1
|
Hadj Abed L, Tak T, Cosgrove J, Perié L. CellDestiny: A RShiny application for the visualization and analysis of single-cell lineage tracing data. Front Med (Lausanne) 2022; 9:919345. [PMID: 36275810 PMCID: PMC9581332 DOI: 10.3389/fmed.2022.919345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Single-cell lineage tracing permits the labeling of individual cells with a heritable marker to follow the fate of each cell’s progeny. Over the last twenty years, several single-cell lineage tracing methods have emerged, enabling major discoveries in developmental biology, oncology and gene therapies. Analytical tools are needed to draw meaningful conclusions from lineage tracing measurements, which are characterized by high variability, sparsity and technical noise. However, the single cell lineage tracing field lacks versatile and easy-to-use tools for standardized and reproducible analyses, in particular tools accessible to biologists. Here we present CellDestiny, a RShiny app and associated web application developed for experimentalists without coding skills to perform visualization and analysis of single cell lineage-tracing datasets through a graphical user interface. We demonstrate the functionality of CellDestiny through the analysis of (i) lentiviral barcoding datasets of murine hematopoietic progenitors; (ii) published integration site data from Wiskott-Aldrich Symdrome patients undergoing gene-therapy treatment; and (iii) simultaneous barcoding and transcriptomic analysis of murine hematopoietic progenitor differentiation in vitro. In summary, CellDestiny is an easy-to-use and versatile toolkit that enables biologists to visualize and analyze single-cell lineage tracing data.
Collapse
Affiliation(s)
- Louisa Hadj Abed
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Centre de Bio-Informatique, MINES ParisTech, Institut Curie, PSL University, Paris, France
| | - Tamar Tak
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France
| | - Jason Cosgrove
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,*Correspondence: Jason Cosgrove,
| | - Leïla Perié
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, Paris, France,Leïla Perié,
| |
Collapse
|
2
|
Dendritic Cells and Their Immunotherapeutic Potential for Treating Type 1 Diabetes. Int J Mol Sci 2022; 23:ijms23094885. [PMID: 35563276 PMCID: PMC9099521 DOI: 10.3390/ijms23094885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/22/2022] [Accepted: 04/26/2022] [Indexed: 12/15/2022] Open
Abstract
Type 1 diabetes (T1D) results from the destruction of pancreatic beta cells through a process that is primarily mediated by T cells. Emerging evidence suggests that dendritic cells (DCs) play a crucial role in initiating and developing this debilitating disease. DCs are professional antigen-presenting cells with the ability to integrate signals arising from tissue infection or injury that present processed antigens from these sites to naïve T cells in secondary lymphoid organs, thereby triggering naïve T cells to differentiate and modulate adaptive immune responses. Recent advancements in our knowledge of the various subsets of DCs and their cellular structures and methods of orchestration over time have resulted in a better understanding of how the T cell response is shaped. DCs employ various arsenal to maintain their tolerance, including the induction of effector T cell deletion or unresponsiveness and the generation and expansion of regulatory T cell populations. Therapies that suppress the immunogenic effects of dendritic cells by blocking T cell costimulatory pathways and proinflammatory cytokine production are currently being sought. Moreover, new strategies are being developed that can regulate DC differentiation and development and harness the tolerogenic capacity of these cells. Here, in this report, we focus on recent advances in the field of DC immunology and evaluate the prospects of DC-based therapeutic strategies to treat T1D.
Collapse
|
3
|
Naik SH. Dendritic cell development at a clonal level within a revised 'continuous' model of haematopoiesis. Mol Immunol 2020; 124:190-197. [PMID: 32593782 DOI: 10.1016/j.molimm.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/17/2022]
Abstract
Understanding development of the dendritic cell (DC) subtypes continues to evolve. The origin and relationship of conventional DC type 1 (cDC1), cDC type 2 (cDC2) and plasmacytoid DCs (pDCs) to each other, and in relation to classic myeloid and lymphoid cells, has had a long and controversial history and is still not fully resolved. This review summarises the technological developments and findings that have been achieved at a clonal level, and how that has enhanced our knowledge of the process. It summarises the single cell lineage tracing technologies that have emerged, their application in in vitro and in vivo studies, in both mouse and human settings, and places the findings in a wider context of understanding haematopoiesis at a single cell or clonal level. In particular, it addresses the fate heterogeneity observed in many phenotypically defined progenitor subsets and how these findings have led to a departure from the classic ball-and-stick models of haematopoiesis to the emerging continuous model. Prior contradictions in DC development may be reconciled if they are framed within this revised model, where commitment to a lineage or cell type does not occur in an all-or-nothing process in defined progenitors but rather can occur at many stages of haematopoiesis in a dynamic process.
Collapse
Affiliation(s)
- Shalin H Naik
- Immunology Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, Australia; The Department of Medical Biology, The University of Melbourne, Parkville, Australia.
| |
Collapse
|
4
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
5
|
The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
6
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
7
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
8
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
9
|
The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
10
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2019. [DOI: 10.1016/j.it.2018.11.007 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
11
|
Hume DA, Irvine KM, Pridans C. The Mononuclear Phagocyte System: The Relationship between Monocytes and Macrophages. Trends Immunol 2018; 40:98-112. [PMID: 30579704 DOI: 10.1016/j.it.2018.11.007] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/18/2018] [Accepted: 11/30/2018] [Indexed: 02/07/2023]
Abstract
The mononuclear phagocyte system (MPS) is defined as a cell lineage in which committed marrow progenitors give rise to blood monocytes and tissue macrophages. Here, we discuss the concept of self-proscribed macrophage territories and homeostatic regulation of tissue macrophage abundance through growth factor availability. Recent studies have questioned the validity of the MPS model and argued that tissue-resident macrophages are a separate lineage seeded during development and maintained by self-renewal. We address this issue; discuss the limitations of inbred mouse models of monocyte-macrophage homeostasis; and summarize the evidence suggesting that during postnatal life, monocytes can replace resident macrophages in all major organs and adopt their tissue-specific gene expression. We conclude that the MPS remains a valid and accurate framework for understanding macrophage development and homeostasis.
Collapse
Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia
| | - Clare Pridans
- University of Edinburgh Centre for Inflammation Research, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| |
Collapse
|
12
|
Complement components as promoters of immunological tolerance in dendritic cells. Semin Cell Dev Biol 2017; 85:143-152. [PMID: 29155220 DOI: 10.1016/j.semcdb.2017.11.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 11/21/2022]
Abstract
Complement and dendritic cells (DCs) share many functional features that drive the outcome of immune-inflammatory processes. Both have a sentinel function, acting as danger sensors specialized for a rapid, comprehensive and selective action against potential threats without damaging the healthy host cells. But while complement has been considered as a "master alarm" system poised for direct pathogen killing, DCs are regarded as "master regulators" or orchestrators of a vast range of effector immune cells for an effective immune response against threatening insults. The original definition of the complement system, coined to denote its auxiliary function to enhance or assist in the role of antibodies or phagocytes to clear microbes or damaged cells, envisaged an important crosstalk between the complement and the mononuclear phagocyte systems. More recent studies have shown that, depending on the microenvironmental conditions, several complement effectors are competent to influence the differentiation and/or function of different DC subsets toward immunogenicity or tolerance. In this review we will infer about the capability of complement activators and inhibitors to "condition" a tolerogenic and anti-inflammatory immune response by direct interaction with DC surface receptors, and about the implications of this knowledge to devise new complement-based therapeutic approaches for autoimmune pathologies.
Collapse
|
13
|
Coles JA, Myburgh E, Brewer JM, McMenamin PG. Where are we? The anatomy of the murine cortical meninges revisited for intravital imaging, immunology, and clearance of waste from the brain. Prog Neurobiol 2017; 156:107-148. [PMID: 28552391 DOI: 10.1016/j.pneurobio.2017.05.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 04/25/2017] [Accepted: 05/08/2017] [Indexed: 12/15/2022]
Abstract
Rapid progress is being made in understanding the roles of the cerebral meninges in the maintenance of normal brain function, in immune surveillance, and as a site of disease. Most basic research on the meninges and the neural brain is now done on mice, major attractions being the availability of reporter mice with fluorescent cells, and of a huge range of antibodies useful for immunocytochemistry and the characterization of isolated cells. In addition, two-photon microscopy through the unperforated calvaria allows intravital imaging of the undisturbed meninges with sub-micron resolution. The anatomy of the dorsal meninges of the mouse (and, indeed, of all mammals) differs considerably from that shown in many published diagrams: over cortical convexities, the outer layer, the dura, is usually thicker than the inner layer, the leptomeninx, and both layers are richly vascularized and innervated, and communicate with the lymphatic system. A membrane barrier separates them and, in disease, inflammation can be localized to one layer or the other, so experimentalists must be able to identify the compartment they are studying. Here, we present current knowledge of the functional anatomy of the meninges, particularly as it appears in intravital imaging, and review their role as a gateway between the brain, blood, and lymphatics, drawing on information that is scattered among works on different pathologies.
Collapse
Affiliation(s)
- Jonathan A Coles
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davis Building, University of Glasgow, Glasgow, G12 8TA, United Kingdom.
| | - Elmarie Myburgh
- Centre for Immunology and Infection Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom
| | - James M Brewer
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Sir Graeme Davis Building, University of Glasgow, Glasgow, G12 8TA, United Kingdom
| | - Paul G McMenamin
- Department of Anatomy & Developmental Biology, School of Biomedical and Psychological Sciences and Monash Biomedical Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, 10 Chancellor's Walk, Clayton, Victoria, 3800, Australia
| |
Collapse
|
14
|
Ginhoux F, Guilliams M, Naik SH. Editorial: Dendritic Cell and Macrophage Nomenclature and Classification. Front Immunol 2016; 7:168. [PMID: 27199991 PMCID: PMC4852170 DOI: 10.3389/fimmu.2016.00168] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/18/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Martin Guilliams
- Laboratory of Immunoregulation, VIB Inflammation Research Center, Ghent University, Ghent, Belgium; Department of Respiratory Medicine, Ghent University, Ghent, Belgium
| | - Shalin H Naik
- Molecular Medicine Division, The Walter + Eliza Hall Institute of Medical Research, The University of Melbourne, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|