101
|
Corbett DC, Fabyan WB, Grigoryan B, O'Connor CE, Johansson F, Batalov I, Regier MC, DeForest CA, Miller JS, Stevens KR. Thermofluidic heat exchangers for actuation of transcription in artificial tissues. SCIENCE ADVANCES 2020; 6:6/40/eabb9062. [PMID: 32998880 PMCID: PMC7527231 DOI: 10.1126/sciadv.abb9062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/13/2020] [Indexed: 05/12/2023]
Abstract
Spatial patterns of gene expression in living organisms orchestrate cell decisions in development, homeostasis, and disease. However, most methods for reconstructing gene patterning in 3D cell culture and artificial tissues are restricted by patterning depth and scale. We introduce a depth- and scale-flexible method to direct volumetric gene expression patterning in 3D artificial tissues, which we call "heat exchangers for actuation of transcription" (HEAT). This approach leverages fluid-based heat transfer from printed networks in the tissues to activate heat-inducible transgenes expressed by embedded cells. We show that gene expression patterning can be tuned both spatially and dynamically by varying channel network architecture, fluid temperature, fluid flow direction, and stimulation timing in a user-defined manner and maintained in vivo. We apply this approach to activate the 3D positional expression of Wnt ligands and Wnt/β-catenin pathway regulators, which are major regulators of development, homeostasis, regeneration, and cancer throughout the animal kingdom.
Collapse
Affiliation(s)
- Daniel C Corbett
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Wesley B Fabyan
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Bagrat Grigoryan
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Colleen E O'Connor
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Fredrik Johansson
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Ivan Batalov
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Mary C Regier
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Jordan S Miller
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Kelly R Stevens
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
102
|
Gómez-Gaviro MV, Sanderson D, Ripoll J, Desco M. Biomedical Applications of Tissue Clearing and Three-Dimensional Imaging in Health and Disease. iScience 2020; 23:101432. [PMID: 32805648 PMCID: PMC7452225 DOI: 10.1016/j.isci.2020.101432] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Three-dimensional (3D) optical imaging techniques can expand our knowledge about physiological and pathological processes that cannot be fully understood with 2D approaches. Standard diagnostic tests frequently are not sufficient to unequivocally determine the presence of a pathological condition. Whole-organ optical imaging requires tissue transparency, which can be achieved by using tissue clearing procedures enabling deeper image acquisition and therefore making possible the analysis of large-scale biological tissue samples. Here, we review currently available clearing agents, methods, and their application in imaging of physiological or pathological conditions in different animal and human organs. We also compare different optical tissue clearing methods discussing their advantages and disadvantages and review the use of different 3D imaging techniques for the visualization and image acquisition of cleared tissues. The use of optical tissue clearing resources for large-scale biological tissues 3D imaging paves the way for future applications in translational and clinical research.
Collapse
Affiliation(s)
- Maria Victoria Gómez-Gaviro
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain.
| | - Daniel Sanderson
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Jorge Ripoll
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Manuel Desco
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain; Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| |
Collapse
|
103
|
Schega Y, Flinner N, Hansmann ML. Quantitative assessment of optical clearing methods on formalin-fixed human lymphoid tissue. Pathol Res Pract 2020; 216:153136. [PMID: 32823235 DOI: 10.1016/j.prp.2020.153136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 12/20/2022]
Abstract
Rising interest in three-dimensional volume imaging of biological tissues for diagnostic and research purposes, calls for appropriate optical clearing methods as an indispensable requirement for high-resolution imaging on a cellular level. In recent years, many clearing protocols have emerged, though most of them focus on murine central nervous tissue. Peripheral organs or tissues of human origin have only been investigated sparsely. Therefore, we tested eight established clearing methods (BABB, Ce3D, CUBIC, ECi, ChemScale, ChemScaleQQ5, SeeDB2 and PACT) on formaldehyde-fixed human tonsils. This application-oriented taxonomy can help researchers restrict the space of their survey on clearing techniques for lymphatic tissue as it provides information on each method in regard to its efficacy, clearing speed, preservation of fluorescence labelling, toxicity, expenditure and monetary costs. We found that all of the applied clearing protocols could render the sample tissues transparent. Ce3D and PACT achieved the highest degrees of tissue transparency. Since it requires less preparing and processing time and is lower in toxicity, we recommend Ce3D for the clearing of human lymphoid tissue.
Collapse
Affiliation(s)
- Yvonne Schega
- University Clinic Frankfurt am Main, Department of Pathology, Goethe University, Germany
| | - Nadine Flinner
- Frankfurt Institute for Advanced Studies (FIAS), Germany; Goethe University, Frankfurt am Main, Department for Informatics, Germany
| | - Martin-Leo Hansmann
- University Clinic Frankfurt am Main, Department of Pathology, Goethe University, Germany; Frankfurt Institute for Advanced Studies (FIAS), Germany.
| |
Collapse
|
104
|
Sample Preparation of Optically Cleared Liver Tissue to Identify Liver Macrophages Using 3D Microscopy. Methods Mol Biol 2020. [PMID: 32607883 DOI: 10.1007/978-1-0716-0704-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Histology, or the study of tissue microanatomy, is essential to understanding the in situ function of varying cell types within an organ. How cells are distributed throughout organs provides an indication of how they interact with other cells and structures within the organ microanatomy. The tortuous shape and large size of liver macrophages limits the value of standard tissue thickness of 5-10 μm. As a result, imaging of specimens ideally thicker than 100 μm is necessary to investigate the liver microanatomy and the how macrophages are distributed within this. Modern methods of microscopy, such as confocal and light sheet microscopy, allow for the analysis of tissue specimens of a thickness well beyond 100 μm in the z-dimension. Liver tissue is an opaque tissue, and as a result, different techniques are needed to ameliorate light diffraction within the tissue. These techniques, in conjunction with antibody staining and refractive index matching of the tissue, have allowed researchers to image liver tissue specimens of more than 100 μm thickness. Two of these techniques are modified versions of the clearing methods known as clearing-enhanced 3D (Ce3D) and fructose, urea, and glycerol for imaging (FUnGI). Here, we discuss the steps involved in preparing tissue specimens for optically clearing tissue using Ce3D and FUnGI for subsequent analysis of the distribution of macrophages in three dimensions using a confocal microscope.
Collapse
|
105
|
Liu CY, Polk DB. Cellular maps of gastrointestinal organs: getting the most from tissue clearing. Am J Physiol Gastrointest Liver Physiol 2020; 319:G1-G10. [PMID: 32421359 PMCID: PMC7468759 DOI: 10.1152/ajpgi.00075.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of modern methods to induce optical transparency ("clearing") in biological tissues has enabled the three-dimensional (3D) reconstruction of intact organs at cellular resolution. New capabilities in visualization of rare cellular events, long-range interactions, and irregular structures will facilitate novel studies in the alimentary tract and gastrointestinal systems. The tubular geometry of the alimentary tract facilitates large-scale cellular reconstruction of cleared tissue without specialized microscopy setups. However, with the rapid pace of development of clearing agents and current relative paucity of research groups in the gastrointestinal field using these techniques, it can be daunting to incorporate tissue clearing into experimental workflows. Here, we give some advice and describe our own experience bringing tissue clearing and whole mount reconstruction into our laboratory's investigations. We present a brief overview of the chemical concepts that underpin tissue clearing, what sorts of questions whole mount imaging can answer, how to choose a clearing agent, an example of how to clear and image alimentary tissue, and what to do after obtaining the image. This short review will encourage other gastrointestinal researchers to consider how utilizing tissue clearing and creating 3D "maps" of tissue might deepen the impact of their studies.
Collapse
Affiliation(s)
- Cambrian Y. Liu
- 1Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Saban Research Institute Children’s Hospital Los Angeles, Los Angeles, California
| | - D. Brent Polk
- 1Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Saban Research Institute Children’s Hospital Los Angeles, Los Angeles, California,2Department of Pediatrics, Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California Los Angeles, California
| |
Collapse
|
106
|
Kinstlinger IS, Saxton SH, Calderon GA, Ruiz KV, Yalacki DR, Deme PR, Rosenkrantz JE, Louis-Rosenberg JD, Johansson F, Janson KD, Sazer DW, Panchavati SS, Bissig KD, Stevens KR, Miller JS. Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates. Nat Biomed Eng 2020; 4:916-932. [DOI: 10.1038/s41551-020-0566-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/01/2020] [Indexed: 12/11/2022]
|
107
|
Tan Y, Chiam CPL, Zhang Y, Tey HL, Ng LG. Research Techniques Made Simple: Optical Clearing and Three-Dimensional Volumetric Imaging of Skin Biopsies. J Invest Dermatol 2020; 140:1305-1314.e1. [PMID: 32571496 DOI: 10.1016/j.jid.2020.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/31/2020] [Accepted: 04/27/2020] [Indexed: 11/25/2022]
Abstract
Skin histology is traditionally carried out using two-dimensional tissue sections, which allows for rapid staining, but these sections cannot accurately represent three-dimensional structures in skin such as nerves, vasculature, hair follicles, and sebaceous glands. Although it may be ideal to image skin in a three-dimensional manner, it is technically challenging to image deep into tissue because of light scattering from collagen fibrils in the dermis and refractive index mismatch owing to the presence of differing biological materials such as cytoplasm, and lipids in the skin. Different optical clearing methods have been developed recently, making it possible to render tissues transparent using different approaches. Here, we discuss the steps involved in tissue preparation for three-dimensional volumetric imaging and provide a brief overview of the different optical clearing methods as well as different imaging modalities for three-dimensional imaging.
Collapse
Affiliation(s)
- Yingrou Tan
- Department of Research, National Skin Centre, Singapore; Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore
| | - Carolyn Pei Lyn Chiam
- School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, United Kingdom
| | - Yuning Zhang
- Faculty of Science, National University of Singapore, Singapore
| | - Hong Liang Tey
- Department of Research, National Skin Centre, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore.
| |
Collapse
|
108
|
Hildebrand S, Schueth A, Wangenheim KV, Mattheyer C, Pampaloni F, Bratzke H, Roebroeck AF, Galuske RAW. hFRUIT: An optimized agent for optical clearing of DiI-stained adult human brain tissue. Sci Rep 2020; 10:9950. [PMID: 32561795 PMCID: PMC7305111 DOI: 10.1038/s41598-020-66999-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 05/28/2020] [Indexed: 11/09/2022] Open
Abstract
Here, we describe a new immersion-based clearing method suitable for optical clearing of thick adult human brain samples while preserving its lipids and lipophilic labels such as 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI). This clearing procedure is simple, easy to implement, and allowed for clearing of 5 mm thick human brain tissue samples within 12 days. Furthermore, we show for the first time the advantageous effect of the Periodate-Lysine-Paraformaldehyde (PLP) fixation as compared to the more commonly used 4% paraformaldehyde (PFA) on clearing performance.
Collapse
Affiliation(s)
- Sven Hildebrand
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, 6229 EV, Maastricht, the Netherlands.
| | - Anna Schueth
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, 6229 EV, Maastricht, the Netherlands
| | - Klaus von Wangenheim
- Department of Systemic Neurophysiology, Technische Universität Darmstadt, Schnittspahnstraße 3, Darmstadt, 64287, Germany
| | - Christian Mattheyer
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Faculty 15 Biological Sciences, Institute for Cell Biology and Neuroscience, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Francesco Pampaloni
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Faculty 15 Biological Sciences, Institute for Cell Biology and Neuroscience, Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, Frankfurt am Main, D-60438, Germany
| | - Hansjürgen Bratzke
- Johann Wolfgang Goethe-Universität Frankfurt am Main, Institute for Forensic Medicine, Kennedy Allee 104, 60596, Frankfurt am Main, Germany
| | - Alard F Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht University, 6229 EV, Maastricht, the Netherlands
| | - Ralf A W Galuske
- Department of Systemic Neurophysiology, Technische Universität Darmstadt, Schnittspahnstraße 3, Darmstadt, 64287, Germany.
| |
Collapse
|
109
|
Ruhland MK, Roberts EW, Cai E, Mujal AM, Marchuk K, Beppler C, Nam D, Serwas NK, Binnewies M, Krummel MF. Visualizing Synaptic Transfer of Tumor Antigens among Dendritic Cells. Cancer Cell 2020; 37:786-799.e5. [PMID: 32516589 PMCID: PMC7671443 DOI: 10.1016/j.ccell.2020.05.002] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/07/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Generation of tumor-infiltrating lymphocytes begins when tumor antigens reach the lymph node (LN) to stimulate T cells, yet we know little of how tumor material is disseminated among the large variety of antigen-presenting dendritic cell (DC) subsets in the LN. Here, we demonstrate that tumor proteins are carried to the LN within discrete vesicles inside DCs and are then transferred among DC subsets. A synapse is formed between interacting DCs and vesicle transfer takes place in the absence of free exosomes. DCs -containing vesicles can uniquely activate T cells, whereas DCs lacking them do not. Understanding this restricted sharing of tumor identity provides substantial room for engineering better anti-tumor immunity.
Collapse
Affiliation(s)
- Megan K Ruhland
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Edward W Roberts
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - En Cai
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Adriana M Mujal
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kyle Marchuk
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA; Biological Imaging Development CoLab, University of California, San Francisco, CA 94143, USA
| | - Casey Beppler
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - David Nam
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nina K Serwas
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mikhail Binnewies
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew F Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
110
|
Wills JW, Robertson J, Summers HD, Miniter M, Barnes C, Hewitt RE, Keita ÅV, Söderholm JD, Rees P, Powell JJ. Image-Based Cell Profiling Enables Quantitative Tissue Microscopy in Gastroenterology. Cytometry A 2020; 97:1222-1237. [PMID: 32445278 DOI: 10.1002/cyto.a.24042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022]
Abstract
Immunofluorescence microscopy is an essential tool for tissue-based research, yet data reporting is almost always qualitative. Quantification of images, at the per-cell level, enables "flow cytometry-type" analyses with intact locational data but achieving this is complex. Gastrointestinal tissue, for example, is highly diverse: from mixed-cell epithelial layers through to discrete lymphoid patches. Moreover, different species (e.g., rat, mouse, and humans) and tissue preparations (paraffin/frozen) are all commonly studied. Here, using field-relevant examples, we develop open, user-friendly methodology that can encompass these variables to provide quantitative tissue microscopy for the field. Antibody-independent cell labeling approaches, compatible across preparation types and species, were optimized. Per-cell data were extracted from routine confocal micrographs, with semantic machine learning employed to tackle densely packed lymphoid tissues. Data analysis was achieved by flow cytometry-type analyses alongside visualization and statistical definition of cell locations, interactions and established microenvironments. First, quantification of Escherichia coli passage into human small bowel tissue, following Ussing chamber incubations exemplified objective quantification of rare events in the context of lumen-tissue crosstalk. Second, in rat jejenum, precise histological context revealed distinct populations of intraepithelial lymphocytes between and directly below enterocytes enabling quantification in context of total epithelial cell numbers. Finally, mouse mononuclear phagocyte-T cell interactions, cell expression and significant spatial cell congregations were mapped to shed light on cell-cell communication in lymphoid Peyer's patch. Accessible, quantitative tissue microscopy provides a new window-of-insight to diverse questions in gastroenterology. It can also help combat some of the data reproducibility crisis associated with antibody technologies and over-reliance on qualitative microscopy. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.
Collapse
Affiliation(s)
- John W Wills
- Biominerals Research, Cambridge University Department of Veterinary Medicine, School of Biological Sciences, Cambridge, UK
| | - Jack Robertson
- Biominerals Research, Cambridge University Department of Veterinary Medicine, School of Biological Sciences, Cambridge, UK
| | - Huw D Summers
- Centre for Nanohealth, Swansea University College of Engineering, Swansea, UK
| | - Michelle Miniter
- Biominerals Research, Cambridge University Department of Veterinary Medicine, School of Biological Sciences, Cambridge, UK
| | - Claire Barnes
- Centre for Nanohealth, Swansea University College of Engineering, Swansea, UK
| | - Rachel E Hewitt
- Biominerals Research, Cambridge University Department of Veterinary Medicine, School of Biological Sciences, Cambridge, UK
| | - Åsa V Keita
- Department of Surgery and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Johan D Söderholm
- Department of Surgery and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Paul Rees
- Centre for Nanohealth, Swansea University College of Engineering, Swansea, UK.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA
| | - Jonathan J Powell
- Biominerals Research, Cambridge University Department of Veterinary Medicine, School of Biological Sciences, Cambridge, UK
| |
Collapse
|
111
|
Kelly HG, Tan HX, Juno JA, Esterbauer R, Ju Y, Jiang W, Wimmer VC, Duckworth BC, Groom JR, Caruso F, Kanekiyo M, Kent SJ, Wheatley AK. Self-assembling influenza nanoparticle vaccines drive extended germinal center activity and memory B cell maturation. JCI Insight 2020; 5:136653. [PMID: 32434990 DOI: 10.1172/jci.insight.136653] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/15/2020] [Indexed: 01/10/2023] Open
Abstract
Protein-based, self-assembling nanoparticles elicit superior immunity compared with soluble protein vaccines, but the immune mechanisms underpinning this effect remain poorly defined. Here, we investigated the immunogenicity of a prototypic ferritin-based nanoparticle displaying influenza hemagglutinin (HA) in mice and macaques. Vaccination of mice with HA-ferritin nanoparticles elicited higher serum antibody titers and greater protection against experimental influenza challenge compared with soluble HA protein. Germinal centers in the draining lymph nodes were expanded and persistent following HA-ferritin vaccination, with greater deposition of antigen that colocalized with follicular dendritic cells. Our findings suggest that a highly ordered and repetitive antigen array may directly drive germinal centers through a B cell-intrinsic mechanism that does not rely on ferritin-specific T follicular helper cells. In contrast to mice, enhanced immunogenicity of HA-ferritin was not observed in pigtail macaques, where antibody titers and lymph node immunity were comparable to soluble vaccination. An improved understanding of factors that drive nanoparticle vaccine immunogenicity in small and large animal models will facilitate the clinical development of nanoparticle vaccines for broad and durable protection against diverse pathogens.
Collapse
Affiliation(s)
- Hannah G Kelly
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Jennifer A Juno
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Robyn Esterbauer
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and
| | - Yi Ju
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and.,Department of Chemical Engineering, University of Melbourne, Parkville, Victoria, Australia
| | - Wenbo Jiang
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Brigette C Duckworth
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Frank Caruso
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and.,Department of Chemical Engineering, University of Melbourne, Parkville, Victoria, Australia
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Stephen J Kent
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and.,Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Adam K Wheatley
- Department of Microbiology and Immunology, University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and
| |
Collapse
|
112
|
Ueda HR, Dodt HU, Osten P, Economo MN, Chandrashekar J, Keller PJ. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron 2020; 106:369-387. [PMID: 32380050 PMCID: PMC7213014 DOI: 10.1016/j.neuron.2020.03.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/11/2020] [Accepted: 03/04/2020] [Indexed: 01/12/2023]
Abstract
Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.
Collapse
Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, The University of Tokyo, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN BDR, Suita, Osaka 565-0871, Japan.
| | - Hans-Ulrich Dodt
- Department of Bioelectronics, FKE, Vienna University of Technology-TU Wien, Vienna, Austria; Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Michael N Economo
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| |
Collapse
|
113
|
Liu T, Yang L, Han X, Ding X, Li J, Yang J. Local sympathetic innervations modulate the lung innate immune responses. SCIENCE ADVANCES 2020; 6:eaay1497. [PMID: 32426489 PMCID: PMC7220323 DOI: 10.1126/sciadv.aay1497] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 05/14/2023]
Abstract
Local immunity of the lung needs to be under tight control. However, how efferent neural signals influence lung immunity remains incompletely understood. Here, we report the development of a modified iDISCO-based protocol, iDISCO(ace), for whole-tissue 3D assessment of neural innervations and immune reactions in intact, unsectioned lung tissues. We observed that genetic, pharmacologic, or surgical removal of local sympathetic innervations promoted LPS-elicited innate immune response in the lung. Also, sympathetic ablation enhanced IL-33-elicited type 2 innate immunity. We further show that the sympathetic neurotransmitter norepinephrine, or specific agonists of the β2-adrenergic receptor, can inhibit the LPS- or IL-33-elicited immune response in a cell-intrinsic manner. Moreover, genetic deletion of the β2-adrenergic receptor produced immunomodulatory effects similar to those observed with sympathetic ablation. Together, this study elucidates the critical function of local sympathetic innervations in negatively modulating the lung innate immune responses.
Collapse
Affiliation(s)
- Tingting Liu
- Center for Life Sciences, Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lu Yang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiangli Han
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaofan Ding
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiali Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jing Yang
- Center for Life Sciences, Peking University, Beijing 100871, China
- School of Life Sciences, Peking University, Beijing 100871, China
- IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China
- Corresponding author.
| |
Collapse
|
114
|
Lee BJ, Mace EM. From stem cell to immune effector: how adhesion, migration, and polarity shape T-cell and natural killer cell lymphocyte development in vitro and in vivo. Mol Biol Cell 2020; 31:981-991. [PMID: 32352896 PMCID: PMC7346728 DOI: 10.1091/mbc.e19-08-0424] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/10/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022] Open
Abstract
Lymphocyte development is a complex and coordinated pathway originating from pluripotent stem cells during embryogenesis and continuing even as matured lymphocytes are primed and educated in adult tissue. Hematopoietic stem cells develop in a specialized niche that includes extracellular matrix and supporting stromal and endothelial cells that both maintain stem cell pluripotency and enable the generation of differentiated cells. Cues for lymphocyte development include changes in integrin-dependent cell motility and adhesion which ultimately help to determine cell fate. The capacity of lymphocytes to adhere and migrate is important for modulating these developmental signals both by regulating the cues that the cell receives from the local microenvironment as well as facilitating the localization of precursors to tissue niches throughout the body. Here we consider how changing migratory and adhesive phenotypes contribute to human natural killer (NK)- and T-cell development as they undergo development from precursors to mature, circulating cells and how our understanding of this process is informed by in vitro models of T- and NK cell generation.
Collapse
Affiliation(s)
- Barclay J. Lee
- Department of Bioengineering, Rice University, Houston, TX 77005
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032
| |
Collapse
|
115
|
Stoltzfus CR, Filipek J, Gern BH, Olin BE, Leal JM, Wu Y, Lyons-Cohen MR, Huang JY, Paz-Stoltzfus CL, Plumlee CR, Pöschinger T, Urdahl KB, Perro M, Gerner MY. CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues. Cell Rep 2020; 31:107523. [PMID: 32320656 PMCID: PMC7233132 DOI: 10.1016/j.celrep.2020.107523] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 12/21/2022] Open
Abstract
Recently developed approaches for highly multiplexed imaging have revealed complex patterns of cellular positioning and cell-cell interactions with important roles in both cellular- and tissue-level physiology. However, tools to quantitatively study cellular patterning and tissue architecture are currently lacking. Here, we develop a spatial analysis toolbox, the histo-cytometric multidimensional analysis pipeline (CytoMAP), which incorporates data clustering, positional correlation, dimensionality reduction, and 2D/3D region reconstruction to identify localized cellular networks and reveal features of tissue organization. We apply CytoMAP to study the microanatomy of innate immune subsets in murine lymph nodes (LNs) and reveal mutually exclusive segregation of migratory dendritic cells (DCs), regionalized compartmentalization of SIRPα- dermal DCs, and preferential association of resident DCs with select LN vasculature. The findings provide insights into the organization of myeloid cells in LNs and demonstrate that CytoMAP is a comprehensive analytics toolbox for revealing features of tissue organization in imaging datasets.
Collapse
Affiliation(s)
- Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jakub Filipek
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Benjamin H Gern
- Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Brandy E Olin
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Joseph M Leal
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Yajun Wu
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | | | - Jessica Y Huang
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | | | | | - Thomas Pöschinger
- Roche Innovation Center Munich, Pharmaceutical Research & Early Development (pRED), Discovery Pharmacology, Nonnenwald 2, 82377 Penzberg, Germany
| | - Kevin B Urdahl
- Department of Immunology, University of Washington, Seattle, WA 98109, USA; Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Mario Perro
- Roche Innovation Center Zurich, Pharmaceutical Research & Early Development (pRED), Wagistrasse 10, 8952 Schlieren, Switzerland
| | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA 98109, USA.
| |
Collapse
|
116
|
Garriock RJ, Chalamalasetty RB, Zhu J, Kennedy MW, Kumar A, Mackem S, Yamaguchi TP. A dorsal-ventral gradient of Wnt3a/β-catenin signals controls mouse hindgut extension and colon formation. Development 2020; 147:dev.185108. [PMID: 32156757 DOI: 10.1242/dev.185108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/19/2020] [Indexed: 12/20/2022]
Abstract
Despite the importance of Wnt signaling for adult intestinal stem cell homeostasis and colorectal cancer, relatively little is known about its role in colon formation during embryogenesis. The development of the colon starts with the formation and extension of the hindgut. We show that Wnt3a is expressed in the caudal embryo in a dorsal-ventral (DV) gradient across all three germ layers, including the hindgut. Using genetic and lineage-tracing approaches, we describe novel dorsal and ventral hindgut domains, and show that ventrolateral hindgut cells populate the majority of the colonic epithelium. A Wnt3a-β-catenin-Sp5/8 pathway, which is active in the dorsal hindgut endoderm, is required for hindgut extension and colon formation. Interestingly, the absence of Wnt activity in the ventral hindgut is crucial for proper hindgut morphogenesis, as ectopic stabilization of β-catenin in the ventral hindgut via gain- or loss-of-function mutations in Ctnnb1 or Apc, respectively, leads to severe colonic hyperplasia. Thus, the DV Wnt gradient is required to coordinate growth between dorsal and ventral hindgut domains to regulate the extension of the hindgut that leads to colon formation.
Collapse
Affiliation(s)
- Robert J Garriock
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Ravindra B Chalamalasetty
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - JianJian Zhu
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Mark W Kennedy
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Amit Kumar
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Susan Mackem
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| | - Terry P Yamaguchi
- Center for Cancer Research, Cancer and Developmental Biology Laboratory, Cell Signaling in Vertebrate Development Section, NCI-Frederick, NIH, Frederick, MD 21702, USA
| |
Collapse
|
117
|
Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
Collapse
Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| |
Collapse
|
118
|
Tan WCC, Nerurkar SN, Cai HY, Ng HHM, Wu D, Wee YTF, Lim JCT, Yeong J, Lim TKH. Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy. Cancer Commun (Lond) 2020; 40:135-153. [PMID: 32301585 PMCID: PMC7170662 DOI: 10.1002/cac2.12023] [Citation(s) in RCA: 289] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 12/17/2022] Open
Abstract
Conventional immunohistochemistry (IHC) is a widely used diagnostic technique in tissue pathology. However, this technique is associated with a number of limitations, including high inter-observer variability and the capacity to label only one marker per tissue section. This review details various highly multiplexed techniques that have emerged to circumvent these constraints, allowing simultaneous detection of multiple markers on a single tissue section and the comprehensive study of cell composition, cellular functional and cell-cell interactions. Among these techniques, multiplex Immunohistochemistry/Immunofluorescence (mIHC/IF) has emerged to be particularly promising. mIHC/IF provides high-throughput multiplex staining and standardized quantitative analysis for highly reproducible, efficient and cost-effective tissue studies. This technique has immediate potential for translational research and clinical practice, particularly in the era of cancer immunotherapy.
Collapse
Affiliation(s)
- Wei Chang Colin Tan
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | | | - Hai Yun Cai
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | - Harry Ho Man Ng
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
- Duke‐NUS Medical SchoolSingapore169856Singapore
| | - Duoduo Wu
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore169856Singapore
| | - Yu Ting Felicia Wee
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR)Singapore169856Singapore
| | - Joe Yeong
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
- Institute of Molecular Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR)Singapore169856Singapore
- Singapore Immunology NetworkAgency of Science (SIgN)Technology and Research (A*STAR)Singapore169856Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical PathologySingapore General HospitalSingapore169856Singapore
| |
Collapse
|
119
|
Zhu J, Yu T, Li Y, Xu J, Qi Y, Yao Y, Ma Y, Wan P, Chen Z, Li X, Gong H, Luo Q, Zhu D. MACS: Rapid Aqueous Clearing System for 3D Mapping of Intact Organs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903185. [PMID: 32328422 PMCID: PMC7175264 DOI: 10.1002/advs.201903185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/16/2020] [Indexed: 05/21/2023]
Abstract
Tissue optical clearing techniques have provided important tools for large-volume imaging. Aqueous-based clearing methods are known for good fluorescence preservation and scalable size maintenance, but are limited by long incubation time, insufficient clearing performance, or requirements for specialized devices. Additionally, few clearing methods are compatible with widely used lipophilic dyes while maintaining high clearing performance. Here, to address these issues, m-xylylenediamine (MXDA) is firstly introduced into tissue clearing and used to develop a rapid, highly efficient aqueous clearing method with robust lipophilic dyes compatibility, termed MXDA-based Aqueous Clearing System (MACS). MACS can render whole adult brains highly transparent within 2.5 days and is also applicable for other intact organs. Meanwhile, MACS possesses ideal compatibility with multiple probes, especially for lipophilic dyes. MACS achieves 3D imaging of the intact neural structures labeled by various techniques. Combining MACS with DiI labeling, MACS allows reconstruction of the detailed vascular structures of various organs and generates 3D pathology of glomeruli tufts in healthy and diabetic kidneys. Therefore, MACS provides a useful method for 3D mapping of intact tissues and is expected to facilitate morphological, physiological, and pathological studies of various organs.
Collapse
Affiliation(s)
- Jingtan Zhu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Tingting Yu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yusha Li
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Jianyi Xu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yisong Qi
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yingtao Yao
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Yilin Ma
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Peng Wan
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Zhilong Chen
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Xiangning Li
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Hui Gong
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Qingming Luo
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| | - Dan Zhu
- Britton Chance Center for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- MoE Key Laboratory for Biomedical PhotonicsHuazhong University of Science and TechnologyWuhan430074China
| |
Collapse
|
120
|
Pincus AB, Adhikary S, Lebold KM, Fryer AD, Jacoby DB. Optogenetic Control of Airway Cholinergic Neurons In Vivo. Am J Respir Cell Mol Biol 2020; 62:423-429. [PMID: 31899655 PMCID: PMC7110977 DOI: 10.1165/rcmb.2019-0378ma] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/03/2020] [Indexed: 01/21/2023] Open
Abstract
Dysregulation of airway nerves leads to airway hyperreactivity, a hallmark of asthma. Although changes to nerve density and phenotype have been described in asthma, the relevance of these changes to nerve function has not been investigated due to anatomical limitations where afferent and efferent nerves run in the same nerve trunk, making it difficult to assess their independent contributions. We developed a unique and accessible system to activate specific airway nerves to investigate their function in mouse models of airway disease. We describe a method to specifically activate cholinergic neurons using light, resulting in immediate, measurable increases in airway inflation pressure and decreases in heart rate. Expression of light-activated channelrhodopsin 2 in these neurons is governed by Cre expression under the endogenous choline acetyltransferase promoter, and we describe a method to decrease variability in channelrhodopsin expression in future experiments. Optogenetic activation of specific subsets of airway neurons will be useful for studying the functional relevance of other observed changes, such as changes to nerve morphology and protein expression, across many airway diseases, and may be used to study the function of subpopulations of autonomic neurons in lungs and other organs.
Collapse
Affiliation(s)
- Alexandra B. Pincus
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Sweta Adhikary
- Vollum Institute, Oregon Health and Science University, Portland, Oregon
| | - Katherine M. Lebold
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Allison D. Fryer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - David B. Jacoby
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| |
Collapse
|
121
|
Lloyd-Lewis B. Multidimensional Imaging of Mammary Gland Development: A Window Into Breast Form and Function. Front Cell Dev Biol 2020; 8:203. [PMID: 32296702 PMCID: PMC7138012 DOI: 10.3389/fcell.2020.00203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/09/2020] [Indexed: 12/14/2022] Open
Abstract
An in-depth appreciation of organ form and function relies on the ability to image intact tissues across multiple scales. Difficulties associated with imaging deep within organs, however, can preclude high-resolution multidimensional imaging of live and fixed tissues. This is particularly challenging in the mammary gland, where the epithelium lies deeply encased within a stromal matrix. Recent advances in deep-tissue and live imaging methodologies are increasingly facilitating the visualization of complex cellular structures within their native environment. Alongside, refinements in optical tissue clearing and immunostaining methods are enabling 3D fluorescence imaging of whole organs at unprecedented resolutions. Collectively, these methods are illuminating the dynamic biological processes underlying tissue morphogenesis, homeostasis, and disease. This review provides a snapshot of the current and state-of-the-art multidimensional imaging techniques applied to the postnatal mammary gland, illustrating how these approaches have revealed important new insights into mammary gland ductal development and lactation. Continual evolution of multidimensional image acquisition and analysis methods will undoubtedly offer further insights into mammary gland biology that promises to shed new light on the perturbations leading to breast cancer.
Collapse
Affiliation(s)
- Bethan Lloyd-Lewis
- School of Cellular and Molecular Medicine, Biomedical Sciences Building, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
122
|
Husna N, Gascoigne NRJ, Tey HL, Ng LG, Tan Y. Reprint of "Multi-modal image cytometry approach - From dynamic to whole organ imaging". Cell Immunol 2020; 350:104086. [PMID: 32169249 DOI: 10.1016/j.cellimm.2020.104086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022]
Abstract
Optical imaging is a valuable tool to visualise biological processes in the context of the tissue. Each imaging modality provides the biologist with different types of information - cell dynamics and migration over time can be tracked with time-lapse imaging (e.g. intra-vital imaging); an overview of whole tissues can be acquired using optical clearing in conjunction with light sheet microscopy; finer details such as cellular morphology and fine nerve tortuosity can be imaged at higher resolution using the confocal microscope. Multi-modal imaging combined with image cytometry - a form of quantitative analysis of image datasets - provides an objective basis for comparing between sample groups. Here, we provide an overview of technical aspects to look out for in an image cytometry workflow, and discuss issues related to sample preparation, image post-processing and analysis for intra-vital and whole organ imaging.
Collapse
Affiliation(s)
- Nazihah Husna
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, 8A Biomedical Grove, Singapore 138648, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Nicholas R J Gascoigne
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
| | - Hong Liang Tey
- National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 117597, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, 8A Biomedical Grove, Singapore 138648, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore.
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), A*STAR (Agency for Science, Technology and Research), Biopolis, 8A Biomedical Grove, Singapore 138648, Singapore; National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore.
| |
Collapse
|
123
|
Grant SM, Lou M, Yao L, Germain RN, Radtke AJ. The lymph node at a glance - how spatial organization optimizes the immune response. J Cell Sci 2020; 133:133/5/jcs241828. [PMID: 32144196 DOI: 10.1242/jcs.241828] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A hallmark of the mammalian immune system is its ability to respond efficiently to foreign antigens without eliciting an inappropriate response to self-antigens. Furthermore, a robust immune response requires the coordination of a diverse range of cells present at low frequencies within the host. This problem is solved, in part, by concentrating antigens, antigen-presenting cells and antigen-responsive cells in lymph nodes (LNs). Beyond housing these cell types in one location, LNs are highly organized structures consisting of pre-positioned cells within well-defined microanatomical niches. In this Cell Science at a Glance article and accompanying poster, we outline the key cellular populations and components of the LN microenvironment that are present at steady state and chronicle the dynamic changes in these elements following an immune response. This review highlights the LN as a staging ground for both innate and adaptive immune responses, while providing an elegant example of how structure informs function.
Collapse
Affiliation(s)
- Spencer M Grant
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Memorial Dr, Bethesda, MD 20892, USA
| | - Meng Lou
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Memorial Dr, Bethesda, MD 20892, USA
| | - Li Yao
- Science Education Department, Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Memorial Dr, Bethesda, MD 20892, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Memorial Dr, Bethesda, MD 20892, USA
| |
Collapse
|
124
|
Brady EL, Kirby MA, Olszewski E, Grosjean P, Johansson F, Davis J, Wang RK, Stevens KR. Guided vascularization in the rat heart leads to transient vessel patterning. APL Bioeng 2020; 4:016105. [PMID: 32161835 PMCID: PMC7058427 DOI: 10.1063/1.5122804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/10/2020] [Indexed: 12/29/2022] Open
Abstract
Recent progress in the production and maturation of iPSC-cardiomyocytes has facilitated major advances in building bioartificial heart tissue with functional cardiomyocytes. Despite this progress, vascularizing these constructs continues to be a barrier to clinical application. One emerging strategy for vascularization uses aligned "cords" of endothelial cells in tissue grafts to guide assembly of chimeric microvessels upon graft implantation. Here, we test whether this approach can guide vascularization of a bioartificial tissue implanted on the rat heart. We find that patterned cords of human endothelial cells anastomose and become perfused with host blood by 3 days post-implantation. Immunohistochemical staining confirmed that graft-derived micro-vessels persist in the patch for 7 days. Furthermore, we noted a shift in distribution of vessels in the patch from patterned cord-associated clustering at 3 days to a more diffuse distribution pattern at 7 days. This loss of patterning corresponded to an infiltration of CD68+ cells and an increase in collagen within the patch. Upon further engraftment of patches containing both cords and human cardiomyocytes, we identified human cardiomyocytes and graft derived vasculature at the time of explant. Our findings show that patterned endothelial cords guide transient vessel patterning on the rat heart. Our results also suggest that future work should be directed at further adapting vascularization strategies to the epicardial environment and add to an important emerging dialog in cardiac cell therapy that points to the need to characterize host response prior to or in parallel with efficacy studies.
Collapse
Affiliation(s)
| | - Mitchell A. Kirby
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | | | - Parker Grosjean
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Fredrik Johansson
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | | | | | | |
Collapse
|
125
|
Abstract
The influx and efflux of cells and antigens to and from the draining lymph nodes largely take place through the subcapsular, cortical and medullary sinus systems. Recent analyses in mice and humans have revealed unexpected diversity in the lymphatic endothelial cells, which form the distinct regions of the sinuses. As a semipermeable barrier, the lymphatic endothelial cells regulate the sorting of lymph-borne antigens to the lymph node parenchyma and can themselves serve as antigen-presenting cells. The leukocytes entering the lymph node via the sinus system and the lymphocytes egressing from the parenchyma migrate through the lymphatic endothelial cell layer. The sinus lymphatic endothelial cells also orchestrate the organogenesis of lymph nodes, and they undergo bidirectional signalling with other sinus-resident cells, such as subcapsular sinus macrophages, to generate a unique lymphatic niche. In this Review, we consider the structural and functional basis of how the lymph node sinus system coordinates immune responses under physiological conditions, and in inflammation and cancer.
Collapse
|
126
|
Abstract
In this study we have utilized an optical clearing method to allow visualization of a heretofore undescribed subpleural acinar structural organization in the mammalian lung. The clearing method enables visualization of the lung structure deep below the visceral pleura in intact inflated lungs. In addition to confirming previous observations that the immediate subpleural alveoli are uniform in appearance, we document for the first time that the subpleural lung parenchyma is much more uniformly organized than the internal parenchyma. Specifically, we report that below the surface layer of alveoli, there is a striking parallel arrangement of alveolar ducts that all run perpendicular to the visceral pleural surface. A three dimensional visualization of alveolar ducts allowed for a calculation of the average inner to outer duct diameter ratio of 0.53 in these subpleural ducts. This unique, self-organizing parallel duct structure likely impacts both elastic recoil and the transmission of tethering forces in healthy and diseased lungs.
Collapse
|
127
|
Nürnberg E, Vitacolonna M, Klicks J, von Molitor E, Cesetti T, Keller F, Bruch R, Ertongur-Fauth T, Riedel K, Scholz P, Lau T, Schneider R, Meier J, Hafner M, Rudolf R. Routine Optical Clearing of 3D-Cell Cultures: Simplicity Forward. Front Mol Biosci 2020; 7:20. [PMID: 32154265 PMCID: PMC7046628 DOI: 10.3389/fmolb.2020.00020] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/04/2020] [Indexed: 12/11/2022] Open
Abstract
Three-dimensional cell cultures, such as spheroids and organoids, serve as increasingly important models in fundamental and applied research and start to be used for drug screening purposes. Optical tissue clearing procedures are employed to enhance visualization of fluorescence-stained organs, tissues, and three-dimensional cell cultures. To get a more systematic overview about the effects and applicability of optical tissue clearing on three-dimensional cell cultures, we compared six different clearing/embedding protocols on seven types of spheroid- and chip-based three-dimensional cell cultures of approximately 300 μm in size that were stained with nuclear dyes, immunofluorescence, cell trackers, and cyan fluorescent protein. Subsequent whole mount confocal microscopy and semi-automated image analysis were performed to quantify the effects. Quantitative analysis included fluorescence signal intensity and signal-to-noise ratio as a function of z-depth as well as segmentation and counting of nuclei and immunopositive cells. In general, these analyses revealed five key points, which largely confirmed current knowledge and were quantified in this study. First, there was a massive variability of effects of different clearing protocols on sample transparency and shrinkage as well as on dye quenching. Second, all tested clearing protocols worked more efficiently on samples prepared with one cell type than on co-cultures. Third, z-compensation was imperative to minimize variations in signal-to-noise ratio. Fourth, a combination of sample-inherent cell density, sample shrinkage, uniformity of signal-to-noise ratio, and image resolution had a strong impact on data segmentation, cell counts, and relative numbers of immunofluorescence-positive cells. Finally, considering all mentioned aspects and including a wish for simplicity and speed of protocols - in particular, for screening purposes - clearing with 88% Glycerol appeared to be the most promising option amongst the ones tested.
Collapse
Affiliation(s)
- Elina Nürnberg
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany.,Zentralinstitut für Seelische Gesundheit, Department of Translational Brain Research, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Mario Vitacolonna
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Julia Klicks
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Elena von Molitor
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Tiziana Cesetti
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Florian Keller
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Roman Bruch
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | | | | | | | - Thorsten Lau
- Zentralinstitut für Seelische Gesundheit, Department of Translational Brain Research, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Julia Meier
- TIP Oncology, Merck Healthcare KGaA, Darmstadt, Germany
| | - Mathias Hafner
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Faculty of Biotechnology, Mannheim University of Applied Sciences, Mannheim, Germany
| |
Collapse
|
128
|
Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci 2020; 21:61-79. [PMID: 31896771 PMCID: PMC8121164 DOI: 10.1038/s41583-019-0250-1] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2019] [Indexed: 02/06/2023]
Abstract
State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.
Collapse
Affiliation(s)
- Hiroki R Ueda
- Department of Systems Pharmacology, University of Tokyo, Tokyo, Japan.
- Laboratory for Synthetic Biology, RIKEN BDR, Suita, Japan.
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University of Munich, Munich, Germany
- Institute of Tissue Engineering and Regenerative Medicine, Helmholtz Zentrum München, Neuherberg, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Eli & Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for NanoMedicine, Institute for Basic Science, Seoul, Republic of Korea
- Graduate Program of Nano Biomedical Engineering, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alain Chédotal
- Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- IT4Innovations, Technical University of Ostrava, Ostrava, Czech Republic
| | - Philipp J Keller
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| |
Collapse
|
129
|
Amodio D, Santilli V, Zangari P, Cotugno N, Manno EC, Rocca S, Rossi P, Cancrini C, Finocchi A, Chassiakos A, Petrovas C, Palma P. How to dissect the plasticity of antigen-specific immune response: a tissue perspective. Clin Exp Immunol 2020; 199:119-130. [PMID: 31626717 PMCID: PMC6954674 DOI: 10.1111/cei.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/01/2022] Open
Abstract
Generation of antigen-specific humoral responses following vaccination or infection requires the maturation and function of highly specialized immune cells in secondary lymphoid organs (SLO), such as lymph nodes or tonsils. Factors that orchestrate the dynamics of these cells are still poorly understood. Currently, experimental approaches that enable a detailed description of the function of the immune system in SLO have been mainly developed and optimized in animal models. Conversely, methodological approaches in humans are mainly based on the use of blood-associated material because of the challenging access to tissues. Indeed, only few studies in humans were able to provide a discrete description of the complex network of cytokines, chemokines and lymphocytes acting in tissues after antigenic challenge. Furthermore, even fewer data are currently available on the interaction occurring within the complex micro-architecture of the SLO. This information is crucial in order to design particular vaccination strategies, especially for patients affected by chronic and immune compromising medical conditions who are under-vaccinated or who respond poorly to immunizations. Analysis of immune cells in different human tissues by high-throughput technologies, able to obtain data ranging from gene signature to protein expression and cell phenotypes, is needed to dissect the peculiarity of each immune cell in a definite human tissue. The main aim of this review is to provide an in-depth description of the current available methodologies, proven evidence and future perspectives in the analysis of immune mechanisms following immunization or infections in SLO.
Collapse
Affiliation(s)
- D. Amodio
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - V. Santilli
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - P. Zangari
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - N. Cotugno
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - E. C. Manno
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - S. Rocca
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - P. Rossi
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - C. Cancrini
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - A. Finocchi
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - A. Chassiakos
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - C. Petrovas
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - P. Palma
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| |
Collapse
|
130
|
Matryba P, Sosnowska A, Wolny A, Bozycki L, Greig A, Grzybowski J, Stefaniuk M, Nowis D, Gołąb J. Systematic Evaluation of Chemically Distinct Tissue Optical Clearing Techniques in Murine Lymph Nodes. THE JOURNAL OF IMMUNOLOGY 2020; 204:1395-1407. [PMID: 31953352 DOI: 10.4049/jimmunol.1900847] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022]
Abstract
Activation of adaptive immunity is a complex process coordinated at multiple levels in both time and the three-dimensional context of reactive lymph nodes (LNs). Although microscopy-based visualization of its spatiotemporal dynamics unravels complexities of developing immune response, such approach is highly limited by light-obstructing nature of tissue components. Recently, tissue optical clearing (TOC) techniques were established to bypass this obstacle and now allow to image and quantify the entire murine organs with cellular resolution. However, the spectrum of TOC is represented by wide variety of chemically distinct methods, each having certain advantages and disadvantages that were unsatisfactorily compared for suitability to LNs clearing. In this study, we have systematically tested 13 typical TOC techniques and assessed their impact on a number of critical factors such as LN transparency, imaging depth, change in size, compatibility with proteinaceous fluorophores, immunostaining, H&E staining, and light-sheet fluorescence microscopy. Based on the detailed data specific to TOC process of murine LNs, we provide a reliable reference for most suitable methods in an application-dependent manner.
Collapse
Affiliation(s)
- Paweł Matryba
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland; .,Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Anna Sosnowska
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Artur Wolny
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Lukasz Bozycki
- Laboratory of Biochemistry of Lipids, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Alan Greig
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1 6DE, United Kingdom
| | - Jakub Grzybowski
- Department of Pathology, Medical University of Warsaw, 02-004 Warsaw, Poland
| | - Marzena Stefaniuk
- Laboratory of Neurobiology, BRAINCITY, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dominika Nowis
- Department of Genomic Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland; and.,Laboratory of Experimental Medicine, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Jakub Gołąb
- Department of Immunology, Medical University of Warsaw, 02-097 Warsaw, Poland;
| |
Collapse
|
131
|
Porter DDL, Morton PD. Clearing techniques for visualizing the nervous system in development, injury, and disease. J Neurosci Methods 2020; 334:108594. [PMID: 31945400 PMCID: PMC10674098 DOI: 10.1016/j.jneumeth.2020.108594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 01/05/2023]
Abstract
Modern clearing techniques enable high resolution visualization and 3D reconstruction of cell populations and their structural details throughout large biological samples, including intact organs and even entire organisms. In the past decade, these methods have become more tractable and are now being utilized to provide unforeseen insights into the complexities of the nervous system. While several iterations of optical clearing techniques have been developed, some are more suitable for specific applications than others depending on the type of specimen under study. Here we review findings from select studies utilizing clearing methods to visualize the developing, injured, and diseased nervous system within numerous model systems and species. We note trends and imbalances in the types of research questions being addressed with clearing methods across these fields in neuroscience. In addition, we discuss restrictions in applying optical clearing methods for postmortem tissue from humans and large animals and emphasize the lack in continuity between studies of these species. We aim for this review to serve as a key outline of available tissue clearing methods used successfully to address issues across neuronal development, injury/repair, and aging/disease.
Collapse
Affiliation(s)
- Demisha D L Porter
- Virginia Tech Graduate Program in Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Paul D Morton
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| |
Collapse
|
132
|
Salei N, Rambichler S, Salvermoser J, Papaioannou NE, Schuchert R, Pakalniškytė D, Li N, Marschner JA, Lichtnekert J, Stremmel C, Cernilogar FM, Salvermoser M, Walzog B, Straub T, Schotta G, Anders HJ, Schulz C, Schraml BU. The Kidney Contains Ontogenetically Distinct Dendritic Cell and Macrophage Subtypes throughout Development That Differ in Their Inflammatory Properties. J Am Soc Nephrol 2020; 31:257-278. [PMID: 31932472 DOI: 10.1681/asn.2019040419] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/20/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mononuclear phagocytes (MPs), including macrophages, monocytes, and dendritic cells (DCs), are phagocytic cells with important roles in immunity. The developmental origin of kidney DCs has been highly debated because of the large phenotypic overlap between macrophages and DCs in this tissue. METHODS We used fate mapping, RNA sequencing, flow cytometry, confocal microscopy, and histo-cytometry to assess the origin and phenotypic and functional properties of renal DCs in healthy kidney and of DCs after cisplatin and ischemia reperfusion-induced kidney injury. RESULTS Adult kidney contains at least four subsets of MPs with prominent Clec9a-expression history indicating a DC origin. We demonstrate that these populations are phenotypically, functionally, and transcriptionally distinct from each other. We also show these kidney MPs exhibit unique age-dependent developmental heterogeneity. Kidneys from newborn mice contain a prominent population of embryonic-derived MHCIInegF4/80hiCD11blow macrophages that express T cell Ig and mucin domain containing 4 (TIM-4) and MER receptor tyrosine kinase (MERTK). These macrophages are replaced within a few weeks after birth by phenotypically similar cells that express MHCII but lack TIM-4 and MERTK. MHCII+F4/80hi cells exhibit prominent Clec9a-expression history in adulthood but not early life, indicating additional age-dependent developmental heterogeneity. In AKI, MHCIInegF4/80hi cells reappear in adult kidneys as a result of MHCII downregulation by resident MHCII+F4/80hi cells, possibly in response to prostaglandin E2 (PGE2). RNA sequencing further suggests MHCII+F4/80hi cells help coordinate the recruitment of inflammatory cells during renal injury. CONCLUSIONS Distinct developmental programs contribute to renal DC and macrophage populations throughout life, which could have important implications for therapies targeting these cells.
Collapse
Affiliation(s)
- Natallia Salei
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Stephan Rambichler
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Johanna Salvermoser
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Nikos E Papaioannou
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Ronja Schuchert
- Medical Clinic and Polyclinic I and.,DZHK (Deutsches Zentrum für Herz-Kreislaufforschung [German Center for Cardiovascular Research]), Partner Site Munich Heart Alliance, Munich, Germany; and
| | - Dalia Pakalniškytė
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Na Li
- Division of Nephrology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shen Zhen, China.,Division of Nephrology, Medical Clinic and Polyclinic IV, University Hospital Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Julian A Marschner
- Division of Nephrology, Medical Clinic and Polyclinic IV, University Hospital Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Julia Lichtnekert
- Division of Nephrology, Medical Clinic and Polyclinic IV, University Hospital Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christopher Stremmel
- Medical Clinic and Polyclinic I and.,DZHK (Deutsches Zentrum für Herz-Kreislaufforschung [German Center for Cardiovascular Research]), Partner Site Munich Heart Alliance, Munich, Germany; and
| | | | - Melanie Salvermoser
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | - Barbara Walzog
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich.,Institute for Cardiovascular Physiology and Pathophysiology
| | | | - Gunnar Schotta
- Division of Molecular Biology.,Center for Integrated Protein Science Munich, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Martinsried, Germany
| | - Hans-Joachim Anders
- Division of Nephrology, Medical Clinic and Polyclinic IV, University Hospital Munich, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christian Schulz
- Medical Clinic and Polyclinic I and.,DZHK (Deutsches Zentrum für Herz-Kreislaufforschung [German Center for Cardiovascular Research]), Partner Site Munich Heart Alliance, Munich, Germany; and
| | - Barbara U Schraml
- Walter Brendel Centre of Experimental Medicine, University Hospital Munich, .,Institute for Cardiovascular Physiology and Pathophysiology
| |
Collapse
|
133
|
The neuropeptide VIP confers anticipatory mucosal immunity by regulating ILC3 activity. Nat Immunol 2019; 21:168-177. [DOI: 10.1038/s41590-019-0567-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/22/2019] [Indexed: 12/25/2022]
|
134
|
Matsumoto T, Wakefield L, Tarlow BD, Grompe M. In Vivo Lineage Tracing of Polyploid Hepatocytes Reveals Extensive Proliferation during Liver Regeneration. Cell Stem Cell 2019; 26:34-47.e3. [PMID: 31866222 DOI: 10.1016/j.stem.2019.11.014] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/06/2019] [Accepted: 11/21/2019] [Indexed: 12/22/2022]
Abstract
The identity of cellular populations that drive liver regeneration after injury is the subject of intense study, and the contributions of polyploid hepatocytes to organ regeneration and homeostasis have not been systematically assessed. Here, we developed a multicolor reporter allele system to genetically label and trace polyploid cells in situ. Multicolored polyploid hepatocytes undergo ploidy reduction and subsequent re-polyploidization after transplantation, providing direct evidence of the hepatocyte ploidy conveyor model. Marker segregation revealed that ploidy reduction rarely involves chromosome missegregation in vivo. We also traced polyploid hepatocytes in several different liver injury models and found robust proliferation in all settings. Importantly, ploidy reduction was seen in all injury models studied. We therefore conclude that polyploid hepatocytes have extensive regenerative capacity in situ and routinely undergo reductive mitoses during regenerative responses.
Collapse
Affiliation(s)
- Tomonori Matsumoto
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA; Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Leslie Wakefield
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Markus Grompe
- Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.
| |
Collapse
|
135
|
Dunn KW, Fu C, Ho DJ, Lee S, Han S, Salama P, Delp EJ. DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data. Sci Rep 2019; 9:18295. [PMID: 31797882 PMCID: PMC6892824 DOI: 10.1038/s41598-019-54244-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022] Open
Abstract
The scale of biological microscopy has increased dramatically over the past ten years, with the development of new modalities supporting collection of high-resolution fluorescence image volumes spanning hundreds of microns if not millimeters. The size and complexity of these volumes is such that quantitative analysis requires automated methods of image processing to identify and characterize individual cells. For many workflows, this process starts with segmentation of nuclei that, due to their ubiquity, ease-of-labeling and relatively simple structure, make them appealing targets for automated detection of individual cells. However, in the context of large, three-dimensional image volumes, nuclei present many challenges to automated segmentation, such that conventional approaches are seldom effective and/or robust. Techniques based upon deep-learning have shown great promise, but enthusiasm for applying these techniques is tempered by the need to generate training data, an arduous task, particularly in three dimensions. Here we present results of a new technique of nuclear segmentation using neural networks trained on synthetic data. Comparisons with results obtained using commonly-used image processing packages demonstrate that DeepSynth provides the superior results associated with deep-learning techniques without the need for manual annotation.
Collapse
Affiliation(s)
- Kenneth W Dunn
- Department of Medicine, Division of Nephrology Indiana University School of Medicine, 950 West Walnut St, R2-202, Indianapolis, IN, 46202, USA.
| | - Chichen Fu
- Video and Image Processing Laboratory, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - David Joon Ho
- Video and Image Processing Laboratory, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Soonam Lee
- Video and Image Processing Laboratory, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Shuo Han
- Video and Image Processing Laboratory, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Paul Salama
- Department of Electrical and Computer Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
| | - Edward J Delp
- Video and Image Processing Laboratory, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
136
|
Mayorca-Guiliani AE, Willacy O, Madsen CD, Rafaeva M, Elisabeth Heumüller S, Bock F, Sengle G, Koch M, Imhof T, Zaucke F, Wagener R, Sasaki T, Erler JT, Reuten R. Decellularization and antibody staining of mouse tissues to map native extracellular matrix structures in 3D. Nat Protoc 2019; 14:3395-3425. [DOI: 10.1038/s41596-019-0225-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/09/2019] [Indexed: 12/15/2022]
|
137
|
Serizawa T, Isotani A, Matsumura T, Nakanishi K, Nonaka S, Shibata S, Ikawa M, Okano H. Developmental analyses of mouse embryos and adults using a non-overlapping tracing system for all three germ layers. Development 2019; 146:dev.174938. [PMID: 31597657 DOI: 10.1242/dev.174938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 09/30/2019] [Indexed: 12/24/2022]
Abstract
Genetic lineage-tracing techniques are powerful tools for studying specific cell populations in development and pathogenesis. Previous techniques have mainly involved systems for tracing a single gene, which are limited in their ability to facilitate direct comparisons of the contributions of different cell lineages. We have developed a new combinatorial system for tracing all three germ layers using self-cleaving 2A peptides and multiple site-specific recombinases (SSRs). In the resulting TRiCK (TRiple Coloured germ layer Knock-in) mice, the three germ layers are conditionally and simultaneously labelled with distinct fluorescent proteins via embryogenesis. We show that previously reported ectopic expressions of lineage markers are the outcome of secondary gene expression. The results presented here also indicate that the commitment of caudal axial stem cells to neural or mesodermal fate proceeds without lineage fluctuations, contrary to the notion of their bi-potency. Moreover, we developed IMES, an optimized tissue clearing method that is highly compatible with a variety of fluorescent proteins and immunostaining, and the combined use of TRiCK mice and IMES can facilitate comprehensive analyses of dynamic contributions of all three germ layers.
Collapse
Affiliation(s)
- Takashi Serizawa
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ayako Isotani
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan.,Organ developmental engineering, Division of Biomedical Science, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takafumi Matsumura
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Katsuyuki Nakanishi
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shigenori Nonaka
- Spatiotemporal Regulations Group, Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, Aichi 444-8585, Japan.,Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shinsuke Shibata
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Masahito Ikawa
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| |
Collapse
|
138
|
Husna N, Gascoigne NR, Tey HL, Ng LG, Tan Y. Multi-modal image cytometry approach – From dynamic to whole organ imaging. Cell Immunol 2019; 344:103946. [DOI: 10.1016/j.cellimm.2019.103946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 12/27/2022]
|
139
|
Lee SSY, Bindokas VP, Lingen MW, Kron SJ. Nondestructive, multiplex three-dimensional mapping of immune infiltrates in core needle biopsy. J Transl Med 2019; 99:1400-1413. [PMID: 30401959 PMCID: PMC6502706 DOI: 10.1038/s41374-018-0156-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/18/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022] Open
Abstract
Enumeration of tumor-infiltrating lymphocytes (TILs) in H&E stained tissue sections has demonstrated limited value in predicting immune responses to cancer immunotherapy, likely reflecting the diversity of cell types and immune activation states among tumor infiltrates. Multiparametric flow cytometry enables robust phenotypic and functional analysis to distinguish suppression from activation, but tissue dissociation eliminates spatial context. Multiplex methods for immunohistochemistry (IHC) are emerging, but these interrogate only a single tissue section at a time. Here, we report transparent tissue tomography (T3) as a tool for three-dimensional (3D) imaging cytometry in the complex architecture of the tumor microenvironment, demonstrating multiplexed immunofluorescent analysis in core needle biopsies. Using T3 imaging, image processing and machine learning to map CD3+CD8+ cytotoxic T cells (CTLs) in whole core needle biopsies from Her2+ murine mammary tumors and human head and neck surgical specimens revealed marked inhomogeneity within single needle cores, confirmed by serial section IHC. Applying T3 imaging cytometry, we discovered a strong spatial correlation between CD3+CD8+ CTLs and microvasculature in the EGFR+ parenchyma, revealing significant differences among head and neck cancer patients. These results show that T3 offers simple and rapid access to three-dimensional and quantitative maps of the tumor microenvironment and immune infiltrate, offering a new diagnostic tool for personalized cancer immunotherapy.
Collapse
Affiliation(s)
- Steve Seung-Young Lee
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL.,Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL
| | | | - Mark W. Lingen
- Department of Pathology, The University of Chicago, Chicago, IL
| | - Stephen J. Kron
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL.,Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL.,Correspondence to:
| |
Collapse
|
140
|
Takeda A, Hollmén M, Dermadi D, Pan J, Brulois KF, Kaukonen R, Lönnberg T, Boström P, Koskivuo I, Irjala H, Miyasaka M, Salmi M, Butcher EC, Jalkanen S. Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils. Immunity 2019; 51:561-572.e5. [PMID: 31402260 DOI: 10.1016/j.immuni.2019.06.027] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/17/2019] [Accepted: 06/27/2019] [Indexed: 01/28/2023]
Abstract
Lymphatic vessels form a critical component in the regulation of human health and disease. While their functional significance is increasingly being recognized, the comprehensive heterogeneity of lymphatics remains uncharacterized. Here, we report the profiling of 33,000 lymphatic endothelial cells (LECs) in human lymph nodes (LNs) by single-cell RNA sequencing. Unbiased clustering revealed six major types of human LECs. LECs lining the subcapsular sinus (SCS) of LNs abundantly expressed neutrophil chemoattractants, whereas LECs lining the medullary sinus (MS) expressed a C-type lectin CD209. Binding of a carbohydrate Lewis X (CD15) to CD209 mediated neutrophil binding to the MS. The neutrophil-selective homing by MS LECs may retain neutrophils in the LN medulla and allow lymph-borne pathogens to clear, preventing their spread through LNs in humans. Our study provides a comprehensive characterization of LEC heterogeneity and unveils a previously undefined role for medullary LECs in human immunity.
Collapse
Affiliation(s)
- Akira Takeda
- MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Maija Hollmén
- MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Denis Dermadi
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Junliang Pan
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System and The Palo Alto Veterans Institute for Research, Palo Alto, CA, USA
| | - Kevin Francis Brulois
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Riina Kaukonen
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Tapio Lönnberg
- Turku Centre for Biotechnology, University of Turku, Turku, Finland
| | - Pia Boström
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - Ilkka Koskivuo
- Department of Plastic and General Surgery, Turku University Hospital, Turku, Finland
| | - Heikki Irjala
- Department of Otorhinolaryngology, Turku University Hospital and University of Turku, Finland
| | - Masayuki Miyasaka
- MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland; Interdisciplinary Program for Biomedical Sciences, Institute for Academic Initiatives, Osaka University, Suita, Japan
| | - Marko Salmi
- MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eugene C Butcher
- Laboratory of Immunology and Vascular Biology, Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Veterans Affairs Palo Alto Health Care System and The Palo Alto Veterans Institute for Research, Palo Alto, CA, USA
| | - Sirpa Jalkanen
- MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland.
| |
Collapse
|
141
|
Ramaglia V, Sheikh-Mohamed S, Legg K, Park C, Rojas OL, Zandee S, Fu F, Ornatsky O, Swanson EC, Pitt D, Prat A, McKee TD, Gommerman JL. Multiplexed imaging of immune cells in staged multiple sclerosis lesions by mass cytometry. eLife 2019; 8:48051. [PMID: 31368890 PMCID: PMC6707785 DOI: 10.7554/elife.48051] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/01/2019] [Indexed: 01/19/2023] Open
Abstract
Multiple sclerosis (MS) is characterized by demyelinated and inflammatory lesions in the brain and spinal cord that are highly variable in terms of cellular content. Here, we used imaging mass cytometry (IMC) to enable the simultaneous imaging of 15+ proteins within staged MS lesions. To test the potential for IMC to discriminate between different types of lesions, we selected a case with severe rebound MS disease activity after natalizumab cessation. With post-acquisition analysis pipelines we were able to: (1) Discriminate demyelinating macrophages from the resident microglial pool; (2) Determine which types of lymphocytes reside closest to blood vessels; (3) Identify multiple subsets of T and B cells, and (4) Ascertain dynamics of T cell phenotypes vis-à-vis lesion type and location. We propose that IMC will enable a comprehensive analysis of single-cell phenotypes, their functional states and cell-cell interactions in relation to lesion morphometry and demyelinating activity in MS patients. It takes an army of immune cells to defend the body against infection. But sometimes the body’s immune system mistakenly attacks its own cells and chronic inflammatory conditions develop. In multiple sclerosis – also known as “MS” – a horde of immune cells infiltrate the brain and spinal cord, forming lesions which strip nerve cells of their insultation, a protective fatty material called myelin. Nerve cells become damaged, scarred and exposed, and this interferes with messages between the brain and other parts of the body. Advanced imaging techniques have revolutionized the diagnosis of multiple sclerosis by capturing lesions as they develop in the brain and spinal cord. Researchers have also focused their efforts on understanding how immune cells activated in the blood stream invade the central nervous system. To better understand how a mistaken immune response leads to nerve damage in multiple sclerosis, a forensic examination of which immune cells accumulate in brain tissue to form lesions is needed. Standard techniques for analyzing whole tissue samples are however limited by design, capable of detecting only a few cell markers in one section of tissue. Ramaglia et al. have now validated a new imaging technique for looking at an array of cell types in brain tissue in a single sample. The technique – called imaging mass cytometry (or IMC for short) – was used to look at post-mortem brain tissue from a multiple sclerosis patient with an acute form of the illness. The tissue examined had multiple sclerosis lesions present. Different types of immune cells were simultaneously identified and characterized using a panel of antibodies which recognize the signature proteins each immune cell makes when active. The state of the underlying myelin content of the tissue was also characterized. The imaging approach could distinguish between the immune cells of the brain (known as resident microglia) and a type of white blood cell summoned as part of the immune response (infiltrating macrophages). The analysis showed that, in the particular patient examined, microglia are abundant in active lesions in multiple sclerosis; also, different subsets of white blood cells were detected. Measuring how far different immune cells had migrated from nearby blood vessels added insights as to how immune cells move through the brain and which cells may have arrived first. Altogether, Ramaglia et al. have shown that IMC can be used as a discovery tool to gain a deeper understanding of multiple sclerosis lesions and immune cells active in the inflamed brain. Further work will apply this now validated imaging approach to large cohorts of multiple sclerosis patients.
Collapse
Affiliation(s)
- Valeria Ramaglia
- Department of Immunology, University of Toronto, Toronto, Canada
| | | | - Karen Legg
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Calvin Park
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Olga L Rojas
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Stephanie Zandee
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Fred Fu
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | | | | | - David Pitt
- Department of Neurology, Yale School of Medicine, New Haven, United States
| | - Alexandre Prat
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Trevor D McKee
- STTARR Innovation Centre, University Health Network, Toronto, Canada
| | | |
Collapse
|
142
|
Glaser AK, Reder NP, Chen Y, Yin C, Wei L, Kang S, Barner LA, Xie W, McCarty EF, Mao C, Halpern AR, Stoltzfus CR, Daniels JS, Gerner MY, Nicovich PR, Vaughan JC, True LD, Liu JTC. Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. Nat Commun 2019; 10:2781. [PMID: 31273194 PMCID: PMC6609674 DOI: 10.1038/s41467-019-10534-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022] Open
Abstract
Recent advances in optical clearing and light-sheet microscopy have provided unprecedented access to structural and molecular information from intact tissues. However, current light-sheet microscopes have imposed constraints on the size, shape, number of specimens, and compatibility with various clearing protocols. Here we present a multi-immersion open-top light-sheet microscope that enables simple mounting of multiple specimens processed with a variety of clearing protocols, which will facilitate wide adoption by preclinical researchers and clinical laboratories. In particular, the open-top geometry provides unsurpassed versatility to interface with a wide range of accessory technologies in the future.
Collapse
Affiliation(s)
- Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Nicholas P Reder
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ye Chen
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Chengbo Yin
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Linpeng Wei
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Lindsey A Barner
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Weisi Xie
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Erin F McCarty
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Chenyi Mao
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Caleb R Stoltzfus
- Department of Immunology, University of Washington, Seattle, WA, 98109, USA
| | | | - Michael Y Gerner
- Department of Immunology, University of Washington, Seattle, WA, 98109, USA
| | | | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, 98195, USA
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, 98195, USA.
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
143
|
Panicle-Shaped Sympathetic Architecture in the Spleen Parenchyma Modulates Antibacterial Innate Immunity. Cell Rep 2019; 27:3799-3807.e3. [DOI: 10.1016/j.celrep.2019.05.082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/22/2019] [Accepted: 05/22/2019] [Indexed: 01/21/2023] Open
|
144
|
Chudnovskiy A, Pasqual G, Victora GD. Studying interactions between dendritic cells and T cells in vivo. Curr Opin Immunol 2019; 58:24-30. [PMID: 30884422 PMCID: PMC6927575 DOI: 10.1016/j.coi.2019.02.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 12/12/2022]
Abstract
Antigen presentation is the key first step in the establishment of an antigen-specific T cell response. Among professional antigen presenting cells (APCs), dendritic cells (DCs) are the major population responsible for the priming of both CD4+ and CD8+ naïve T cells. This priming requires physical interaction between the DC and the T cell; during which signals are exchanged that determine both the magnitude and the quality of the ensuing response. The nature of these signals varies widely depending on the nature of the antigen, the anatomical site in which they take place, and the phenotype of the antigen-presenting DC, making the study of the dynamics, microanatomical distribution and phenotypic variation of DCs a key part of our understanding of adaptive immunity. Here, we provide a brief survey of how our view of T cell activation by DCs has evolved over recent years as intravital multiphoton microscopy and other emerging technologies have expanded our ability to study these events in vivo.
Collapse
Affiliation(s)
- Aleksey Chudnovskiy
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
| | - Giulia Pasqual
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
145
|
Bossolani GDP, Pintelon I, Detrez JD, Buckinx R, Thys S, Zanoni JN, De Vos WH, Timmermans JP. Comparative analysis reveals Ce3D as optimal clearing method for in toto imaging of the mouse intestine. Neurogastroenterol Motil 2019; 31:e13560. [PMID: 30761698 DOI: 10.1111/nmo.13560] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 12/26/2018] [Accepted: 01/03/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND The intestinal wall has a complex topographical architecture. The multi-layered network of the enteric nervous system and its intercellular interactions are difficult to map using traditional section-based or whole-mount histology. With the advent of optical clearing techniques, it has become feasible to visualize intact tissue and organs in 3D. However, as yet, a gap still needs to be filled in that no in-depth analysis has been performed yet on the potential of different clearing techniques for the small intestine. AIM The goal of this study was to identify an optimal clearing protocol for in toto imaging of mouse intestinal tissue. METHODS Five aqueous-based clearing protocols (SeeDB2, CUBIC, ScaleS, Ce3D, and UbasM) and four organic reagent-based clearing protocols (3DISCO, iDISCO+, uDISCO, and Visikol® ) were assessed in segments of small intestine from CX3CR1GFP/GFP and wild-type mice. Following clearing, optical transparency, tissue morphology, green fluorescent protein (GFP) fluorescence retention, and compatibility with (immuno-)labeling were analyzed. KEY RESULTS All organic reagent-based clearing protocols-except for Visikol-rendered tissue highly transparent but led to substantial tissue shrinkage and deformation. Of the aqueous-based protocols, only Ce3D yielded full-thickness tissue transparency. In addition, Ce3D displayed excellent GFP retention and preservation of tissue morphology. CONCLUSIONS Ce3D emerged as a most efficient protocol for enabling rapid full-thickness 3D mapping of the mouse intestinal wall.
Collapse
Affiliation(s)
- Gleison D P Bossolani
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium.,Department of Morphological Sciences, State University of Maringá, Maringá, Brasil
| | - Isabel Pintelon
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Jan D Detrez
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Roeland Buckinx
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sofie Thys
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
146
|
High-dimensional cell-level analysis of tissues with Ce3D multiplex volume imaging. Nat Protoc 2019; 14:1708-1733. [DOI: 10.1038/s41596-019-0156-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/22/2019] [Indexed: 01/19/2023]
|
147
|
Jing D, Yi Y, Luo W, Zhang S, Yuan Q, Wang J, Lachika E, Zhao Z, Zhao H. Tissue Clearing and Its Application to Bone and Dental Tissues. J Dent Res 2019; 98:621-631. [PMID: 31009584 DOI: 10.1177/0022034519844510] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Opaqueness of animal tissue can be attributed mostly to light absorption and light scattering. In most noncleared tissue samples, confocal images can be acquired at no more than a 100-µm depth. Tissue-clearing techniques have emerged in recent years in the neuroscience field. Many tissue-clearing methods have been developed, and they all follow similar working principles. During the tissue-clearing process, chemical or physical treatments are applied to remove components blocking or scattering the light. Finally, samples are immersed in a designated clearing medium to achieve a uniform refractive index and to gain transparency. Once the transparency is reached, images can be acquired even at several millimeters of depth with high resolution. Tissue clearing has become an essential tool for neuroscientists to investigate the neural connectome or to analyze spatial information of various types of brain cells. Other than neural science research, tissue-clearing techniques also have applications for bone research. Several methods have been developed for clearing bones. Clearing treatment enables 3-dimensional imaging of bones without sectioning and provides important new insights that are difficult or impossible to acquire with conventional approaches. Application of tissue-clearing technique on dental research remains limited. This review will provide an overview of the recent literature related to the methods and application of various tissue-clearing methods. The following aspects will be covered: general principles for the tissue-clearing technique, current available methods for clearing bones and teeth, general principles of 3-dimensional imaging acquisition and data processing, applications of tissue clearing on studying biological processes within bones and teeth, and future directions for 3-dimensional imaging.
Collapse
Affiliation(s)
- D Jing
- 1 Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA.,2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Y Yi
- 1 Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA.,2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - W Luo
- 1 Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| | - S Zhang
- 2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Q Yuan
- 2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - J Wang
- 2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - E Lachika
- 3 Intelligent Imaging Innovations (3i), Denver, CO, USA
| | - Z Zhao
- 2 State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P.R. China
| | - H Zhao
- 1 Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
| |
Collapse
|
148
|
Teh YC, Ding JL, Ng LG, Chong SZ. Capturing the Fantastic Voyage of Monocytes Through Time and Space. Front Immunol 2019; 10:834. [PMID: 31040854 PMCID: PMC6476989 DOI: 10.3389/fimmu.2019.00834] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/29/2019] [Indexed: 02/02/2023] Open
Abstract
Monocytes are a subset of cells that are categorized together with dendritic cells (DCs) and macrophages in the mononuclear phagocyte system (MPS). Despite sharing several phenotypic and functional characteristics with MPS cells, monocytes are unique cells with the ability to function as both precursor and effector cells in their own right. Before the development of hematopoietic stem cells (HSCs) in utero, monocytes are derived from erythro-myeloid precursors (EMPs) in the fetal liver that are important for populating the majority of tissue resident macrophages. After birth, monocytes arise from bone marrow (BM)-derived HSCs and are released into the circulation upon their maturation, where they survey peripheral tissues and maintain endothelial integrity. Upon sensing of microbial breaches or inflammatory stimuli, monocytes migrate into tissues where their plasticity allows them to differentiate into cells that resemble macrophages or DCs according to the environmental niche. Alternatively, they may also migrate into tissues in the absence of inflammation and remain in an undifferentiated state where they perform homeostatic roles. As monocytes are typically on the move, the availability of intravital imaging approaches has provided further insights into their trafficking patterns in distinct tissue compartments. In this review, we outline the importance of understanding their functional behavior in the context of tissue compartments, and how these studies may contribute towards improved vaccine and future therapeutic strategies.
Collapse
Affiliation(s)
- Ye Chean Teh
- Functional Immune Imaging, Singapore Immunology Network (SIgN), ASTAR (Agency for Science, Technology and Research), Biopolis, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), Singapore, Singapore
| | - Jeak Ling Ding
- Department of Biological Sciences, National University of Singapore (NUS), Singapore, Singapore
| | - Lai Guan Ng
- Functional Immune Imaging, Singapore Immunology Network (SIgN), ASTAR (Agency for Science, Technology and Research), Biopolis, Singapore.,Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shu Zhen Chong
- Functional Immune Imaging, Singapore Immunology Network (SIgN), ASTAR (Agency for Science, Technology and Research), Biopolis, Singapore
| |
Collapse
|
149
|
Rios AC, Capaldo BD, Vaillant F, Pal B, van Ineveld R, Dawson CA, Chen Y, Nolan E, Fu NY, Jackling FC, Devi S, Clouston D, Whitehead L, Smyth GK, Mueller SN, Lindeman GJ, Visvader JE. Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging. Cancer Cell 2019; 35:618-632.e6. [PMID: 30930118 DOI: 10.1016/j.ccell.2019.02.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/31/2018] [Accepted: 02/26/2019] [Indexed: 12/31/2022]
Abstract
Breast tumors are inherently heterogeneous, but the evolving cellular organization through neoplastic progression is poorly understood. Here we report a rapid, large-scale single-cell resolution 3D imaging protocol based on a one-step clearing agent that allows visualization of normal tissue architecture and entire tumors at cellular resolution. Imaging of multicolor lineage-tracing models of breast cancer targeted to either basal or luminal progenitor cells revealed profound clonal restriction during progression. Expression profiling of clones arising in Pten/Trp53-deficient tumors identified distinct molecular signatures. Strikingly, most clones harbored cells that had undergone an epithelial-to-mesenchymal transition, indicating widespread, inherent plasticity. Hence, an integrative pipeline that combines lineage tracing, 3D imaging, and clonal RNA sequencing technologies offers a comprehensive path for studying mechanisms underlying heterogeneity in whole tumors.
Collapse
MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Cell Line, Tumor
- Cell Lineage/genetics
- Cell Plasticity/genetics
- Epithelial-Mesenchymal Transition/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Heterogeneity
- Humans
- Imaging, Three-Dimensional
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Microscopy, Confocal
- Sequence Analysis, RNA
- Single-Cell Analysis/methods
- Transcriptome
- Tumor Burden
Collapse
Affiliation(s)
- Anne C Rios
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands.
| | - Bianca D Capaldo
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - François Vaillant
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Bhupinder Pal
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ravian van Ineveld
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands
| | - Caleb A Dawson
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Yunshun Chen
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia; Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Emma Nolan
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nai Yang Fu
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | -
- 3D Tissue Clearing and Lightsheet Microscopy Group, Hunter Medical Research Institute, Newcastle, NSW 2305, Australia
| | - Felicity C Jackling
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sapna Devi
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3050, Australia; The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3000, Australia
| | | | - Lachlan Whitehead
- Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Gordon K Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3050, Australia; The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Geoffrey J Lindeman
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Department of Medicine, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E Visvader
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia.
| |
Collapse
|
150
|
Uderhardt S, Martins AJ, Tsang JS, Lämmermann T, Germain RN. Resident Macrophages Cloak Tissue Microlesions to Prevent Neutrophil-Driven Inflammatory Damage. Cell 2019; 177:541-555.e17. [PMID: 30955887 DOI: 10.1016/j.cell.2019.02.028] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/02/2019] [Accepted: 02/15/2019] [Indexed: 12/21/2022]
Abstract
Neutrophils are attracted to and generate dense swarms at sites of cell damage in diverse tissues, often extending the local disruption of organ architecture produced by the initial insult. Whether the inflammatory damage resulting from such neutrophil accumulation is an inescapable consequence of parenchymal cell death has not been explored. Using a combination of dynamic intravital imaging and confocal multiplex microscopy, we report here that tissue-resident macrophages rapidly sense the death of individual cells and extend membrane processes that sequester the damage, a process that prevents initiation of the feedforward chemoattractant signaling cascade that results in neutrophil swarms. Through this "cloaking" mechanism, the resident macrophages prevent neutrophil-mediated inflammatory damage, maintaining tissue homeostasis in the face of local cell injury that occurs on a regular basis in many organs because of mechanical and other stresses. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Stefan Uderhardt
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Andrew J Martins
- Systems Genomics and Bioinformatics Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Group Immune Cell Dynamics, 79108 Freibcurg, Germany
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|