sword. On the one hand, neutrophil reverse migration can promote the resolution of local inflammation by accelerating the clearance of neutrophils from local wounds. On the other hand, neutrophils re-enter the circulatory system may lead to the spread of systemic inflammation. Therefore, accurate regulation of neutrophil reverse migration is of great significance for the treatment of various neutrophil- mediated diseases. However, the mechanism of neutrophil reverse migration and its relationship with inflammation resolution is unknown. In this review, we reviewed the relevant knowledge of neutrophil reverse migration to elucidate the potential mechanisms and factors influencing reverse migration and its impact on inflammation in different disease processes.
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Affiliation(s)
- Qichao Xu
- grid.417384.d0000 0004 1764 2632Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, Zhejiang Province People’s Republic of China 325027 ,grid.417384.d0000 0004 1764 2632Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Zhejiang, China
| | - Wenqi Zhao
- grid.417384.d0000 0004 1764 2632Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, Zhejiang Province People’s Republic of China 325027 ,grid.417384.d0000 0004 1764 2632Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Zhejiang, China
| | - Mingyang Yan
- grid.417384.d0000 0004 1764 2632Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, Zhejiang Province People’s Republic of China 325027 ,grid.417384.d0000 0004 1764 2632Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Zhejiang, China
| | - Hongxia Mei
- grid.417384.d0000 0004 1764 2632Department of Anesthesia and Critical Care, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, 109 Xueyuan Road, Wenzhou, Zhejiang Province People’s Republic of China 325027 ,grid.417384.d0000 0004 1764 2632Key Laboratory of Anesthesiology of Zhejiang Province, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Zhejiang, China
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6
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GZMK high CD8 + T effector memory cells are associated with CD15 high neutrophil abundance in non-metastatic colorectal tumors and predict poor clinical outcome. Nat Commun 2022; 13:6752. [PMID: 36347862 PMCID: PMC9643357 DOI: 10.1038/s41467-022-34467-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
CD8+ T cells are a major prognostic determinant in solid tumors, including colorectal cancer (CRC). However, understanding how the interplay between different immune cells impacts on clinical outcome is still in its infancy. Here, we describe that the interaction of tumor infiltrating neutrophils expressing high levels of CD15 with CD8+ T effector memory cells (TEM) correlates with tumor progression. Mechanistically, stromal cell-derived factor-1 (CXCL12/SDF-1) promotes the retention of neutrophils within tumors, increasing the crosstalk with CD8+ T cells. As a consequence of the contact-mediated interaction with neutrophils, CD8+ T cells are skewed to produce high levels of GZMK, which in turn decreases E-cadherin on the intestinal epithelium and favors tumor progression. Overall, our results highlight the emergence of GZMKhigh CD8+ TEM in non-metastatic CRC tumors as a hallmark driven by the interaction with neutrophils, which could implement current patient stratification and be targeted by novel therapeutics.
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7
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Georgantzoglou A, Matthews J, Sarris M. Neutrophil motion in numbers: How to analyse complex migration patterns. Cells Dev 2021; 168:203734. [PMID: 34461315 DOI: 10.1016/j.cdev.2021.203734] [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: 05/15/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
In vivo imaging has revolutionised the study of leukocyte trafficking and revealed many insights on the dynamic behaviour of immune cells in their native environment. Neutrophil migration represents a prominent example whereby live imaging led to discovery of unanticipated cell migration patterns. These cells are the first to enter inflammatory sites and their recruitment had once been thought to be driven primarily by extrinsic signals and resolved by apoptosis in these lesions. However, in vivo imaging in zebrafish and mice indicated that neutrophils are also able to self-organise their migration to a large extent, through collective generation of gradients, in a process referred to as 'swarming', and that they can leave sites of inflammation, in a process referred to as 'reverse migration'. An important step in understanding these newly defined behaviours is the ability to detect and quantify them through statistical analysis. Here we provide a summary of considerations and recommendations for quantitative analysis of neutrophil swarming and reverse migration, with the purpose of introducing relevant analysis tools to new researchers in the field and establishing common frameworks and standards.
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Affiliation(s)
- Antonios Georgantzoglou
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK.
| | - Joanna Matthews
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK
| | - Milka Sarris
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Site, Cambridge CB2 3DY, UK.
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8
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Kaveh A, Bruton FA, Buckley C, Oremek MEM, Tucker CS, Mullins JJ, Taylor JM, Rossi AG, Denvir MA. Live Imaging of Heart Injury in Larval Zebrafish Reveals a Multi-Stage Model of Neutrophil and Macrophage Migration. Front Cell Dev Biol 2020; 8:579943. [PMID: 33195220 PMCID: PMC7604347 DOI: 10.3389/fcell.2020.579943] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/11/2020] [Indexed: 01/11/2023] Open
Abstract
Neutrophils and macrophages are crucial effectors and modulators of repair and regeneration following myocardial infarction, but they cannot be easily observed in vivo in mammalian models. Hence many studies have utilized larval zebrafish injury models to examine neutrophils and macrophages in their tissue of interest. However, to date the migratory patterns and ontogeny of these recruited cells is unknown. In this study, we address this need by comparing our larval zebrafish model of cardiac injury to the archetypal tail fin injury model. Our in vivo imaging allowed comprehensive mapping of neutrophil and macrophage migration from primary hematopoietic sites, to the wound. Early following injury there is an acute phase of neutrophil recruitment that is followed by sustained macrophage recruitment. Both cell types are initially recruited locally and subsequently from distal sites, primarily the caudal hematopoietic tissue (CHT). Once liberated from the CHT, some neutrophils and macrophages enter circulation, but most use abluminal vascular endothelium to crawl through the larva. In both injury models the innate immune response resolves by reverse migration, with very little apoptosis or efferocytosis of neutrophils. Furthermore, our in vivo imaging led to the finding of a novel wound responsive mpeg1+ neutrophil subset, highlighting previously unrecognized heterogeneity in neutrophils. Our study provides a detailed analysis of the modes of immune cell migration in larval zebrafish, paving the way for future studies examining tissue injury and inflammation.
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Affiliation(s)
- Aryan Kaveh
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Finnius A. Bruton
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlotte Buckley
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Magdalena E. M. Oremek
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Carl S. Tucker
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - John J. Mullins
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Adriano G. Rossi
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin A. Denvir
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
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Bernut A, Loynes CA, Floto RA, Renshaw SA. Deletion of cftr Leads to an Excessive Neutrophilic Response and Defective Tissue Repair in a Zebrafish Model of Sterile Inflammation. Front Immunol 2020; 11:1733. [PMID: 32849617 PMCID: PMC7412881 DOI: 10.3389/fimmu.2020.01733] [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: 05/15/2020] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Inflammation-related progressive lung destruction is the leading causes of premature death in cystic fibrosis (CF), a genetic disorder caused by a defective cystic fibrosis transmembrane conductance regulator (CFTR). However, therapeutic targeting of inflammation has been hampered by a lack of understanding of the links between a dysfunctional CFTR and the deleterious innate immune response in CF. Herein, we used a CFTR-depleted zebrafish larva, as an innovative in vivo vertebrate model, to understand how CFTR dysfunction leads to abnormal inflammatory status in CF. We show that impaired CFTR-mediated inflammation correlates with an exuberant neutrophilic response after injury: CF zebrafish exhibit enhanced and sustained accumulation of neutrophils at wounds. Excessive epithelial oxidative responses drive enhanced neutrophil recruitment towards wounds. Persistence of neutrophils at inflamed sites is associated with impaired reverse migration of neutrophils and reduction in neutrophil apoptosis. As a consequence, the increased number of neutrophils at wound sites causes tissue damage and abnormal tissue repair. Importantly, the molecule Tanshinone IIA successfully accelerates inflammation resolution and improves tissue repair in CF animal. Our findings bring important new understanding of the mechanisms underlying the inflammatory pathology in CF, which could be addressed therapeutically to prevent inflammatory lung damage in CF patients with potential improvements in disease outcomes.
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Affiliation(s)
- Audrey Bernut
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Catherine A. Loynes
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - R. Andres Floto
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Francis Crick Avenue, Cambridge Biomedical, Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Stephen A. Renshaw
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, United Kingdom
- Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
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Meier P, Purshouse R, Bain M, Bambra C, Bentall R, Birkin M, Brazier J, Brennan A, Bryan M, Cox J, Fell G, Goyder E, Heppenstall A, Holmes J, Hughes C, Ishaq A, Kadirkamanathan V, Lomax N, Lupton R, Paisley S, Smith K, Stewart E, Strong M, Such E, Tsuchiya A, Watkins C. The SIPHER Consortium: Introducing the new UK hub for systems science in public health and health economic research. Wellcome Open Res 2019; 4:174. [PMID: 31815191 PMCID: PMC6880277 DOI: 10.12688/wellcomeopenres.15534.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2019] [Indexed: 01/08/2023] Open
Abstract
The conditions in which we are born, grow, live, work and age are key drivers of health and inequalities in life chances. To maximise health and wellbeing across the whole population, we need well-coordinated action across government sectors, in areas including economic, education, welfare, labour market and housing policy. Current research struggles to offer effective decision support on the cross-sector strategic alignment of policies, and to generate evidence that gives budget holders the confidence to change the way major investment decisions are made. This open letter introduces a new research initiative in this space. The SIPHER (
Systems Science in
Public
Health and Health
Economics
Research) Consortium brings together a multi-disciplinary group of scientists from across six universities, three government partners at local, regional and national level, and ten practice partner organisations. The Consortium’s vision is a shift from health policy to healthy public policy, where the wellbeing impacts of policies are a core consideration across government sectors. Researchers and policy makers will jointly tackle fundamental questions about: a) the complex causal relationships between upstream policies and wellbeing, economic and equality outcomes; b) the multi-sectoral appraisal of costs and benefits of alternative investment options; c) public values and preferences for different outcomes, and how necessary trade-offs can be negotiated; and d) creating the conditions for intelligence-led adaptive policy design that maximises progress against economic, social and health goals. Whilst our methods will be adaptable across policy topics and jurisdictions, we will initially focus on four policy areas: Inclusive Economic Growth, Adverse Childhood Experiences, Mental Wellbeing and Housing.
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Affiliation(s)
- Petra Meier
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Robin Purshouse
- Department of Automatic Control & Systems Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Marion Bain
- Population Health Directorate, Scottish Government, Edinburgh, EH1 3DG, UK
| | - Clare Bambra
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, NE1 4LP, UK
| | - Richard Bentall
- Clinical Psychology Unit, Department of Psychology, University of Sheffield, Sheffield, S1 2LT, UK
| | - Mark Birkin
- Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9NL, UK
| | - John Brazier
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Alan Brennan
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Mark Bryan
- Department of Economics, University of Sheffield, Sheffield, S1 4DT, UK
| | - Julian Cox
- Greater Manchester Combined Authority, Manchester, M1 6EU, UK
| | - Greg Fell
- Sheffield City Council, Sheffield, S1 2HH, UK
| | - Elizabeth Goyder
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Alison Heppenstall
- Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9NL, UK
| | - John Holmes
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Ceri Hughes
- Inclusive Growth Analysis Unit, University of Manchester, Manchester, M13 9PL, UK
| | - Asif Ishaq
- Population Health Directorate, Scottish Government, Edinburgh, EH1 3DG, UK
| | - Visakan Kadirkamanathan
- Department of Automatic Control & Systems Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - Nik Lomax
- Leeds Institute for Data Analytics, University of Leeds, Leeds, LS2 9NL, UK
| | - Ruth Lupton
- Inclusive Growth Analysis Unit, University of Manchester, Manchester, M13 9PL, UK
| | - Suzy Paisley
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Katherine Smith
- School of Social Work & Social Policy, University of Strathclyde, Glasgow, G4 0LT, UK
| | - Ellen Stewart
- Centre for Biomedicine, Self & Society, University of Edinburgh, Edinburgh, EH8 9AG, UK
| | - Mark Strong
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Elizabeth Such
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK
| | - Aki Tsuchiya
- School of Health and Related Research, University of Sheffield, Sheffield, S1 4DA, UK.,Department of Economics, University of Sheffield, Sheffield, S1 4DT, UK
| | - Craig Watkins
- Department of Urban Studies and Planning, University of Sheffield, Sheffield, S1 4DP, UK
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11
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Bekeschus S, Seebauer C, Wende K, Schmidt A. Physical plasma and leukocytes - immune or reactive? Biol Chem 2019; 400:63-75. [PMID: 30030959 DOI: 10.1515/hsz-2018-0224] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022]
Abstract
Leukocytes are professionals in recognizing and removing pathogenic or unwanted material. They are present in virtually all tissues, and highly motile to enter or leave specific sites throughout the body. Less than a decade ago, physical plasmas entered the field of medicine to deliver their delicate mix of reactive species and other physical agents for mainly dermatological or oncological therapy. Plasma treatment thus affects leukocytes via direct or indirect means: immune cells are either present in tissues during treatment, or infiltrate or exfiltrate plasma-treated areas. The immune system is crucial for human health and resolution of many types of diseases. It is therefore vital to study the response of leukocytes after plasma treatment in vitro and in vivo. This review gathers together the major themes in the plasma treatment of innate and adaptive immune cells, and puts these into the context of wound healing and oncology, the two major topics in plasma medicine.
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Affiliation(s)
- Sander Bekeschus
- Leibniz-Institute for Plasma Science and Technology (INP Greifswald), ZIK plasmatis, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
| | - Christian Seebauer
- Greifswald University Medical Center, Department of Oral and Maxillofacial Surgery/Plastic Surgery, Ferdinand-Sauerbruch-Str. DZ 7, D-17475 Greifswald, Germany
| | - Kristian Wende
- Leibniz-Institute for Plasma Science and Technology (INP Greifswald), ZIK plasmatis, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
| | - Anke Schmidt
- Leibniz-Institute for Plasma Science and Technology (INP Greifswald), ZIK plasmatis, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
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12
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Isles HM, Herman KD, Robertson AL, Loynes CA, Prince LR, Elks PM, Renshaw SA. The CXCL12/CXCR4 Signaling Axis Retains Neutrophils at Inflammatory Sites in Zebrafish. Front Immunol 2019; 10:1784. [PMID: 31417560 PMCID: PMC6684839 DOI: 10.3389/fimmu.2019.01784] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022] Open
Abstract
The inappropriate retention of neutrophils at inflammatory sites is a major driver of the excessive tissue damage characteristic of respiratory inflammatory diseases including COPD, ARDS, and cystic fibrosis. The molecular programmes which orchestrate neutrophil recruitment to inflammatory sites through chemotactic guidance have been well-studied. However, how neutrophil sensitivity to these cues is modulated during inflammation resolution is not understood. The identification of neutrophil reverse migration as a mechanism of inflammation resolution and the ability to modulate this therapeutically has identified a new target to treat inflammatory disease. Here we investigate the role of the CXCL12/CXCR4 signaling axis in modulating neutrophil retention at inflammatory sites. We used an in vivo tissue injury model to study neutrophilic inflammation using transgenic zebrafish larvae. Expression of cxcl12a and cxcr4b during the tissue damage response was assessed using in situ hybridization and analysis of RNA sequencing data. CRISPR/Cas9 was used to knockdown cxcl12a and cxcr4b in zebrafish larvae. The CXCR4 antagonist AMD3100 was used to block the Cxcl12/Cxcr4 signaling axis pharmacologically. We identified that cxcr4b and cxcl12a are expressed at the wound site in zebrafish larvae during the inflammatory response. Following tail-fin transection, removal of neutrophils from inflammatory sites is significantly increased in cxcr4b and cxcl12a CRISPR knockdown larvae. Pharmacological inhibition of the Cxcl12/Cxcr4 signaling axis accelerated resolution of the neutrophil component of inflammation, an effect caused by an increase in neutrophil reverse migration. The findings of this study suggest that CXCR4/CXCL12 signaling may play an important role in neutrophil retention at inflammatory sites, identifying a potential new target for the therapeutic removal of neutrophils from the lung in chronic inflammatory disease.
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Affiliation(s)
- Hannah M. Isles
- Renshaw Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Elks Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Kimberly D. Herman
- Renshaw Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Prince Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Anne L. Robertson
- Renshaw Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
- Zon Laboratory, Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Catherine A. Loynes
- Renshaw Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Lynne R. Prince
- Prince Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom
| | - Philip M. Elks
- Elks Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Stephen A. Renshaw
- Renshaw Laboratory, Department of Infection, Immunity, and Cardiovascular Disease, The Bateson Centre, University of Sheffield, Sheffield, United Kingdom
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13
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Malhotra D, Shin J, Solnica-Krezel L, Raz E. Spatio-temporal regulation of concurrent developmental processes by generic signaling downstream of chemokine receptors. eLife 2018; 7:33574. [PMID: 29873633 PMCID: PMC5990360 DOI: 10.7554/elife.33574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/19/2018] [Indexed: 01/09/2023] Open
Abstract
Chemokines are secreted proteins that regulate a range of processes in eukaryotic organisms. Interestingly, different chemokine receptors control distinct biological processes, and the same receptor can direct different cellular responses, but the basis for this phenomenon is not known. To understand this property of chemokine signaling, we examined the function of the chemokine receptors Cxcr4a, Cxcr4b, Ccr7, Ccr9 in the context of diverse processes in embryonic development in zebrafish. Our results reveal that the specific response to chemokine signaling is dictated by cell-type-specific chemokine receptor signal interpretation modules (CRIM) rather than by chemokine-receptor-specific signals. Thus, a generic signal provided by different receptors leads to discrete responses that depend on the specific identity of the cell that receives the signal. We present the implications of employing generic signals in different contexts such as gastrulation, axis specification and single-cell migration. Every process in the body is regulated by a complex network of interactions between different molecules and cells. Chemokines, for example, are tiny molecules produced by a cell that are involved in a range of processes, from development to immune responses and cancer. When chemokines bind to a specific protein on another cell, called the chemokine receptor, it stimulates different signaling pathways inside the cell. Consequently, chemokine receptors are equally important for regulating processes as diverse as the movement of cells during development and growth, or activating immune responses. Mammals have over 20 different chemokine receptors, and the same receptor can have different roles depending in which cell type it is found in. For example, in one cell type it may stimulate an action such as cell growth, but in another, it may block this process. Until now, it was unclear how chemokine receptors can achieve such different effects. One theory was that chemokine receptors initiate a distinct signaling cascade, a phenomenon termed ‘signaling bias’, depending on the type of chemokine or receptor. Here, Malhotra et al. used zebrafish embryos to investigate how four specific chemokine receptors regulate different events during early development. They found that the same chemokine receptor could direct different reactions in distinct cell types, while different receptors could also cause the same response in a specific cell type. In other words, the effect of a chemokine receptor depends on the cell type rather than the type of receptor. Since each of these receptors was able to control processes that it normally does not regulate in other cells, Malhotra et al. suggest that different chemokine receptors provide the same generic signal when activated, which the specific cell types then interpret accordingly. A next step will be to test how other chemokine receptors behave in different contexts, for example during an immune response. If the receptors work on the same principle regardless of the process, it could help to explain why faulty expression of chemokine receptors play such an important role during development and in disease. It could further highlight why blocking one receptor may not have any consequences, as they are dispensable and can be replaced by other receptors in the cell.
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Affiliation(s)
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri
| | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St Louis, Missouri
| | - Erez Raz
- Institute for Cell Biology, ZMBE, Muenster, Germany
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14
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Wang J, Hossain M, Thanabalasuriar A, Gunzer M, Meininger C, Kubes P. Visualizing the function and fate of neutrophils in sterile injury and repair. Science 2018; 358:111-116. [PMID: 28983053 DOI: 10.1126/science.aam9690] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 07/03/2017] [Accepted: 08/30/2017] [Indexed: 12/12/2022]
Abstract
Neutrophils have been implicated as harmful cells in a variety of inappropriate inflammatory conditions where they injure the host, leading to the death of the neutrophils and their subsequent phagocytosis by monocytes and macrophages. Here we show that in a fully repairing sterile thermal hepatic injury, neutrophils also penetrate the injury site and perform the critical tasks of dismantling injured vessels and creating channels for new vascular regrowth. Upon completion of these tasks, they neither die at the injury site nor are phagocytosed. Instead, many of these neutrophils reenter the vasculature and have a preprogrammed journey that entails a sojourn in the lungs to up-regulate CXCR4 (C-X-C motif chemokine receptor 4) before entering the bone marrow, where they undergo apoptosis.
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Affiliation(s)
- Jing Wang
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Division of Inflammation Biology, Tokushima University, Tokushima 7708503, Japan.,Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Mokarram Hossain
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Ajitha Thanabalasuriar
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Essen 45147, Germany
| | - Cynthia Meininger
- Department of Medical Physiology, Texas A&M University Health Science Center, Temple, TX 76504, USA
| | - Paul Kubes
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta T2N 4N1, Canada. .,Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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15
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Neutrophil migration in infection and wound repair: going forward in reverse. Nat Rev Immunol 2017; 16:378-91. [PMID: 27231052 DOI: 10.1038/nri.2016.49] [Citation(s) in RCA: 640] [Impact Index Per Article: 91.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neutrophil migration and its role during inflammation has been the focus of increased interest in the past decade. Advances in live imaging and the use of new model systems have helped to uncover the behaviour of neutrophils in injured and infected tissues. Although neutrophils were considered to be short-lived effector cells that undergo apoptosis in damaged tissues, recent evidence suggests that neutrophil behaviour is more complex and, in some settings, neutrophils might leave sites of tissue injury and migrate back into the vasculature. The role of reverse migration and its contribution to resolution of inflammation remains unclear. In this Review, we discuss the different cues within tissues that mediate neutrophil forward and reverse migration in response to injury or infection and the implications of these mechanisms to human disease.
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16
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Powell D, Tauzin S, Hind LE, Deng Q, Beebe DJ, Huttenlocher A. Chemokine Signaling and the Regulation of Bidirectional Leukocyte Migration in Interstitial Tissues. Cell Rep 2017; 19:1572-1585. [PMID: 28538177 PMCID: PMC5505660 DOI: 10.1016/j.celrep.2017.04.078] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/17/2017] [Accepted: 04/28/2017] [Indexed: 01/02/2023] Open
Abstract
Motile cells navigate through complex tissue environments that include both attractive and repulsive cues. In response to tissue wounding, neutrophils, primary cells of the innate immune response, exhibit bidirectional migration that is orchestrated by chemokines and their receptors. Although progress has been made in identifying signals that mediate the recruitment phase, the mechanisms that regulate neutrophil reverse migration remain largely unknown. Here, we visualize bidirectional neutrophil migration to sterile wounds in zebrafish larvae and identify specific roles for the chemokine receptors Cxcr1 and Cxcr2 in neutrophil recruitment to sterile injury and infection. Notably, we also identify Cxcl8a/Cxcr2 as a specific ligand-receptor pair that orchestrates neutrophil chemokinesis in interstitial tissues during neutrophil reverse migration and resolution of inflammation. Taken together, our findings identify distinct receptors that mediate bidirectional leukocyte motility during interstitial migration depending on the context and type of tissue damage in vivo.
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Affiliation(s)
- Davalyn Powell
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sebastien Tauzin
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laurel E Hind
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Qing Deng
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - David J Beebe
- Department of Biomedical Engineering and University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna Huttenlocher
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53706, USA.
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17
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Weavers H, Liepe J, Sim A, Wood W, Martin P, Stumpf MPH. Systems Analysis of the Dynamic Inflammatory Response to Tissue Damage Reveals Spatiotemporal Properties of the Wound Attractant Gradient. Curr Biol 2016; 26:1975-1989. [PMID: 27426513 PMCID: PMC4985561 DOI: 10.1016/j.cub.2016.06.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 05/11/2016] [Accepted: 06/10/2016] [Indexed: 01/23/2023]
Abstract
In the acute inflammatory phase following tissue damage, cells of the innate immune system are rapidly recruited to sites of injury by pro-inflammatory mediators released at the wound site. Although advances in live imaging allow us to directly visualize this process in vivo, the precise identity and properties of the primary immune damage attractants remain unclear, as it is currently impossible to directly observe and accurately measure these signals in tissues. Here, we demonstrate that detailed information about the attractant signals can be extracted directly from the in vivo behavior of the responding immune cells. By applying inference-based computational approaches to analyze the in vivo dynamics of the Drosophila inflammatory response, we gain new detailed insight into the spatiotemporal properties of the attractant gradient. In particular, we show that the wound attractant is released by wound margin cells, rather than by the wounded tissue per se, and that it diffuses away from this source at rates far slower than those of previously implicated signals such as H2O2 and ATP, ruling out these fast mediators as the primary chemoattractant. We then predict, and experimentally test, how competing attractant signals might interact in space and time to regulate multi-step cell navigation in the complex environment of a healing wound, revealing a period of receptor desensitization after initial exposure to the damage attractant. Extending our analysis to model much larger wounds, we uncover a dynamic behavioral change in the responding immune cells in vivo that is prognostic of whether a wound will subsequently heal or not. Video Abstract
Computational modeling of in vivo inflammatory response to tissue damage is applied The model infers novel spatiotemporal properties of the wound attractant gradient Wound signal is released from the wound edge for 30 min and diffuses at 200 μm2/min Modeling two competing wounds reveals a period of immune cell desensitization
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Affiliation(s)
- Helen Weavers
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK; School of Cellular and Molecular Medicine, Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Juliane Liepe
- Theoretical Systems Biology, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
| | - Aaron Sim
- Theoretical Systems Biology, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK
| | - Will Wood
- School of Cellular and Molecular Medicine, Medical Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Paul Martin
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK; Department of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol BS8 1TD, UK; School of Medicine, Cardiff University, Cardiff CF14 4XN, UK; Lee Kong Chian School of Medicine, Nanyang Technologicial University, Singapore 636921, Singapore.
| | - Michael P H Stumpf
- Theoretical Systems Biology, Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, UK.
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18
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Cox process representation and inference for stochastic reaction-diffusion processes. Nat Commun 2016; 7:11729. [PMID: 27222432 PMCID: PMC4894951 DOI: 10.1038/ncomms11729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/26/2016] [Indexed: 01/30/2023] Open
Abstract
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction–diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction–diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction–diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling. Stochastic reaction-diffusion systems are used for modelling spatial dynamics in many disciplines, but parameter inference and model selection remain challenging. Here the authors offer a solution enabled by a connection between reaction-diffusion and the well-studied spatio-temporal Cox processes.
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19
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Nourshargh S, Renshaw SA, Imhof BA. Reverse Migration of Neutrophils: Where, When, How, and Why? Trends Immunol 2016; 37:273-286. [PMID: 27055913 DOI: 10.1016/j.it.2016.03.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023]
Abstract
Neutrophil migration to injured and pathogen-infected tissues is a fundamental component of innate immunity. An array of cellular and molecular events mediate this response to collectively guide neutrophils out of the vasculature and towards the core of the ensuing inflammatory reaction where they exert effector functions. Advances in imaging modalities have revealed that neutrophils can also exhibit motility away from sites of inflammation and injury, although it is unclear under what circumstances this reverse migration is a physiological protective response, and when it has pathophysiological relevance. Here we review different types of neutrophil reverse migration and discuss the current understanding of the associated mechanisms. In this context we propose clarifications to the existing terminology used to describe the many facets of neutrophil reverse migration.
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Affiliation(s)
- Sussan Nourshargh
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Stephen A Renshaw
- Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, Firth Court, University of Sheffield, Western Bank, Sheffield S10 2TN, UK.
| | - Beat A Imhof
- Centre Médical Universitaire, Rue Michel-Servet 1, Geneva 1211, Switzerland.
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20
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Tolosa EJ, Fernández-Zapico ME, Battiato NL, Rovasio RA. Sonic hedgehog is a chemotactic neural crest cell guide that is perturbed by ethanol exposure. Eur J Cell Biol 2016; 95:136-52. [DOI: 10.1016/j.ejcb.2016.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 01/23/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022] Open
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21
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Marjoram P, Hamblin S, Foley B. Simulation-based Bayesian Analysis of Complex Data. SUMMER COMPUTER SIMULATION CONFERENCE : (SCSC 2015) : 2015 SUMMER SIMULATION MULTI-CONFERENCE (SUMMERSIM'15) : CHICAGO, ILLINOIS, USA, 26-29 JULY 2015. SUMMER COMPUTER SIMULATION CONFERENCE (2015 : CHICAGO, ILLINOIS) 2015; 47:176-183. [PMID: 27840859 PMCID: PMC5102508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Our ability to collect large datasets is growing rapidly. Such richness of data offers great promise in terms of addressing detailed scientific questions in great depth. However, this benefit is not without scientific difficulty: many traditional analysis methods become computationally intractable for very large datasets. However, one can frequently still simulate data from scientific models for which direct calculation is no longer possible. In this paper we propose a Bayesian perspective for such analyses, and argue for the advantage of a simulation-based approximate Bayesian method that remains tractable when tractability of other methods is lost. This method, which is known as "approximate Bayesian computation" [ABC], has now been used in a variety of contexts, such as the analysis of tumor data (a tumor being a complex population of cells), and the analysis of human genetic variation data (which arise from a population of individual people). We review a number of ABC methods, with specific attention to the use of ABC in agent-based models, and give pointers to software that allows straightforward implementation of the ABC approach. In this way we demonstrate the utility of simulation-based analyses of large datasets within a rigorous statistical framework.
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Affiliation(s)
- Paul Marjoram
- University of Southern California, Dept of Preventive Medicine, Keck School of Medicine, Los Angeles, CA
| | - Steven Hamblin
- University of Southern California, Dept. of Molecular and Computational Biology, Los Angeles, CA
| | - Brad Foley
- University of Southern California, Dept. of Molecular and Computational Biology, Los Angeles, CA
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22
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Ellett F, Elks PM, Robertson AL, Ogryzko NV, Renshaw SA. Defining the phenotype of neutrophils following reverse migration in zebrafish. J Leukoc Biol 2015; 98:975-81. [PMID: 26071567 PMCID: PMC4661044 DOI: 10.1189/jlb.3ma0315-105r] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/02/2015] [Indexed: 01/01/2023] Open
Abstract
Stimulation of neutrophil reverse migration presents an attractive, alternative therapeutic pathway to driving inflammation resolution. However, little is known about whether the activity of wound-experienced neutrophils is altered and whether encouraging dispersal of such neutrophils back into the body may have undesirable consequences. This study used a zebrafish tail transection inflammation model, in combination with a photoconvertible neutrophil transgenic line, to allow internally controlled, simultaneous comparison of reverse-migrated neutrophils with naïve neutrophils in the presence and absence of secondary insult. Detailed microscopy revealed that reverse-migrated neutrophils exhibited an activated morphology but responded normally to secondary insult and are able to mount an effective antimicrobial response to Staphylococcus aureus. These results support a model in which reverse-migrated neutrophils exhibit no long-term behavioral alterations and encourage the notion of enhanced reverse migration as a viable target for pharmaceutical manipulation.
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Affiliation(s)
- Felix Ellett
- Bateson Centre and Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Philip M Elks
- Bateson Centre and Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Anne L Robertson
- Bateson Centre and Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Nikolay V Ogryzko
- Bateson Centre and Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Stephen A Renshaw
- Bateson Centre and Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
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23
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Kamenyeva O, Boularan C, Kabat J, Cheung GYC, Cicala C, Yeh AJ, Chan JL, Periasamy S, Otto M, Kehrl JH. Neutrophil recruitment to lymph nodes limits local humoral response to Staphylococcus aureus. PLoS Pathog 2015; 11:e1004827. [PMID: 25884622 PMCID: PMC4401519 DOI: 10.1371/journal.ppat.1004827] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 03/23/2015] [Indexed: 12/25/2022] Open
Abstract
Neutrophils form the first line of host defense against bacterial pathogens. They are rapidly mobilized to sites of infection where they help marshal host defenses and remove bacteria by phagocytosis. While splenic neutrophils promote marginal zone B cell antibody production in response to administered T cell independent antigens, whether neutrophils shape humoral immunity in other lymphoid organs is controversial. Here we investigate the neutrophil influx following the local injection of Staphylococcus aureus adjacent to the inguinal lymph node and determine neutrophil impact on the lymph node humoral response. Using intravital microscopy we show that local immunization or infection recruits neutrophils from the blood to lymph nodes in waves. The second wave occurs temporally with neutrophils mobilized from the bone marrow. Within lymph nodes neutrophils infiltrate the medulla and interfollicular areas, but avoid crossing follicle borders. In vivo neutrophils form transient and long-lived interactions with B cells and plasma cells, and their depletion augments production of antigen-specific IgG and IgM in the lymph node. In vitro activated neutrophils establish synapse- and nanotube-like interactions with B cells and reduce B cell IgM production in a TGF- β1 dependent manner. Our data reveal that neutrophils mobilized from the bone marrow in response to a local bacterial challenge dampen the early humoral response in the lymph node. Highly antibiotic resistant Staphylococcus aureus (S. aureus) are an important human pathogen and major cause of hospital acquired infections. An early host defense mechanism against bacterial infection is neutrophil recruitment, which helps eliminate the bacteria at the site of invasion. However, unless quickly neutralized, pathogens such as S. aureus can gain access to nearby lymph nodes via draining lymphatics. Lymph nodes protect the host by mobilizing additional resources that limit further pathogen dissemination. These include recruitment of neutrophils to the lymph node to directly target pathogens and the initiation of adaptive immune mechanisms, such as the humoral immune response, which transforms B lymphocytes capable of making pathogen specific antibodies into antibody producing plasma cells. Using a mouse model that allows direct visualization of lymphocytes, neutrophils, and fluorescently-labeled S. aureus in lymph nodes, we document the rapid appearance of bacteria in the lymph node following local S. aureus infection. We characterize the dynamic influx of neutrophils that occurs as a consequence and reveal direct B cell-neutrophil interactions within the lymph node parenchyma. We find that while lymph node neutrophils rapidly engage bacteria, they limit the subsequent humoral immune response likely by producing Transforming Growth Factor-β1, a factor known to limit B cell responses. These finding have important implication for our understanding of B cell responses against potent pathogens such as S. aureus and for the design of effective vaccines.
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Affiliation(s)
- Olena Kamenyeva
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Cedric Boularan
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Juraj Kabat
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gordon Y C Cheung
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Claudia Cicala
- Immunopathogenesis Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Anthony J Yeh
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - June L Chan
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Saravanan Periasamy
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Human Bacterial Pathogenesis, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John H Kehrl
- B-Cell Molecular Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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24
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Mori DN, Kreisel D, Fullerton JN, Gilroy DW, Goldstein DR. Inflammatory triggers of acute rejection of organ allografts. Immunol Rev 2015; 258:132-44. [PMID: 24517430 DOI: 10.1111/imr.12146] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Solid organ transplantation is a vital therapy for end stage diseases. Decades of research have established that components of the adaptive immune system are critical for transplant rejection, but the role of the innate immune system in organ transplantation is just emerging. Accumulating evidence indicates that the innate immune system is activated at the time of organ implantation by the release of endogenous inflammatory triggers. This review discusses the nature of these triggers in organ transplantation and also potential mediators that may enhance inflammation resolution after organ implantation.
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Affiliation(s)
- Daniel N Mori
- Departments of Internal Medicine and Immunobiology, Yale School of Medicine, New Haven, CT, USA
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Hamza B, Wong E, Patel S, Cho H, Martel J, Irimia D. Retrotaxis of human neutrophils during mechanical confinement inside microfluidic channels. Integr Biol (Camb) 2014; 6:175-83. [PMID: 24419464 DOI: 10.1039/c3ib40175h] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The current paradigm of unidirectional migration of neutrophils from circulation to sites of injury in tissues has been recently challenged by observations in zebrafish showing that neutrophils can return from tissues back into the circulation. However, the relevance of these observations to human neutrophils remains unclear, the forward and reverse migration of neutrophils is difficult to quantify, and the precise conditions modulating the reverse migration cannot be isolated. Here, we designed a microfluidic platform inside which we observed human neutrophil migration in response to chemoattractant sources inside channels, simulating the biochemical and mechanical confinement conditions at sites of injury in tissues. We observed that, after initially following the direction of chemoattractant gradients, more than 90% of human neutrophils can reverse their direction and migrate persistently and for distances longer than one thousand micrometers away from chemoattractant sources (retrotaxis). Retrotaxis is enhanced in the presence of lipoxin A4 (LXA4), a well-established mediator of inflammation resolution, or Tempol, a standard antioxidant. Retrotaxis stops after neutrophils encounter targets which they phagocytise or on surfaces presenting high concentrations of fibronectin. Our microfluidic model suggests a new paradigm for neutrophil accumulation at sites of inflammation, which depends on the balance of three simultaneous processes: chemotaxis along diffusion gradients, retrotaxis following mechanical guides, and stopping triggered by phagocytosis.
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Affiliation(s)
- Bashar Hamza
- BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, and Shriners Hospital for Children, Charlestown, MA 02129, USA.
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26
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Robertson AL, Holmes GR, Bojarczuk AN, Burgon J, Loynes CA, Chimen M, Sawtell AK, Hamza B, Willson J, Walmsley SR, Anderson SR, Coles MC, Farrow SN, Solari R, Jones S, Prince LR, Irimia D, Rainger GE, Kadirkamanathan V, Whyte MKB, Renshaw SA. A zebrafish compound screen reveals modulation of neutrophil reverse migration as an anti-inflammatory mechanism. Sci Transl Med 2014; 6:225ra29. [PMID: 24574340 PMCID: PMC4247228 DOI: 10.1126/scitranslmed.3007672] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Diseases of failed inflammation resolution are common and largely incurable. Therapeutic induction of inflammation resolution is an attractive strategy to bring about healing without increasing susceptibility to infection. However, therapeutic targeting of inflammation resolution has been hampered by a lack of understanding of the underlying molecular controls. To address this drug development challenge, we developed an in vivo screen for proresolution therapeutics in a transgenic zebrafish model. Inflammation induced by sterile tissue injury was assessed for accelerated resolution in the presence of a library of known compounds. Of the molecules with proresolution activity, tanshinone IIA, derived from a Chinese medicinal herb, potently induced inflammation resolution in vivo both by induction of neutrophil apoptosis and by promoting reverse migration of neutrophils. Tanshinone IIA blocked proinflammatory signals in vivo, and its effects are conserved in human neutrophils, supporting a potential role in treating human inflammation and providing compelling evidence of the translational potential of this screening strategy.
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Affiliation(s)
- Anne L. Robertson
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Geoffrey R. Holmes
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Aleksandra N. Bojarczuk
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
| | - Joseph Burgon
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
| | - Catherine A. Loynes
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Myriam Chimen
- Centre for Cardiovascular Sciences, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Amy K. Sawtell
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | - Bashar Hamza
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Joseph Willson
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Sarah R. Walmsley
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean R. Anderson
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Mark C. Coles
- Centre for Immunology and Infection, Department of Biology, University of York, York YO10 5DD, UK
| | - Stuart N. Farrow
- Respiratory Therapy Area, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Roberto Solari
- National Heart and Lung Institute, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Simon Jones
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | - Lynne R. Prince
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Daniel Irimia
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - G. Ed Rainger
- Centre for Cardiovascular Sciences, School of Clinical and Experimental Medicine, University of Birmingham, Birmingham B15 2TT, UK
| | - Visakan Kadirkamanathan
- Department of Automatic Control and Systems Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Moira K. B. Whyte
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Stephen A. Renshaw
- Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, UK
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
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Zanin JP, Battiato NL, Rovasio RA. Neurotrophic factor NT-3 displays a non-canonical cell guidance signaling function for cephalic neural crest cells. Eur J Cell Biol 2013; 92:264-79. [PMID: 24252516 DOI: 10.1016/j.ejcb.2013.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/08/2013] [Accepted: 10/13/2013] [Indexed: 12/30/2022] Open
Abstract
Chemotactic cell migration is triggered by extracellular concentration gradients of molecules segregated by target fields. Neural crest cells (NCCs), paradigmatic as an accurately moving cell population, undergo wide dispersion along multiple pathways, invading with precision defined sites of the embryo to differentiate into many derivatives. This report addresses the involvement of NT-3 in early colonization by cephalic NCCs invading the optic vesicle region. The results of in vitro and in vivo approaches showed that NCCs migrate directionally up an NT-3 concentration gradient. We also demonstrated the expression of NT-3 in the ocular region as well as their functional TrkB, TrkC and p75 receptors on cephalic NCCs. On whole-mount embryo, a perturbed distribution of NCCs colonizing the optic vesicle target field was shown after morpholino cancelation of cephalic NT-3 or TrkC receptor on NCCs, as well as in situ blocking of TrkC receptor of mesencephalic NCCs by specific antibody released from inserted microbeads. The present results strongly suggest that, among other complementary cell guidance factor(s), the chemotactic response of NCCs toward the ocular region NT-3 gradient is essential for spatiotemporal cell orientation, amplifying the functional scope of this neurotrophic factor as a molecular guide for the embryo cells, besides its well-known canonical functions.
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Affiliation(s)
- Juan P Zanin
- Center for Cellular and Molecular Biology - IIBYT (CONICET, UNC), FCEFN, National University of Cordoba, Av. Vélez Sarsfield 1611, 5016 Córdoba, Argentina
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Holmes GR, Anderson SR, Dixon G, Renshaw SA, Kadirkamanathan V. A Bayesian framework for identifying cell migration dynamics. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:3455-8. [PMID: 24110472 DOI: 10.1109/embc.2013.6610285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cell migration is a vital process in living organisms. In particular we are interested in the way that white blood cells such as neutrophils migrate during episodes of inflammation which are important events in the working of the innate immune system. Migration of populations of many kinds can be modelled using drift-diffusion models by drawing analogies between the individual agents and the molecules in a fluid. It is challenging to arrive at a data-driven estimate of the parameters of this kind of process, particularly so if the individual agents have time varying properties that are not uniform over the population. In this paper, we offer a novel framework to estimate migration dynamics in this context. It makes use of the Approximate Bayesian Computation approach for parameter estimation and model selection. The Framework is applied to zebrafish neutrophil dynamics but is applicable for general migration scenarios.
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Kirk P, Thorne T, Stumpf MPH. Model selection in systems and synthetic biology. Curr Opin Biotechnol 2013; 24:767-74. [PMID: 23578462 DOI: 10.1016/j.copbio.2013.03.012] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 03/07/2013] [Accepted: 03/14/2013] [Indexed: 11/17/2022]
Abstract
Developing mechanistic models has become an integral aspect of systems biology, as has the need to differentiate between alternative models. Parameterizing mathematical models has been widely perceived as a formidable challenge, which has spurred the development of statistical and optimisation routines for parameter inference. But now focus is increasingly shifting to problems that require us to choose from among a set of different models to determine which one offers the best description of a given biological system. We will here provide an overview of recent developments in the area of model selection. We will focus on approaches that are both practical as well as build on solid statistical principles and outline the conceptual foundations and the scope for application of such methods in systems biology.
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Affiliation(s)
- Paul Kirk
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Vanlier J, Tiemann CA, Hilbers PAJ, van Riel NAW. Parameter uncertainty in biochemical models described by ordinary differential equations. Math Biosci 2013; 246:305-14. [PMID: 23535194 DOI: 10.1016/j.mbs.2013.03.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/07/2013] [Accepted: 03/12/2013] [Indexed: 12/21/2022]
Abstract
Improved mechanistic understanding of biochemical networks is one of the driving ambitions of Systems Biology. Computational modeling allows the integration of various sources of experimental data in order to put this conceptual understanding to the test in a quantitative manner. The aim of computational modeling is to obtain both predictive as well as explanatory models for complex phenomena, hereby providing useful approximations of reality with varying levels of detail. As the complexity required to describe different system increases, so does the need for determining how well such predictions can be made. Despite efforts to make tools for uncertainty analysis available to the field, these methods have not yet found widespread use in the field of Systems Biology. Additionally, the suitability of the different methods strongly depends on the problem and system under investigation. This review provides an introduction to some of the techniques available as well as gives an overview of the state-of-the-art methods for parameter uncertainty analysis.
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Affiliation(s)
- J Vanlier
- Eindhoven University of Technology, Department of Biomedical Engineering, Eindhoven, The Netherlands; Netherlands Consortium for Systems Biology, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands.
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Henry KM, Loynes CA, Whyte MKB, Renshaw SA. Zebrafish as a model for the study of neutrophil biology. J Leukoc Biol 2013; 94:633-42. [PMID: 23463724 DOI: 10.1189/jlb.1112594] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
To understand inflammation and immunity, we need to understand the biology of the neutrophil. Whereas these cells can readily be extracted from peripheral blood, their short lifespan makes genetic manipulations impractical. Murine knockout models have been highly informative, and new imaging techniques are allowing neutrophils to be seen during inflammation in vivo for the first time. However, there is a place for a new model of neutrophil biology, which readily permits imaging of individual neutrophils during inflammation in vivo, combined with the ease of genetic and chemical manipulation. The zebrafish has long been the model of choice for the developmental biology community, and the availability of genomic resources and tools for gene manipulation makes this an attractive model. Zebrafish innate immunity shares many features with mammalian systems, including neutrophils with morphological, biochemical, and functional features, also shared with mammalian neutrophils. Transgenic zebrafish with neutrophils specifically labeled with fluorescent proteins have been generated, and this advance has led to the adoption of zebrafish, alongside existing models, by a number of groups around the world. The use of these models has underpinned a number of key advances in the field, including the identification of a tissue gradient of hydrogen peroxide for neutrophil recruitment following tissue injury and direct evidence for reverse migration as a regulatable mechanism of inflammation resolution. In this review, we discuss the importance of zebrafish models in neutrophil biology and describe how the understanding of neutrophil biology has been advanced by the use of these models.
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