251
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Mari B, Crestani B. Dysregulated balance of lung macrophage populations in idiopathic pulmonary fibrosis revealed by single-cell RNA seq: an unstable "ménage-à-trois". Eur Respir J 2019; 54:54/2/1901229. [PMID: 31439723 DOI: 10.1183/13993003.01229-2019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 06/26/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Bernard Mari
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | - Bruno Crestani
- Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, INSERM U1152, Université de Paris, LABEX Inflamex, DHU FIRE, Paris, France
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252
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Lloyd CM, Saglani S. Opening the Window of Immune Opportunity: Treating Childhood Asthma. Trends Immunol 2019; 40:786-798. [PMID: 31420279 DOI: 10.1016/j.it.2019.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022]
Abstract
Asthma is an increasingly common childhood disease and although most patients can control their symptoms with medication, a proportion experience life-threatening symptoms. The advent of novel biologic therapies represents a giant leap forward for asthma treatment, but efficacy is rarely tested in children. Recent mechanistic work in mice suggests that early life is a key period for immune development and, therefore, allergen sensitization. Although children with severe asthma experience significant comorbidities and are at increased risk for serious diseases such as chronic obstructive pulmonary disease as adults, no specific investigation into tailored treatment for young children with severe asthma exists. Here, we propose how new information regarding early life immunity could be used to inform modified treatments for children.
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Affiliation(s)
- Clare M Lloyd
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
| | - Sejal Saglani
- Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College, London, UK.
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253
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Scott CL, Guilliams M. Tissue Unit-ed: Lung Cells Team up to Drive Alveolar Macrophage Development. Cell 2019; 175:898-900. [PMID: 30388447 DOI: 10.1016/j.cell.2018.10.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Using single-cell RNA sequencing of both immune and non-immune cells in the developing lung, Cohen et al. map candidate cell-cell interactions during alveolar macrophage development. This revealed potential cross-talk between epithelial cells, ILC2s, basophils, and the developing macrophages, which were validated both in vitro and in vivo.
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Affiliation(s)
- Charlotte L Scott
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB-UGent Centre for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK.
| | - Martin Guilliams
- Laboratory of Myeloid Cell Ontogeny and Functional Specialization, VIB-UGent Centre for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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254
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Poczobutt JM, Eickelberg O. Defining the Cell Types That Drive Idiopathic Pulmonary Fibrosis Using Single-Cell RNA Sequencing. Am J Respir Crit Care Med 2019; 199:1454-1456. [PMID: 30715901 PMCID: PMC6580670 DOI: 10.1164/rccm.201901-0197ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Joanna M Poczobutt
- 1 Department of Medicine University of Colorado Anschutz Medical Campus Denver, Colorado
| | - Oliver Eickelberg
- 1 Department of Medicine University of Colorado Anschutz Medical Campus Denver, Colorado
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255
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Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB, Strunz M, Vieira Braga FA, Timens W, Koppelman GH, Budinger GRS, Burgess JK, Waghray A, van den Berge M, Theis FJ, Regev A, Kaminski N, Rajagopal J, Teichmann SA, Misharin AV, Nawijn MC. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. Am J Respir Cell Mol Biol 2019; 61:31-41. [PMID: 30995076 PMCID: PMC6604220 DOI: 10.1165/rcmb.2018-0416tr] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Lung disease accounts for every sixth death globally. Profiling the molecular state of all lung cell types in health and disease is currently revolutionizing the identification of disease mechanisms and will aid the design of novel diagnostic and personalized therapeutic regimens. Recent progress in high-throughput techniques for single-cell genomic and transcriptomic analyses has opened up new possibilities to study individual cells within a tissue, classify these into cell types, and characterize variations in their molecular profiles as a function of genetics, environment, cell-cell interactions, developmental processes, aging, or disease. Integration of these cell state definitions with spatial information allows the in-depth molecular description of cellular neighborhoods and tissue microenvironments, including the tissue resident structural and immune cells, the tissue matrix, and the microbiome. The Human Cell Atlas consortium aims to characterize all cells in the healthy human body and has prioritized lung tissue as one of the flagship projects. Here, we present the rationale, the approach, and the expected impact of a Human Lung Cell Atlas.
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Affiliation(s)
- Herbert B. Schiller
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Daniel T. Montoro
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Lukas M. Simon
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Emma L. Rawlins
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Maximilian Strunz
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Wim Timens
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, and
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - G. R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Janette K. Burgess
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Avinash Waghray
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Maarten van den Berge
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Fabian J. Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Department of Biology, Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts; and
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Jayaraj Rajagopal
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology
- Groningen Research Institute for Asthma and COPD at the University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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256
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Luecken MD, Theis FJ. Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol 2019; 15:e8746. [PMID: 31217225 PMCID: PMC6582955 DOI: 10.15252/msb.20188746] [Citation(s) in RCA: 976] [Impact Index Per Article: 195.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/15/2019] [Accepted: 04/03/2019] [Indexed: 12/21/2022] Open
Abstract
Single-cell RNA-seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single-cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up-to-date workflow to analyse one's data. Here, we detail the steps of a typical single-cell RNA-seq analysis, including pre-processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell- and gene-level downstream analysis. We formulate current best-practice recommendations for these steps based on independent comparison studies. We have integrated these best-practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github.com/theislab/single-cell-tutorial This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines.
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Affiliation(s)
- Malte D Luecken
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Mathematics, Technische Universität München, Garching bei München, Germany
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257
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Gu W, Ni Z, Tan YQ, Deng J, Zhang SJ, Lv ZC, Wang XJ, Chen T, Zhang Z, Hu Y, Jing ZC, Xu Q. Adventitial Cell Atlas of wt (Wild Type) and ApoE (Apolipoprotein E)-Deficient Mice Defined by Single-Cell RNA Sequencing. Arterioscler Thromb Vasc Biol 2019; 39:1055-1071. [PMID: 30943771 PMCID: PMC6553510 DOI: 10.1161/atvbaha.119.312399] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022]
Abstract
Objective- Vascular adventitia encompasses progenitors and is getting recognized as the major site of inflammation in early stage of atherosclerosis. However, the cellular atlas of the heterogeneous adventitial cells, the intercellular communication, the cellular response of adventitia to hyperlipidemia, and its contribution to atherosclerosis have been elusive. Approach and Results- Single-cell RNA sequencing was applied to wt (wild type) and ApoE (apolipoprotein E)-deficient aortic adventitia from 12-week-old C57BL/6J mice fed on normal laboratory diet with early stage of atherosclerosis. Unbiased clustering analysis revealed that the landscape of adventitial cells encompassed adventitial mesenchyme cells, immune cells (macrophages, T cells, and B cells), and some types of rare cells, for example, neuron, lymphatic endothelial cells, and innate lymphoid cells. Seurat clustering analysis singled out 6 nonimmune clusters with distinct transcriptomic profiles, in which there predominantly were stem/progenitor cell-like and proinflammatory population (Mesen II). In ApoE-deficient adventitia, resident macrophages were activated and related to increased myeloid cell infiltration in the adventitia. Cell communication analysis further elucidated enhanced interaction between a mesenchyme cluster and inflammatory macrophages in ApoE-deficient adventitia. In vitro transwell assay confirmed the proinflammatory role of SCA1+ (stem cell antigen 1 positive) Mesen II population with increased CCL2 (chemokine [C-C motif] ligand 2) secretion and thus increased capacity to attract immune cells in ApoE-deficient adventitia. Conclusions- Cell atlas defined by single-cell RNA sequencing depicted the heterogeneous cellular landscape of the adventitia and uncovered several types of cell populations. Furthermore, resident cell interaction with immune cells appears crucial at the early stage of atherosclerosis.
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Affiliation(s)
- Wenduo Gu
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
| | - Zhichao Ni
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
| | - Yuan-Qing Tan
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing (Y.-Q.T., S.-J.Z., Z.-C.L., X.-J.W., Z.-C.J.)
| | - Jiacheng Deng
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
| | - Si-Jin Zhang
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing (Y.-Q.T., S.-J.Z., Z.-C.L., X.-J.W., Z.-C.J.)
| | - Zi-Chao Lv
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing (Y.-Q.T., S.-J.Z., Z.-C.L., X.-J.W., Z.-C.J.)
| | - Xiao-Jian Wang
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing (Y.-Q.T., S.-J.Z., Z.-C.L., X.-J.W., Z.-C.J.)
| | - Ting Chen
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University, China (T.C., Q.X.)
| | - Zhongyi Zhang
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
| | - Yanhua Hu
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
| | - Zhi-Cheng Jing
- Key Laboratory of Pulmonary Vascular Medicine and FuWai Hospital, State Key Laboratory of Cardiovascular Disease, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing (Y.-Q.T., S.-J.Z., Z.-C.L., X.-J.W., Z.-C.J.)
| | - Qingbo Xu
- From the School of Cardiovascular Medicine and Sciences, King's College London British Heart Foundation Centre, United Kingdom (W.G., Z.N., J.D., Z.Z., Y.H., Q.X.)
- Department of Cardiology, The First Affiliated Hospital, Zhejiang University, China (T.C., Q.X.)
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258
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Abstract
Single-cell transcriptome profiling has enabled high-resolution analysis of cellular populations in tissues during development, health, and disease. Recent studies make innovative use of single-cell RNA sequencing (scRNAseq) to investigate mechanisms that allow immune cells to interact with tissue components in the lung during development and fibrotic lung disease.
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Affiliation(s)
- Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Surgery, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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259
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Schmitt P, Girard JP, Cayrol C. [Interleukin-33: from biology to potential treatments]. Med Sci (Paris) 2019; 35:440-451. [PMID: 31115327 DOI: 10.1051/medsci/2019078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Interleukin-33 is a member of the IL-1 cytokine family, expressed in the nucleus of endothelial cells and epithelial cells of barrier tissues. After cellular damage, IL-33 is released in the extracellular space and functions as an alarmin that alerts the immune system. IL-33 plays a critical role in type-2 innate immunity and allergic inflammation, by activating various target cells including mast cells and innate lymphoid cells that secrete high amounts of IL-5 and IL-13, two cytokines involved in allergic reactions. Recent studies suggest that IL-33 can also play other important roles, for example in homeostasis and during viral infection. It is implicated in numerous diseases, including allergic, inflammatory and infectious diseases and it constitutes a promising therapeutic target for treatment of severe asthma.
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Affiliation(s)
- Pauline Schmitt
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205, route de Narbonne, 31077 Toulouse, France
| | - Jean-Philippe Girard
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205, route de Narbonne, 31077 Toulouse, France
| | - Corinne Cayrol
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 205, route de Narbonne, 31077 Toulouse, France
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260
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Lakhdari O, Yamamura A, Hernandez GE, Anderson KK, Lund SJ, Oppong-Nonterah GO, Hoffman HM, Prince LS. Differential Immune Activation in Fetal Macrophage Populations. Sci Rep 2019; 9:7677. [PMID: 31118442 PMCID: PMC6531440 DOI: 10.1038/s41598-019-44181-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
Distinct macrophage subsets populate the developing embryo and fetus in distinct waves. However little is known about the functional differences between in utero macrophage populations or how they might contribute to fetal and neonatal immunity. Here we tested the innate immune response of mouse macrophages derived from the embryonic yolk sac and from fetal liver. When isolated from liver or lung, CD11bHI fetal liver derived macrophages responded to the TLR4 agonist LPS by expressing and releasing inflammatory cytokines. However F4/80HI macrophages from the yolk sac did not respond to LPS treatment. While differences in TLR4 expression did not appear to explain these data, F4/80HI macrophages had much lower NLRP3 inflammasome expression compared to CD11bHI macrophages. Gene expression profiling also demonstrated LPS-induced expression of inflammatory genes in CD11bHI macrophages, but not in F4/80HI cells. Genes expressed in LPS-treated CD11bHI macrophages were more likely to contain predicted NF-κB binding sites in their promoter regions. Our data show that CD11bHI macrophages derived from fetal liver are the major pro-inflammatory cells in the developing fetus. These findings could have important implications in better understanding the fetal inflammatory response and the unique features of neonatal immunity.
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Affiliation(s)
- Omar Lakhdari
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Asami Yamamura
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Gilberto E Hernandez
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Kathryn K Anderson
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Sean J Lund
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Gertrude O Oppong-Nonterah
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Hal M Hoffman
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA
| | - Lawrence S Prince
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, Rady Children's Hospital, San Diego, San Diego, CA, USA.
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261
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Zhang N, Zhang N, Xu Y, Li Z, Yan C, Mei K, Ding M, Ding S, Guan P, Qian L, Du C, Hu X. Molecularly Imprinted Materials for Selective Biological Recognition. Macromol Rapid Commun 2019; 40:e1900096. [PMID: 31111979 DOI: 10.1002/marc.201900096] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/16/2019] [Indexed: 12/11/2022]
Abstract
Molecular imprinting is an approach of generating imprinting cavities in polymer structures that are compatible with the target molecules. The cavities have memory for shape and chemical recognition, similar to the recognition mechanism of antigen-antibody in organisms. Their structures are also called biomimetic receptors or synthetic receptors. Owing to the excellent selectivity and unique structural predictability of molecularly imprinted materials (MIMs), practical MIMs have become a rapidly evolving research area providing key factors for understanding separation, recognition, and regenerative properties toward biological small molecules to biomacromolecules, even cell and microorganism. In this review, the characteristics, morphologies, and applicability of currently popular carrier materials for molecular imprinting, especially the fundamental role of hydrogels, porous materials, hierarchical nanoparticles, and 2D materials in the separation and recognition of biological templates are discussed. Moreover, through a series of case studies, emphasis is given on introducing imprinting strategies for biological templates with different molecular scales. In particular, the differences and connections between small molecular imprinting (bulk imprinting, "dummy" template imprinting, etc.), large molecular imprinting (surface imprinting, interfacial imprinting, etc.), and cell imprinting strategies are demonstrated in detail. Finally, future research directions are provided.
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Affiliation(s)
- Nan Zhang
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.,Department of Mechanical Engineering, National University of Singapore 9 Engineering Drive 1, 117575, Singapore
| | - Nan Zhang
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Yarong Xu
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Zhiling Li
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Chaoren Yan
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Kun Mei
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Minling Ding
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Shichao Ding
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA, 99164, USA
| | - Ping Guan
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
| | - Liwei Qian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, P. R. China
| | - Chunbao Du
- College of Chemistry and Chemical Engineering, Xi'an Shiyou University, Xi'an, 710065, P. R. China
| | - Xiaoling Hu
- School of Natural and Applied Science, Northwestern Polytechnical University, Xi'an, 710072, P. R. China
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262
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Keren-Shaul H, Kenigsberg E, Jaitin DA, David E, Paul F, Tanay A, Amit I. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat Protoc 2019; 14:1841-1862. [PMID: 31101904 DOI: 10.1038/s41596-019-0164-4] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/12/2019] [Indexed: 11/09/2022]
Abstract
Human tissues comprise trillions of cells that populate a complex space of molecular phenotypes and functions and that vary in abundance by 4-9 orders of magnitude. Relying solely on unbiased sampling to characterize cellular niches becomes infeasible, as the marginal utility of collecting more cells diminishes quickly. Furthermore, in many clinical samples, the relevant cell types are scarce and efficient processing is critical. We developed an integrated pipeline for index sorting and massively parallel single-cell RNA sequencing (MARS-seq2.0) that builds on our previously published MARS-seq approach. MARS-seq2.0 is based on >1 million cells sequenced with this pipeline and allows identification of unique cell types across different tissues and diseases, as well as unique model systems and organisms. Here, we present a detailed step-by-step procedure for applying the method. In the improved procedure, we combine sub-microliter reaction volumes, optimization of enzymatic mixtures and an enhanced analytical pipeline to substantially lower the cost, improve reproducibility and reduce well-to-well contamination. Data analysis combines multiple layers of quality assessment and error detection and correction, graphically presenting key statistics for library complexity, noise distribution and sequencing saturation. Importantly, our combined FACS and single-cell RNA sequencing (scRNA-seq) workflow enables intuitive approaches for depletion or enrichment of cell populations in a data-driven manner that is essential to efficient sampling of complex tissues. The experimental protocol, from cell sorting to a ready-to-sequence library, takes 2-3 d. Sequencing and processing the data through the analytical pipeline take another 1-2 d.
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Affiliation(s)
- Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.,Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Ephraim Kenigsberg
- Precision Immunology Institute, Icahn Institute for Data Science and Genomic Technology, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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263
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Low ambient humidity impairs barrier function and innate resistance against influenza infection. Proc Natl Acad Sci U S A 2019; 116:10905-10910. [PMID: 31085641 PMCID: PMC6561219 DOI: 10.1073/pnas.1902840116] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Influenza virus causes seasonal outbreaks in temperate regions, with an increase in disease and mortality in the winter months. Dry air combined with cold temperature is known to enable viral transmission. In this study, we asked whether humidity impacts the host response to influenza virus infections. Exposure of mice to low humidity conditions rendered them more susceptible to influenza disease. Mice housed in dry air had impaired mucociliary clearance, innate antiviral defense, and tissue repair function. Moreover, mice exposed to dry air were more susceptible to disease mediated by inflammasome caspases. Our study provides mechanistic insights for the seasonality of the influenza virus epidemics, whereby inhalation of dry air compromises the host’s ability to restrict influenza virus infection. In the temperate regions, seasonal influenza virus outbreaks correlate closely with decreases in humidity. While low ambient humidity is known to enhance viral transmission, its impact on host response to influenza virus infection and disease outcome remains unclear. Here, we showed that housing Mx1 congenic mice in low relative humidity makes mice more susceptible to severe disease following respiratory challenge with influenza A virus. We find that inhalation of dry air impairs mucociliary clearance, innate antiviral defense, and tissue repair. Moreover, disease exacerbated by low relative humidity was ameliorated in caspase-1/11–deficient Mx1 mice, independent of viral burden. Single-cell RNA sequencing revealed that induction of IFN-stimulated genes in response to viral infection was diminished in multiple cell types in the lung of mice housed in low humidity condition. These results indicate that exposure to dry air impairs host defense against influenza infection, reduces tissue repair, and inflicts caspase-dependent disease pathology.
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264
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Park J, Ivey MJ, Deana Y, Riggsbee KL, Sörensen E, Schwabl V, Sjöberg C, Hjertberg T, Park GY, Swonger JM, Rosengreen T, Morty RE, Ahlbrecht K, Tallquist MD. The Tcf21 lineage constitutes the lung lipofibroblast population. Am J Physiol Lung Cell Mol Physiol 2019; 316:L872-L885. [PMID: 30675802 PMCID: PMC6589586 DOI: 10.1152/ajplung.00254.2018] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/29/2018] [Accepted: 01/18/2019] [Indexed: 01/18/2023] Open
Abstract
Transcription factor 21 (Tcf21) is a basic helix-loop-helix transcription factor required for mesenchymal development in several organs. Others have demonstrated that Tcf21 is expressed in embryonic lung mesenchyme and that loss of Tcf21 results in a pulmonary hypoplasia phenotype. Although recent single-cell transcriptome analysis has described multiple mesenchymal cell types in the lung, few have characterized the Tcf21 expressing population. To explore the Tcf21 mesenchymal lineage, we traced Tcf21-expressing cells during embryogenesis and in the adult. Our results showed that Tcf21 progenitor cells at embryonic day (E)11.5 generated a subpopulation of fibroblasts and lipofibroblasts and a limited number of smooth muscle cells. After E15.5, Tcf21 progenitor cells exclusively become lipofibroblasts and interstitial fibroblasts. Lipid metabolism genes were highly expressed in perinatal and adult Tcf21 lineage cells. Overexpression of Tcf21 in primary neonatal lung fibroblasts led to increases in intracellular neutral lipids, suggesting a regulatory role for Tcf21 in lipofibroblast function. Collectively, our results reveal that Tcf21 expression after E15.5 delineates the lipofibroblast and a population of interstitial fibroblasts. The Tcf21 inducible Cre mouse line provides a novel method for identifying and manipulating the lipofibroblast.
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Affiliation(s)
- Juwon Park
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Malina J Ivey
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Yanik Deana
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Kara L Riggsbee
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Emelie Sörensen
- Department of Medicine and Health Sciences, Linköping University , Linköping , Sweden
| | - Veronika Schwabl
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Caroline Sjöberg
- Department of Medicine and Health Sciences, Linköping University , Linköping , Sweden
| | - Tilda Hjertberg
- Department of Medicine and Health Sciences, Linköping University , Linköping , Sweden
| | - Ga Young Park
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Jessica M Swonger
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Taylor Rosengreen
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
| | - Rory E Morty
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, German Center for Lung Research , Bad Nauheim , Germany
| | - Katrin Ahlbrecht
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, German Center for Lung Research , Bad Nauheim , Germany
| | - Michelle D Tallquist
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii at Manoa , Honolulu, Hawaii
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265
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Skinnider MA, Squair JW, Foster LJ. Evaluating measures of association for single-cell transcriptomics. Nat Methods 2019; 16:381-386. [DOI: 10.1038/s41592-019-0372-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/25/2019] [Accepted: 03/05/2019] [Indexed: 12/13/2022]
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266
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Roan F, Obata-Ninomiya K, Ziegler SF. Epithelial cell-derived cytokines: more than just signaling the alarm. J Clin Invest 2019; 129:1441-1451. [PMID: 30932910 DOI: 10.1172/jci124606] [Citation(s) in RCA: 273] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The epithelial cell-derived cytokines thymic stromal lymphopoietin (TSLP), IL-33, and IL-25 are central regulators of type 2 immunity, which drives a broad array of allergic responses. Often characterized as "alarmins" that are released by the barrier epithelium in response to external insults, these epithelial cell-derived cytokines were initially thought to act only early in allergic inflammation. Indeed, TSLP can condition dendritic cells to initiate type 2 responses, and IL-33 may influence susceptibility to asthma through its role in establishing the immune environment in the perinatal lungs. However, TSLP, IL-33, and IL-25 all regulate a broad spectrum of innate immune cell populations and are particularly potent in eliciting and activating type 2 innate lymphoid cells (ILC2s) that may act throughout allergic inflammation. Recent data suggest that a TSLP/ILC axis may mediate steroid resistance in asthma. Recent identification of memory Th2 cell subsets that are characterized by high receptor expression for TSLP, IL-33, and IL-25 further supports a role for these cytokines in allergic exacerbations. There is therefore growing interest in developing biologics that target TSLP, IL-33, and IL-25. This Review provides an overview of TSLP, IL-33, and IL-25 and the development of blocking antibodies that target these epithelial cell-derived cytokines.
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Affiliation(s)
- Florence Roan
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA.,Division of Allergy and Infectious Diseases and
| | | | - Steven F Ziegler
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA.,Department of Immunology, University of Washington, Seattle, Washington, USA
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267
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Zhang Y, Liu F. Multidimensional Single-Cell Analyses in Organ Development and Maintenance. Trends Cell Biol 2019; 29:477-486. [PMID: 30928527 DOI: 10.1016/j.tcb.2019.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 02/12/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022]
Abstract
The revolution of single-cell analysis tools in epigenomics, transcriptomics, lineage tracing, and transcriptome-scale RNA imaging, has boosted our understanding of the underlying molecular mechanisms during organ development and maintenance. Application of these tools enables the multidimensional study of organs, from cell atlas profiling, spatial organization, to cell-cell interaction. Here, we discuss recent progress in employing multidimensional single-cell analyses to address fundamental questions related to the development and maintenance of hematopoietic organs, brain and lung, which will also help provide insights into a better understanding of relevant diseases.
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Affiliation(s)
- Yifan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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268
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Yu J, Peng J, Chi H. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity. ACTA ACUST UNITED AC 2019; 15:19-29. [PMID: 32789283 DOI: 10.1016/j.coisb.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The immune system is a highly complex and dynamic biological system. It operates through intracellular molecular networks and intercellular (cell-cell) interaction networks. Systems immunology is an emerging discipline that applies systems biology approaches of integrating high-throughput multi-omics measurements with computational network modeling to better understand immunity at various scales. In this review, we summarize key omics technologies and computational approaches used for immunological studies at both population and single-cell levels. We highlight the hidden driver analysis based on data-driven networks and comment on the potential of translating systems immunology discoveries to immunotherapy of cancer and other human diseases.
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Affiliation(s)
- Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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269
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Revolutionizing immunology with single-cell RNA sequencing. Cell Mol Immunol 2019; 16:242-249. [PMID: 30796351 DOI: 10.1038/s41423-019-0214-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 01/30/2019] [Indexed: 12/30/2022] Open
Abstract
The immune system is composed of a complex hierarchy of cell types that protect the organism against disease and maintain homeostasis. Identifying heterogeneity of immune cells is the key to understanding the immune system. Advanced single-cell RNA sequencing (scRNA-seq) technologies are revolutionizing our ability to study immunology. By measuring transcriptomes at the single-cell level, scRNA-seq enables identification of cellular heterogeneity in far greater detail than conventional methods. In this review, we introduce the existing scRNA-seq technologies and present their strengths and weaknesses. We also discuss potential applications and future innovations of scRNA-seq in immunology.
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270
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Blecher-Gonen R, Bost P, Hilligan KL, David E, Salame TM, Roussel E, Connor LM, Mayer JU, Bahar Halpern K, Tóth B, Itzkovitz S, Schwikowski B, Ronchese F, Amit I. Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity. Cell Syst 2019; 8:109-121.e6. [PMID: 30772378 DOI: 10.1016/j.cels.2019.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/20/2018] [Accepted: 01/14/2019] [Indexed: 12/11/2022]
Abstract
The immune system generates pathogen-tailored responses. The precise innate immune cell types and pathways that direct robust adaptive immune responses have not been fully characterized. By using fluorescent pathogens combined with massively parallel single-cell RNA-seq, we comprehensively characterized the initial 48 h of the innate immune response to diverse pathogens. We found that across all pathogens tested, most of the lymph node cell types and states showed little pathogen specificity. In contrast, the rare antigen-positive cells displayed pathogen-specific transcriptional programs as early as 24 h after immunization. In addition, mycobacteria activated a specific NK-driven IFNγ response. Depletion of NK cells and IFNγ showed that IFNγ initiated a monocyte-specific signaling cascade, leading to the production of major chemokines and cytokines that promote Th1 development. Our systems immunology approach sheds light on early events in innate immune responses and may help further development of safe and efficient vaccines.
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Affiliation(s)
| | - Pierre Bost
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; Systems Biology Group, Center for Bioinformatics, Biostatistics, and Integrative Biology (C3BI) and USR 3756, Institut Pasteur CNRS, Paris 75015, France; Sorbonne Universite, Complexite du vivant, F-75005 Paris, France
| | - Kerry L Hilligan
- Malaghan Institute of Medical Research, Wellington 6201, New Zealand; Department of Pathology and Molecular Medicine, University of Otago Wellington, Wellington 6201, New Zealand
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tomer Meir Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elsa Roussel
- Malaghan Institute of Medical Research, Wellington 6201, New Zealand
| | - Lisa M Connor
- Malaghan Institute of Medical Research, Wellington 6201, New Zealand
| | - Johannes U Mayer
- Malaghan Institute of Medical Research, Wellington 6201, New Zealand
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Beáta Tóth
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Benno Schwikowski
- Systems Biology Group, Center for Bioinformatics, Biostatistics, and Integrative Biology (C3BI) and USR 3756, Institut Pasteur CNRS, Paris 75015, France
| | - Franca Ronchese
- Malaghan Institute of Medical Research, Wellington 6201, New Zealand.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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271
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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]
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272
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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]
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273
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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]
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274
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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]
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275
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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]
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276
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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]
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277
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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]
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278
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Loering S, Cameron GJM, Starkey MR, Hansbro PM. Lung development and emerging roles for type 2 immunity. J Pathol 2019; 247:686-696. [PMID: 30506724 DOI: 10.1002/path.5211] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/06/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
Abstract
Lung development is a complex process mediated through the interaction of multiple cell types, factors and mediators. In mice, it starts as early as embryonic day 9 and continues into early adulthood. The process can be separated into five different developmental stages: embryonic, pseudoglandular, canalicular, saccular, and alveolar. Whilst lung bud formation and branching morphogenesis have been studied extensively, the mechanisms of alveolarisation are incompletely understood. Aberrant lung development can lead to deleterious consequences for respiratory health such as bronchopulmonary dysplasia (BPD), a disease primarily affecting preterm neonates, which is characterised by increased pulmonary inflammation and disturbed alveolarisation. While the deleterious effects of type 1-mediated inflammatory responses on lung development have been well established, the role of type 2 responses in postnatal lung development remains poorly understood. Recent studies indicate that type 2-associated immune cells, such as group 2 innate lymphoid cells and alveolar macrophages, are increased in number during postnatal alveolarisation. Here, we present the current state of understanding of the postnatal stages of lung development and the key cell types and mediators known to be involved. We also provide an overview of how stem cells are involved in lung development and regeneration, and the negative influences of respiratory infections. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Svenja Loering
- Priority Research Center's GrowUpWell and Healthy Lungs, School of Biomedical Sciences and Pharmacy, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Guy J M Cameron
- Priority Research Center's GrowUpWell and Healthy Lungs, School of Biomedical Sciences and Pharmacy, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Malcolm R Starkey
- Priority Research Center's GrowUpWell and Healthy Lungs, School of Biomedical Sciences and Pharmacy, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Philip M Hansbro
- Priority Research Center's GrowUpWell and Healthy Lungs, School of Biomedical Sciences and Pharmacy, The University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Center for Inflammation, Centenary Institute and The School of Life Sciences, University of Technology, Sydney, New South Wales, Australia
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279
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Lung Macrophages: Multifunctional Regulator Cells for Metastatic Cells. Int J Mol Sci 2018; 20:ijms20010116. [PMID: 30597969 PMCID: PMC6337639 DOI: 10.3390/ijms20010116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 12/29/2022] Open
Abstract
Metastasis is responsible for most of the cancer-associated deaths and proceeds through multiple steps. Several lines of evidence have established an indispensable involvement of macrophages present at the primary tumor sites in various steps of metastasis, from primary tumor growth to its intravasation into circulation. The lungs encompass a large, dense vascular area and, therefore, are vulnerable to metastasis, particularly, hematogenous ones arising from various types of neoplasms. Lung tissues constitutively contain several types of tissue-resident macrophages and circulating monocytes to counteract potentially harmful exogenous materials, which directly reach through the airway. Recent advances have provided an insight into the ontogenetic, phenotypic, and functional heterogeneity of these lung macrophage and monocyte populations, under resting and inflammatory conditions. In this review, we discuss the ontogeny, trafficking dynamics, and functions of these pulmonary macrophages and monocytes and their potential roles in lung metastasis and measures to combat lung metastasis by targeting these populations.
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280
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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.
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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
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