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Martínez-Greene JA, Gómez-Chavarín M, Ramos-Godínez MDP, Martínez-Martínez E. Isolation of Hepatic and Adipose-Tissue-Derived Extracellular Vesicles Using Density Gradient Separation and Size Exclusion Chromatography. Int J Mol Sci 2023; 24:12704. [PMID: 37628890 PMCID: PMC10454538 DOI: 10.3390/ijms241612704] [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] [Received: 05/06/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
In recent years, the study of extracellular vesicles (EVs) in the context of various diseases has dramatically increased due to their diagnostic and therapeutic potential. Typically, EVs are isolated in vitro from the cell culture of primary cells or cell lines or from bodily fluids. However, these cell culture methods do not represent the whole complexity of an in vivo microenvironment, and bodily fluids contain a high heterogeneous population of vesicles since they originate from different tissues. This highlights the need to develop new methods to isolate EVs directly from tissue samples. In the present study, we established a protocol for isolating EVs from hepatic and adipose tissue of mice, using a combination of ultracentrifugation and iodixanol-sucrose density gradient separation. EV isolation was confirmed with EV protein marker enrichment in Western blot assays, total protein quantification, and transmission electron microscopy. Regarding the liver tissue, we additionally implemented size exclusion chromatography (SEC) to further increase the purity grade of the EVs. The successful isolation of EVs from tissue samples will allow us to uncover a more precise molecular composition and functions, as well as their role in intercellular communication in an in vivo microenvironment.
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Affiliation(s)
- Juan Alfonso Martínez-Greene
- Laboratory of Cell Communication and Extracellular Vesicles, National Institute of Genomic Medicine (INMEGEN), Mexico City 14610, Mexico;
| | - Margarita Gómez-Chavarín
- Physiology Department, School of Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico;
| | | | - Eduardo Martínez-Martínez
- Laboratory of Cell Communication and Extracellular Vesicles, National Institute of Genomic Medicine (INMEGEN), Mexico City 14610, Mexico;
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Guille M, Grainger R. Genetics and Gene Editing Methods in Xenopus laevis and Xenopus tropicalis. Cold Spring Harb Protoc 2023; 2023:pdb.top107045. [PMID: 36283837 DOI: 10.1101/pdb.top107045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Our understanding of biological systems has for many years been heavily influenced by experimental approaches that exploit genetic methods. These include gain-of-function experiments that overexpress transgenes or ectopically express injected RNA and loss-of-function experiments that knock out genes or knock down RNAs. Here, we review how these methods have been applied in Xenopus frogs and introduce a variety of protocols for genetic manipulation of Xenopus laevis and Xenopus tropicalis.
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Affiliation(s)
- Matthew Guille
- European Xenopus Resource Centre, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2UP, United Kingdom
| | - Robert Grainger
- Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
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Montanari M, Burattini S, Ciacci C, Ambrogini P, Carloni S, Balduini W, Lopez D, Panza G, Papa S, Canonico B. Automated–Mechanical Procedure Compared to Gentle Enzymatic Tissue Dissociation in Cell Function Studies. Biomolecules 2022; 12:biom12050701. [PMID: 35625628 PMCID: PMC9138555 DOI: 10.3390/biom12050701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/11/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
The first step to obtain a cellular suspension from tissues is the disaggregation procedure. The cell suspension method has to provide a representative sample of the different cellular subpopulations and to maximize the number of viable functional cells. Here, we analyzed specific cell functions in cell suspensions from several rat tissues obtained by two different methods, automated–mechanical and enzymatic disaggregation. Flow cytometric, confocal, and ultrastructural (TEM) analyses were applied to the spleen, testis, liver and other tissues. Samples were treated by an enzymatic trypsin solution or processed by the Medimachine II (MMII). The automated–mechanical and enzymatic disaggregation procedures have shown to work similarly in some tissues, which displayed comparable amounts of apoptotic/necrotic cells. However, cells obtained by the enzyme-free Medimachine II protocols show a better preservation lysosome and mitochondria labeling, whereas the enzymatic gentle dissociation appears to constantly induce a lower amount of intracellular ROS; nevertheless, lightly increased ROS can be recognized as a complimentary signal to promote cell survival. Therefore, MMII represents a simple, fast, and standardized method for tissue processing, which allows to minimize bias arising from the operator’s ability. Our study points out technical issues to be adopted for specific organs and tissues to obtain functional cells.
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Affiliation(s)
- Mariele Montanari
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Sabrina Burattini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Caterina Ciacci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Patrizia Ambrogini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Silvia Carloni
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Walter Balduini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Daniele Lopez
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
- Department of Pure and Applied Sciences (DiSPeA), University of Urbino Carlo Bo, 61029 Urbino, Italy
| | - Giovanna Panza
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Stefano Papa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
| | - Barbara Canonico
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (M.M.); (S.B.); (C.C.); (P.A.); (S.C.); (W.B.); (D.L.); (G.P.); (S.P.)
- Correspondence:
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Baxi AB, Pade LR, Nemes P. Cell-Lineage Guided Mass Spectrometry Proteomics in the Developing (Frog) Embryo. J Vis Exp 2022:10.3791/63586. [PMID: 35532271 PMCID: PMC9513837 DOI: 10.3791/63586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
Characterization of molecular events as cells give rise to tissues and organs raises a potential to better understand normal development and design efficient remedies for diseases. Technologies enabling accurate identification and quantification of diverse types and large numbers of proteins would provide still missing information on molecular mechanisms orchestrating tissue and organism development in space and time. Here, we present a mass spectrometry-based protocol that enables the measurement of thousands of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The approach builds on reproducible cell-fate maps and established methods to identify, fluorescently label, track, and sample cells and their progeny (clones) from this model of vertebrate development. After collecting cellular contents using microsampling or isolating cells by dissection or fluorescence-activated cell sorting, proteins are extracted and processed for bottom-up proteomic analysis. Liquid chromatography and capillary electrophoresis are used to provide scalable separation for protein detection and quantification with high-resolution mass spectrometry (HRMS). Representative examples are provided for the proteomic characterization of neural-tissue fated cells. Cell-lineage-guided HRMS proteomics is adaptable to different tissues and organisms. It is sufficiently sensitive, specific, and quantitative to peer into the spatio-temporal dynamics of the proteome during vertebrate development.
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Affiliation(s)
- Aparna B Baxi
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University
| | - Leena R Pade
- Department of Chemistry & Biochemistry, University of Maryland
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland; Department of Anatomy & Cell Biology, The George Washington University;
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Sears KE, Gros J, Davey M. Limb development, evolution, and regeneration & repair: Part 1. Dev Dyn 2021; 250:1218-1219. [PMID: 34402127 DOI: 10.1002/dvdy.411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Karen E Sears
- Departments of Ecology and Evolutionary Biology and Molecular, Cell, and Developmental Biology, UCLA, California, Los Angeles, USA
| | - Jerome Gros
- Department of Developmental and Stem Biology, Institute Pasteur, Paris, France
| | - Megan Davey
- Functional Genetics and Development, The Roslin Institute, The University of Edinburgh, Midlothian, Scotland, UK
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